Mock Version: 1.2.14
ENTER do(['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target i686 --nodeps /builddir/build/SPECS/python-biopython.spec'], chrootPath='/srv/build/7/A/mock-root/c7-epel-i686/root'shell=FalseprintOutput=Falseenv={'LANG': 'en_GB', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'}gid=135user='mockbuild'timeout=21600logger=<mockbuild.trace_decorator.getLog object at 0x195b090>uid=501)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target i686 --nodeps /builddir/build/SPECS/python-biopython.spec'] with env {'LANG': 'en_GB', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'} and shell False
warning: Could not canonicalize hostname: worker1.bsys.centos.org
Building target platforms: i686
Building for target i686
Wrote: /builddir/build/SRPMS/python-biopython-1.66-3.el7.src.rpm
Child return code was: 0
LEAVE do --> 

ENTER do(['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target i686 --nodeps  /builddir/build/SPECS/python-biopython.spec '], chrootPath='/srv/build/7/A/mock-root/c7-epel-i686/root'shell=Falseuid=501env={'LANG': 'en_GB', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'}gid=135user='mockbuild'timeout=21600private_network=Truelogger=<mockbuild.trace_decorator.getLog object at 0x195b090>printOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target i686 --nodeps  /builddir/build/SPECS/python-biopython.spec '] with env {'LANG': 'en_GB', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'} and shell False
Building target platforms: i686
Building for target i686
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.r4nYu0
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf python-biopython-1.66
+ /usr/bin/mkdir -p python-biopython-1.66
+ cd python-biopython-1.66
+ /usr/bin/gzip -dc /builddir/build/SOURCES/biopython-1.66.tar.gz
+ /usr/bin/tar -xf -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ mv biopython-1.66 python2
+ pushd python2
~/build/BUILD/python-biopython-1.66/python2 ~/build/BUILD/python-biopython-1.66
+ find Scripts -type f -exec chmod -x '{}' ';'
+ find Doc -type f -exec chmod -x '{}' ';'
+ find Doc -type f -exec sed -i 's/\r//' '{}' ';'
+ find Bio -type f -exec chmod -x '{}' ';'
+ find Bio -type f -name '*.py' -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' '{}' ';'
+ popd
+ exit 0
~/build/BUILD/python-biopython-1.66
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.K3Z3X5
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.66
~/build/BUILD/python-biopython-1.66/python2 ~/build/BUILD/python-biopython-1.66
+ pushd python2
+ CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now'
+ /usr/bin/python2 setup.py build '--executable=/usr/bin/python2 -s'
running build
running build_py
creating build
creating build/lib.linux-i686-2.7
creating build/lib.linux-i686-2.7/Bio
copying Bio/pairwise2.py -> build/lib.linux-i686-2.7/Bio
copying Bio/MaxEntropy.py -> build/lib.linux-i686-2.7/Bio
copying Bio/DocSQL.py -> build/lib.linux-i686-2.7/Bio
copying Bio/bgzf.py -> build/lib.linux-i686-2.7/Bio
copying Bio/triefind.py -> build/lib.linux-i686-2.7/Bio
copying Bio/__init__.py -> build/lib.linux-i686-2.7/Bio
copying Bio/LogisticRegression.py -> build/lib.linux-i686-2.7/Bio
copying Bio/_utils.py -> build/lib.linux-i686-2.7/Bio
copying Bio/Seq.py -> build/lib.linux-i686-2.7/Bio
copying Bio/SeqRecord.py -> build/lib.linux-i686-2.7/Bio
copying Bio/NaiveBayes.py -> build/lib.linux-i686-2.7/Bio
copying Bio/ParserSupport.py -> build/lib.linux-i686-2.7/Bio
copying Bio/File.py -> build/lib.linux-i686-2.7/Bio
copying Bio/MarkovModel.py -> build/lib.linux-i686-2.7/Bio
copying Bio/kNN.py -> build/lib.linux-i686-2.7/Bio
copying Bio/Index.py -> build/lib.linux-i686-2.7/Bio
copying Bio/SeqFeature.py -> build/lib.linux-i686-2.7/Bio
creating build/lib.linux-i686-2.7/Bio/Align
copying Bio/Align/__init__.py -> build/lib.linux-i686-2.7/Bio/Align
copying Bio/Align/AlignInfo.py -> build/lib.linux-i686-2.7/Bio/Align
copying Bio/Align/Generic.py -> build/lib.linux-i686-2.7/Bio/Align
creating build/lib.linux-i686-2.7/Bio/Align/Applications
copying Bio/Align/Applications/_MSAProbs.py -> build/lib.linux-i686-2.7/Bio/Align/Applications
copying Bio/Align/Applications/_Probcons.py -> build/lib.linux-i686-2.7/Bio/Align/Applications
copying Bio/Align/Applications/_Mafft.py -> build/lib.linux-i686-2.7/Bio/Align/Applications
copying Bio/Align/Applications/_ClustalOmega.py -> build/lib.linux-i686-2.7/Bio/Align/Applications
copying Bio/Align/Applications/__init__.py -> build/lib.linux-i686-2.7/Bio/Align/Applications
copying Bio/Align/Applications/_Prank.py -> build/lib.linux-i686-2.7/Bio/Align/Applications
copying Bio/Align/Applications/_Clustalw.py -> build/lib.linux-i686-2.7/Bio/Align/Applications
copying Bio/Align/Applications/_Dialign.py -> build/lib.linux-i686-2.7/Bio/Align/Applications
copying Bio/Align/Applications/_Muscle.py -> build/lib.linux-i686-2.7/Bio/Align/Applications
copying Bio/Align/Applications/_TCoffee.py -> build/lib.linux-i686-2.7/Bio/Align/Applications
creating build/lib.linux-i686-2.7/Bio/AlignIO
copying Bio/AlignIO/NexusIO.py -> build/lib.linux-i686-2.7/Bio/AlignIO
copying Bio/AlignIO/Interfaces.py -> build/lib.linux-i686-2.7/Bio/AlignIO
copying Bio/AlignIO/FastaIO.py -> build/lib.linux-i686-2.7/Bio/AlignIO
copying Bio/AlignIO/StockholmIO.py -> build/lib.linux-i686-2.7/Bio/AlignIO
copying Bio/AlignIO/EmbossIO.py -> build/lib.linux-i686-2.7/Bio/AlignIO
copying Bio/AlignIO/__init__.py -> build/lib.linux-i686-2.7/Bio/AlignIO
copying Bio/AlignIO/ClustalIO.py -> build/lib.linux-i686-2.7/Bio/AlignIO
copying Bio/AlignIO/PhylipIO.py -> build/lib.linux-i686-2.7/Bio/AlignIO
creating build/lib.linux-i686-2.7/Bio/Alphabet
copying Bio/Alphabet/__init__.py -> build/lib.linux-i686-2.7/Bio/Alphabet
copying Bio/Alphabet/IUPAC.py -> build/lib.linux-i686-2.7/Bio/Alphabet
copying Bio/Alphabet/Reduced.py -> build/lib.linux-i686-2.7/Bio/Alphabet
creating build/lib.linux-i686-2.7/Bio/Application
copying Bio/Application/__init__.py -> build/lib.linux-i686-2.7/Bio/Application
creating build/lib.linux-i686-2.7/Bio/Blast
copying Bio/Blast/Record.py -> build/lib.linux-i686-2.7/Bio/Blast
copying Bio/Blast/NCBIXML.py -> build/lib.linux-i686-2.7/Bio/Blast
copying Bio/Blast/__init__.py -> build/lib.linux-i686-2.7/Bio/Blast
copying Bio/Blast/NCBIStandalone.py -> build/lib.linux-i686-2.7/Bio/Blast
copying Bio/Blast/Applications.py -> build/lib.linux-i686-2.7/Bio/Blast
copying Bio/Blast/ParseBlastTable.py -> build/lib.linux-i686-2.7/Bio/Blast
copying Bio/Blast/NCBIWWW.py -> build/lib.linux-i686-2.7/Bio/Blast
creating build/lib.linux-i686-2.7/Bio/CAPS
copying Bio/CAPS/__init__.py -> build/lib.linux-i686-2.7/Bio/CAPS
creating build/lib.linux-i686-2.7/Bio/codonalign
copying Bio/codonalign/codonseq.py -> build/lib.linux-i686-2.7/Bio/codonalign
copying Bio/codonalign/codonalignment.py -> build/lib.linux-i686-2.7/Bio/codonalign
copying Bio/codonalign/codonalphabet.py -> build/lib.linux-i686-2.7/Bio/codonalign
copying Bio/codonalign/__init__.py -> build/lib.linux-i686-2.7/Bio/codonalign
copying Bio/codonalign/chisq.py -> build/lib.linux-i686-2.7/Bio/codonalign
creating build/lib.linux-i686-2.7/Bio/Compass
copying Bio/Compass/__init__.py -> build/lib.linux-i686-2.7/Bio/Compass
creating build/lib.linux-i686-2.7/Bio/Crystal
copying Bio/Crystal/__init__.py -> build/lib.linux-i686-2.7/Bio/Crystal
creating build/lib.linux-i686-2.7/Bio/Data
copying Bio/Data/CodonTable.py -> build/lib.linux-i686-2.7/Bio/Data
copying Bio/Data/IUPACData.py -> build/lib.linux-i686-2.7/Bio/Data
copying Bio/Data/SCOPData.py -> build/lib.linux-i686-2.7/Bio/Data
copying Bio/Data/__init__.py -> build/lib.linux-i686-2.7/Bio/Data
creating build/lib.linux-i686-2.7/Bio/Emboss
copying Bio/Emboss/__init__.py -> build/lib.linux-i686-2.7/Bio/Emboss
copying Bio/Emboss/Primer3.py -> build/lib.linux-i686-2.7/Bio/Emboss
copying Bio/Emboss/Applications.py -> build/lib.linux-i686-2.7/Bio/Emboss
copying Bio/Emboss/PrimerSearch.py -> build/lib.linux-i686-2.7/Bio/Emboss
creating build/lib.linux-i686-2.7/Bio/Entrez
copying Bio/Entrez/Parser.py -> build/lib.linux-i686-2.7/Bio/Entrez
copying Bio/Entrez/__init__.py -> build/lib.linux-i686-2.7/Bio/Entrez
creating build/lib.linux-i686-2.7/Bio/ExPASy
copying Bio/ExPASy/ScanProsite.py -> build/lib.linux-i686-2.7/Bio/ExPASy
copying Bio/ExPASy/Prosite.py -> build/lib.linux-i686-2.7/Bio/ExPASy
copying Bio/ExPASy/Enzyme.py -> build/lib.linux-i686-2.7/Bio/ExPASy
copying Bio/ExPASy/__init__.py -> build/lib.linux-i686-2.7/Bio/ExPASy
copying Bio/ExPASy/Prodoc.py -> build/lib.linux-i686-2.7/Bio/ExPASy
creating build/lib.linux-i686-2.7/Bio/FSSP
copying Bio/FSSP/fssp_rec.py -> build/lib.linux-i686-2.7/Bio/FSSP
copying Bio/FSSP/__init__.py -> build/lib.linux-i686-2.7/Bio/FSSP
copying Bio/FSSP/FSSPTools.py -> build/lib.linux-i686-2.7/Bio/FSSP
creating build/lib.linux-i686-2.7/Bio/GA
copying Bio/GA/Organism.py -> build/lib.linux-i686-2.7/Bio/GA
copying Bio/GA/__init__.py -> build/lib.linux-i686-2.7/Bio/GA
copying Bio/GA/Evolver.py -> build/lib.linux-i686-2.7/Bio/GA
creating build/lib.linux-i686-2.7/Bio/GA/Crossover
copying Bio/GA/Crossover/Point.py -> build/lib.linux-i686-2.7/Bio/GA/Crossover
copying Bio/GA/Crossover/__init__.py -> build/lib.linux-i686-2.7/Bio/GA/Crossover
copying Bio/GA/Crossover/General.py -> build/lib.linux-i686-2.7/Bio/GA/Crossover
copying Bio/GA/Crossover/Uniform.py -> build/lib.linux-i686-2.7/Bio/GA/Crossover
copying Bio/GA/Crossover/TwoPoint.py -> build/lib.linux-i686-2.7/Bio/GA/Crossover
copying Bio/GA/Crossover/GeneralPoint.py -> build/lib.linux-i686-2.7/Bio/GA/Crossover
creating build/lib.linux-i686-2.7/Bio/GA/Mutation
copying Bio/GA/Mutation/__init__.py -> build/lib.linux-i686-2.7/Bio/GA/Mutation
copying Bio/GA/Mutation/General.py -> build/lib.linux-i686-2.7/Bio/GA/Mutation
copying Bio/GA/Mutation/Simple.py -> build/lib.linux-i686-2.7/Bio/GA/Mutation
creating build/lib.linux-i686-2.7/Bio/GA/Repair
copying Bio/GA/Repair/__init__.py -> build/lib.linux-i686-2.7/Bio/GA/Repair
copying Bio/GA/Repair/Stabilizing.py -> build/lib.linux-i686-2.7/Bio/GA/Repair
creating build/lib.linux-i686-2.7/Bio/GA/Selection
copying Bio/GA/Selection/Diversity.py -> build/lib.linux-i686-2.7/Bio/GA/Selection
copying Bio/GA/Selection/Tournament.py -> build/lib.linux-i686-2.7/Bio/GA/Selection
copying Bio/GA/Selection/__init__.py -> build/lib.linux-i686-2.7/Bio/GA/Selection
copying Bio/GA/Selection/Abstract.py -> build/lib.linux-i686-2.7/Bio/GA/Selection
copying Bio/GA/Selection/RouletteWheel.py -> build/lib.linux-i686-2.7/Bio/GA/Selection
creating build/lib.linux-i686-2.7/Bio/GenBank
copying Bio/GenBank/Record.py -> build/lib.linux-i686-2.7/Bio/GenBank
copying Bio/GenBank/utils.py -> build/lib.linux-i686-2.7/Bio/GenBank
copying Bio/GenBank/__init__.py -> build/lib.linux-i686-2.7/Bio/GenBank
copying Bio/GenBank/Scanner.py -> build/lib.linux-i686-2.7/Bio/GenBank
creating build/lib.linux-i686-2.7/Bio/Geo
copying Bio/Geo/Record.py -> build/lib.linux-i686-2.7/Bio/Geo
copying Bio/Geo/__init__.py -> build/lib.linux-i686-2.7/Bio/Geo
creating build/lib.linux-i686-2.7/Bio/Graphics
copying Bio/Graphics/ColorSpiral.py -> build/lib.linux-i686-2.7/Bio/Graphics
copying Bio/Graphics/BasicChromosome.py -> build/lib.linux-i686-2.7/Bio/Graphics
copying Bio/Graphics/KGML_vis.py -> build/lib.linux-i686-2.7/Bio/Graphics
copying Bio/Graphics/__init__.py -> build/lib.linux-i686-2.7/Bio/Graphics
copying Bio/Graphics/Distribution.py -> build/lib.linux-i686-2.7/Bio/Graphics
copying Bio/Graphics/Comparative.py -> build/lib.linux-i686-2.7/Bio/Graphics
copying Bio/Graphics/DisplayRepresentation.py -> build/lib.linux-i686-2.7/Bio/Graphics
creating build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Colors.py -> build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_GraphSet.py -> build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Feature.py -> build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_FeatureSet.py -> build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Graph.py -> build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Track.py -> build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_CrossLink.py -> build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/__init__.py -> build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram
copying Bio/Graphics/GenomeDiagram/_Diagram.py -> build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram
creating build/lib.linux-i686-2.7/Bio/HMM
copying Bio/HMM/Trainer.py -> build/lib.linux-i686-2.7/Bio/HMM
copying Bio/HMM/DynamicProgramming.py -> build/lib.linux-i686-2.7/Bio/HMM
copying Bio/HMM/__init__.py -> build/lib.linux-i686-2.7/Bio/HMM
copying Bio/HMM/MarkovModel.py -> build/lib.linux-i686-2.7/Bio/HMM
copying Bio/HMM/Utilities.py -> build/lib.linux-i686-2.7/Bio/HMM
creating build/lib.linux-i686-2.7/Bio/KEGG
copying Bio/KEGG/__init__.py -> build/lib.linux-i686-2.7/Bio/KEGG
copying Bio/KEGG/REST.py -> build/lib.linux-i686-2.7/Bio/KEGG
creating build/lib.linux-i686-2.7/Bio/KEGG/Compound
copying Bio/KEGG/Compound/__init__.py -> build/lib.linux-i686-2.7/Bio/KEGG/Compound
creating build/lib.linux-i686-2.7/Bio/KEGG/Enzyme
copying Bio/KEGG/Enzyme/__init__.py -> build/lib.linux-i686-2.7/Bio/KEGG/Enzyme
creating build/lib.linux-i686-2.7/Bio/KEGG/Map
copying Bio/KEGG/Map/__init__.py -> build/lib.linux-i686-2.7/Bio/KEGG/Map
creating build/lib.linux-i686-2.7/Bio/KEGG/KGML
copying Bio/KEGG/KGML/__init__.py -> build/lib.linux-i686-2.7/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_parser.py -> build/lib.linux-i686-2.7/Bio/KEGG/KGML
copying Bio/KEGG/KGML/KGML_pathway.py -> build/lib.linux-i686-2.7/Bio/KEGG/KGML
creating build/lib.linux-i686-2.7/Bio/Medline
copying Bio/Medline/__init__.py -> build/lib.linux-i686-2.7/Bio/Medline
creating build/lib.linux-i686-2.7/Bio/Motif
copying Bio/Motif/Thresholds.py -> build/lib.linux-i686-2.7/Bio/Motif
copying Bio/Motif/__init__.py -> build/lib.linux-i686-2.7/Bio/Motif
copying Bio/Motif/_Motif.py -> build/lib.linux-i686-2.7/Bio/Motif
creating build/lib.linux-i686-2.7/Bio/Motif/Parsers
copying Bio/Motif/Parsers/MEME.py -> build/lib.linux-i686-2.7/Bio/Motif/Parsers
copying Bio/Motif/Parsers/AlignAce.py -> build/lib.linux-i686-2.7/Bio/Motif/Parsers
copying Bio/Motif/Parsers/__init__.py -> build/lib.linux-i686-2.7/Bio/Motif/Parsers
copying Bio/Motif/Parsers/MAST.py -> build/lib.linux-i686-2.7/Bio/Motif/Parsers
creating build/lib.linux-i686-2.7/Bio/Motif/Applications
copying Bio/Motif/Applications/__init__.py -> build/lib.linux-i686-2.7/Bio/Motif/Applications
creating build/lib.linux-i686-2.7/Bio/motifs
copying Bio/motifs/thresholds.py -> build/lib.linux-i686-2.7/Bio/motifs
copying Bio/motifs/alignace.py -> build/lib.linux-i686-2.7/Bio/motifs
copying Bio/motifs/mast.py -> build/lib.linux-i686-2.7/Bio/motifs
copying Bio/motifs/meme.py -> build/lib.linux-i686-2.7/Bio/motifs
copying Bio/motifs/matrix.py -> build/lib.linux-i686-2.7/Bio/motifs
copying Bio/motifs/__init__.py -> build/lib.linux-i686-2.7/Bio/motifs
copying Bio/motifs/transfac.py -> build/lib.linux-i686-2.7/Bio/motifs
creating build/lib.linux-i686-2.7/Bio/motifs/applications
copying Bio/motifs/applications/_xxmotif.py -> build/lib.linux-i686-2.7/Bio/motifs/applications
copying Bio/motifs/applications/_alignace.py -> build/lib.linux-i686-2.7/Bio/motifs/applications
copying Bio/motifs/applications/__init__.py -> build/lib.linux-i686-2.7/Bio/motifs/applications
creating build/lib.linux-i686-2.7/Bio/motifs/jaspar
copying Bio/motifs/jaspar/db.py -> build/lib.linux-i686-2.7/Bio/motifs/jaspar
copying Bio/motifs/jaspar/__init__.py -> build/lib.linux-i686-2.7/Bio/motifs/jaspar
creating build/lib.linux-i686-2.7/Bio/NeuralNetwork
copying Bio/NeuralNetwork/StopTraining.py -> build/lib.linux-i686-2.7/Bio/NeuralNetwork
copying Bio/NeuralNetwork/__init__.py -> build/lib.linux-i686-2.7/Bio/NeuralNetwork
copying Bio/NeuralNetwork/Training.py -> build/lib.linux-i686-2.7/Bio/NeuralNetwork
creating build/lib.linux-i686-2.7/Bio/NeuralNetwork/BackPropagation
copying Bio/NeuralNetwork/BackPropagation/Network.py -> build/lib.linux-i686-2.7/Bio/NeuralNetwork/BackPropagation
copying Bio/NeuralNetwork/BackPropagation/__init__.py -> build/lib.linux-i686-2.7/Bio/NeuralNetwork/BackPropagation
copying Bio/NeuralNetwork/BackPropagation/Layer.py -> build/lib.linux-i686-2.7/Bio/NeuralNetwork/BackPropagation
creating build/lib.linux-i686-2.7/Bio/NeuralNetwork/Gene
copying Bio/NeuralNetwork/Gene/Motif.py -> build/lib.linux-i686-2.7/Bio/NeuralNetwork/Gene
copying Bio/NeuralNetwork/Gene/Signature.py -> build/lib.linux-i686-2.7/Bio/NeuralNetwork/Gene
copying Bio/NeuralNetwork/Gene/Schema.py -> build/lib.linux-i686-2.7/Bio/NeuralNetwork/Gene
copying Bio/NeuralNetwork/Gene/__init__.py -> build/lib.linux-i686-2.7/Bio/NeuralNetwork/Gene
copying Bio/NeuralNetwork/Gene/Pattern.py -> build/lib.linux-i686-2.7/Bio/NeuralNetwork/Gene
creating build/lib.linux-i686-2.7/Bio/Nexus
copying Bio/Nexus/Nexus.py -> build/lib.linux-i686-2.7/Bio/Nexus
copying Bio/Nexus/Nodes.py -> build/lib.linux-i686-2.7/Bio/Nexus
copying Bio/Nexus/__init__.py -> build/lib.linux-i686-2.7/Bio/Nexus
copying Bio/Nexus/Trees.py -> build/lib.linux-i686-2.7/Bio/Nexus
creating build/lib.linux-i686-2.7/Bio/NMR
copying Bio/NMR/NOEtools.py -> build/lib.linux-i686-2.7/Bio/NMR
copying Bio/NMR/xpktools.py -> build/lib.linux-i686-2.7/Bio/NMR
copying Bio/NMR/__init__.py -> build/lib.linux-i686-2.7/Bio/NMR
creating build/lib.linux-i686-2.7/Bio/Pathway
copying Bio/Pathway/__init__.py -> build/lib.linux-i686-2.7/Bio/Pathway
creating build/lib.linux-i686-2.7/Bio/Pathway/Rep
copying Bio/Pathway/Rep/MultiGraph.py -> build/lib.linux-i686-2.7/Bio/Pathway/Rep
copying Bio/Pathway/Rep/__init__.py -> build/lib.linux-i686-2.7/Bio/Pathway/Rep
copying Bio/Pathway/Rep/Graph.py -> build/lib.linux-i686-2.7/Bio/Pathway/Rep
creating build/lib.linux-i686-2.7/Bio/PDB
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copying Bio/PDB/StructureAlignment.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/ResidueDepth.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/AbstractPropertyMap.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/Dice.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/Residue.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/PSEA.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/MMCIF2Dict.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/NeighborSearch.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/PDBList.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/NACCESS.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/PDBExceptions.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/Superimposer.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/Chain.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/DSSP.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/Polypeptide.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/Structure.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/__init__.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/FragmentMapper.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/PDBIO.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/StructureBuilder.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/Atom.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/Entity.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/Model.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/MMCIFParser.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/Selection.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/parse_pdb_header.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/HSExposure.py -> build/lib.linux-i686-2.7/Bio/PDB
copying Bio/PDB/PDBParser.py -> build/lib.linux-i686-2.7/Bio/PDB
creating build/lib.linux-i686-2.7/Bio/PopGen
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creating build/lib.linux-i686-2.7/Bio/PopGen/Async
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copying Bio/PopGen/Async/Local.py -> build/lib.linux-i686-2.7/Bio/PopGen/Async
creating build/lib.linux-i686-2.7/Bio/PopGen/FDist
copying Bio/PopGen/FDist/Controller.py -> build/lib.linux-i686-2.7/Bio/PopGen/FDist
copying Bio/PopGen/FDist/Async.py -> build/lib.linux-i686-2.7/Bio/PopGen/FDist
copying Bio/PopGen/FDist/__init__.py -> build/lib.linux-i686-2.7/Bio/PopGen/FDist
copying Bio/PopGen/FDist/Utils.py -> build/lib.linux-i686-2.7/Bio/PopGen/FDist
creating build/lib.linux-i686-2.7/Bio/PopGen/GenePop
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copying Bio/PopGen/GenePop/LargeFileParser.py -> build/lib.linux-i686-2.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/EasyController.py -> build/lib.linux-i686-2.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/__init__.py -> build/lib.linux-i686-2.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/FileParser.py -> build/lib.linux-i686-2.7/Bio/PopGen/GenePop
copying Bio/PopGen/GenePop/Utils.py -> build/lib.linux-i686-2.7/Bio/PopGen/GenePop
creating build/lib.linux-i686-2.7/Bio/PopGen/SimCoal
copying Bio/PopGen/SimCoal/Controller.py -> build/lib.linux-i686-2.7/Bio/PopGen/SimCoal
copying Bio/PopGen/SimCoal/Async.py -> build/lib.linux-i686-2.7/Bio/PopGen/SimCoal
copying Bio/PopGen/SimCoal/__init__.py -> build/lib.linux-i686-2.7/Bio/PopGen/SimCoal
copying Bio/PopGen/SimCoal/Cache.py -> build/lib.linux-i686-2.7/Bio/PopGen/SimCoal
copying Bio/PopGen/SimCoal/Template.py -> build/lib.linux-i686-2.7/Bio/PopGen/SimCoal
creating build/lib.linux-i686-2.7/Bio/Restriction
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copying Bio/Restriction/Restriction.py -> build/lib.linux-i686-2.7/Bio/Restriction
copying Bio/Restriction/__init__.py -> build/lib.linux-i686-2.7/Bio/Restriction
copying Bio/Restriction/Restriction_Dictionary.py -> build/lib.linux-i686-2.7/Bio/Restriction
copying Bio/Restriction/RanaConfig.py -> build/lib.linux-i686-2.7/Bio/Restriction
creating build/lib.linux-i686-2.7/Bio/SCOP
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copying Bio/SCOP/Residues.py -> build/lib.linux-i686-2.7/Bio/SCOP
copying Bio/SCOP/Hie.py -> build/lib.linux-i686-2.7/Bio/SCOP
copying Bio/SCOP/Cla.py -> build/lib.linux-i686-2.7/Bio/SCOP
copying Bio/SCOP/__init__.py -> build/lib.linux-i686-2.7/Bio/SCOP
copying Bio/SCOP/Raf.py -> build/lib.linux-i686-2.7/Bio/SCOP
copying Bio/SCOP/Dom.py -> build/lib.linux-i686-2.7/Bio/SCOP
creating build/lib.linux-i686-2.7/Bio/SearchIO
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copying Bio/SearchIO/BlatIO.py -> build/lib.linux-i686-2.7/Bio/SearchIO
copying Bio/SearchIO/__init__.py -> build/lib.linux-i686-2.7/Bio/SearchIO
copying Bio/SearchIO/_utils.py -> build/lib.linux-i686-2.7/Bio/SearchIO
copying Bio/SearchIO/_index.py -> build/lib.linux-i686-2.7/Bio/SearchIO
creating build/lib.linux-i686-2.7/Bio/SearchIO/_model
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copying Bio/SearchIO/_model/hit.py -> build/lib.linux-i686-2.7/Bio/SearchIO/_model
copying Bio/SearchIO/_model/__init__.py -> build/lib.linux-i686-2.7/Bio/SearchIO/_model
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copying Bio/SearchIO/_model/query.py -> build/lib.linux-i686-2.7/Bio/SearchIO/_model
creating build/lib.linux-i686-2.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_tab.py -> build/lib.linux-i686-2.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_text.py -> build/lib.linux-i686-2.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/__init__.py -> build/lib.linux-i686-2.7/Bio/SearchIO/BlastIO
copying Bio/SearchIO/BlastIO/blast_xml.py -> build/lib.linux-i686-2.7/Bio/SearchIO/BlastIO
creating build/lib.linux-i686-2.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> build/lib.linux-i686-2.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/__init__.py -> build/lib.linux-i686-2.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/_base.py -> build/lib.linux-i686-2.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_text.py -> build/lib.linux-i686-2.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer2_text.py -> build/lib.linux-i686-2.7/Bio/SearchIO/HmmerIO
copying Bio/SearchIO/HmmerIO/hmmer3_tab.py -> build/lib.linux-i686-2.7/Bio/SearchIO/HmmerIO
creating build/lib.linux-i686-2.7/Bio/SearchIO/ExonerateIO
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copying Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> build/lib.linux-i686-2.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/__init__.py -> build/lib.linux-i686-2.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/_base.py -> build/lib.linux-i686-2.7/Bio/SearchIO/ExonerateIO
copying Bio/SearchIO/ExonerateIO/exonerate_text.py -> build/lib.linux-i686-2.7/Bio/SearchIO/ExonerateIO
creating build/lib.linux-i686-2.7/Bio/SeqIO
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copying Bio/SeqIO/SwissIO.py -> build/lib.linux-i686-2.7/Bio/SeqIO
copying Bio/SeqIO/FastaIO.py -> build/lib.linux-i686-2.7/Bio/SeqIO
copying Bio/SeqIO/UniprotIO.py -> build/lib.linux-i686-2.7/Bio/SeqIO
copying Bio/SeqIO/SeqXmlIO.py -> build/lib.linux-i686-2.7/Bio/SeqIO
copying Bio/SeqIO/_convert.py -> build/lib.linux-i686-2.7/Bio/SeqIO
copying Bio/SeqIO/AbiIO.py -> build/lib.linux-i686-2.7/Bio/SeqIO
copying Bio/SeqIO/PdbIO.py -> build/lib.linux-i686-2.7/Bio/SeqIO
copying Bio/SeqIO/__init__.py -> build/lib.linux-i686-2.7/Bio/SeqIO
copying Bio/SeqIO/PhdIO.py -> build/lib.linux-i686-2.7/Bio/SeqIO
copying Bio/SeqIO/SffIO.py -> build/lib.linux-i686-2.7/Bio/SeqIO
copying Bio/SeqIO/TabIO.py -> build/lib.linux-i686-2.7/Bio/SeqIO
copying Bio/SeqIO/IgIO.py -> build/lib.linux-i686-2.7/Bio/SeqIO
copying Bio/SeqIO/PirIO.py -> build/lib.linux-i686-2.7/Bio/SeqIO
copying Bio/SeqIO/_index.py -> build/lib.linux-i686-2.7/Bio/SeqIO
copying Bio/SeqIO/AceIO.py -> build/lib.linux-i686-2.7/Bio/SeqIO
copying Bio/SeqIO/QualityIO.py -> build/lib.linux-i686-2.7/Bio/SeqIO
copying Bio/SeqIO/InsdcIO.py -> build/lib.linux-i686-2.7/Bio/SeqIO
creating build/lib.linux-i686-2.7/Bio/SeqUtils
copying Bio/SeqUtils/ProtParamData.py -> build/lib.linux-i686-2.7/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsageIndices.py -> build/lib.linux-i686-2.7/Bio/SeqUtils
copying Bio/SeqUtils/__init__.py -> build/lib.linux-i686-2.7/Bio/SeqUtils
copying Bio/SeqUtils/MeltingTemp.py -> build/lib.linux-i686-2.7/Bio/SeqUtils
copying Bio/SeqUtils/CodonUsage.py -> build/lib.linux-i686-2.7/Bio/SeqUtils
copying Bio/SeqUtils/CheckSum.py -> build/lib.linux-i686-2.7/Bio/SeqUtils
copying Bio/SeqUtils/lcc.py -> build/lib.linux-i686-2.7/Bio/SeqUtils
copying Bio/SeqUtils/ProtParam.py -> build/lib.linux-i686-2.7/Bio/SeqUtils
copying Bio/SeqUtils/IsoelectricPoint.py -> build/lib.linux-i686-2.7/Bio/SeqUtils
creating build/lib.linux-i686-2.7/Bio/Sequencing
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copying Bio/Sequencing/Phd.py -> build/lib.linux-i686-2.7/Bio/Sequencing
copying Bio/Sequencing/__init__.py -> build/lib.linux-i686-2.7/Bio/Sequencing
creating build/lib.linux-i686-2.7/Bio/Sequencing/Applications
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copying Bio/Sequencing/Applications/__init__.py -> build/lib.linux-i686-2.7/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_bwa.py -> build/lib.linux-i686-2.7/Bio/Sequencing/Applications
copying Bio/Sequencing/Applications/_samtools.py -> build/lib.linux-i686-2.7/Bio/Sequencing/Applications
creating build/lib.linux-i686-2.7/Bio/Statistics
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creating build/lib.linux-i686-2.7/Bio/SubsMat
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copying Bio/SubsMat/FreqTable.py -> build/lib.linux-i686-2.7/Bio/SubsMat
creating build/lib.linux-i686-2.7/Bio/SVDSuperimposer
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creating build/lib.linux-i686-2.7/Bio/PDB/QCPSuperimposer
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creating build/lib.linux-i686-2.7/Bio/SwissProt
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copying Bio/SwissProt/KeyWList.py -> build/lib.linux-i686-2.7/Bio/SwissProt
creating build/lib.linux-i686-2.7/Bio/TogoWS
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creating build/lib.linux-i686-2.7/Bio/Phylo
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copying Bio/Phylo/NexusIO.py -> build/lib.linux-i686-2.7/Bio/Phylo
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copying Bio/Phylo/PhyloXML.py -> build/lib.linux-i686-2.7/Bio/Phylo
copying Bio/Phylo/_cdao_owl.py -> build/lib.linux-i686-2.7/Bio/Phylo
copying Bio/Phylo/Consensus.py -> build/lib.linux-i686-2.7/Bio/Phylo
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copying Bio/Phylo/NeXMLIO.py -> build/lib.linux-i686-2.7/Bio/Phylo
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copying Bio/Phylo/_utils.py -> build/lib.linux-i686-2.7/Bio/Phylo
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copying Bio/Phylo/CDAOIO.py -> build/lib.linux-i686-2.7/Bio/Phylo
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copying Bio/Phylo/CDAO.py -> build/lib.linux-i686-2.7/Bio/Phylo
copying Bio/Phylo/TreeConstruction.py -> build/lib.linux-i686-2.7/Bio/Phylo
copying Bio/Phylo/PhyloXMLIO.py -> build/lib.linux-i686-2.7/Bio/Phylo
creating build/lib.linux-i686-2.7/Bio/Phylo/Applications
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copying Bio/Phylo/Applications/_Phyml.py -> build/lib.linux-i686-2.7/Bio/Phylo/Applications
copying Bio/Phylo/Applications/__init__.py -> build/lib.linux-i686-2.7/Bio/Phylo/Applications
copying Bio/Phylo/Applications/_Fasttree.py -> build/lib.linux-i686-2.7/Bio/Phylo/Applications
creating build/lib.linux-i686-2.7/Bio/Phylo/PAML
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copying Bio/Phylo/PAML/_paml.py -> build/lib.linux-i686-2.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/yn00.py -> build/lib.linux-i686-2.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/baseml.py -> build/lib.linux-i686-2.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/chi2.py -> build/lib.linux-i686-2.7/Bio/Phylo/PAML
copying Bio/Phylo/PAML/__init__.py -> build/lib.linux-i686-2.7/Bio/Phylo/PAML
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copying Bio/Phylo/PAML/_parse_yn00.py -> build/lib.linux-i686-2.7/Bio/Phylo/PAML
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creating build/lib.linux-i686-2.7/Bio/UniGene
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creating build/lib.linux-i686-2.7/Bio/UniProt
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creating build/lib.linux-i686-2.7/Bio/Wise
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creating build/lib.linux-i686-2.7/BioSQL
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creating build/lib.linux-i686-2.7/Bio/Affy
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creating build/lib.linux-i686-2.7/Bio/Cluster
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creating build/lib.linux-i686-2.7/Bio/KDTree
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creating build/lib.linux-i686-2.7/Bio/Entrez/DTDs
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copying Bio/Entrez/DTDs/MMDB.dtd -> build/lib.linux-i686-2.7/Bio/Entrez/DTDs
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copying Bio/Entrez/DTDs/list.ent -> build/lib.linux-i686-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isogrk4.ent -> build/lib.linux-i686-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/common.ent -> build/lib.linux-i686-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/isomfrk.ent -> build/lib.linux-i686-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/chars.ent -> build/lib.linux-i686-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/archivecustom-models.ent -> build/lib.linux-i686-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/default-mixes.ent -> build/lib.linux-i686-2.7/Bio/Entrez/DTDs
copying Bio/Entrez/DTDs/mathml2-qname-1.mod -> build/lib.linux-i686-2.7/Bio/Entrez/DTDs
creating build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/split_island.par -> build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/split_ssm_1d.par -> build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/ssm_1d.par -> build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/split_ssm_2d.par -> build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/decline_split.par -> build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/simple.par -> build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/ssm_2d.par -> build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/bottle.par -> build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/island.par -> build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data
copying Bio/PopGen/SimCoal/data/decline_lambda.par -> build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data
running build_ext
building 'Bio.cpairwise2' extension
creating build/temp.linux-i686-2.7
creating build/temp.linux-i686-2.7/Bio
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now -fPIC -I/usr/include/python2.7 -c Bio/cpairwise2module.c -o build/temp.linux-i686-2.7/Bio/cpairwise2module.o
gcc -pthread -shared -Wl,-z,relro -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now build/temp.linux-i686-2.7/Bio/cpairwise2module.o -L/usr/lib -lpython2.7 -o build/lib.linux-i686-2.7/Bio/cpairwise2.so
building 'Bio.trie' extension
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now -fPIC -IBio -I/usr/include/python2.7 -c Bio/triemodule.c -o build/temp.linux-i686-2.7/Bio/triemodule.o
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now -fPIC -IBio -I/usr/include/python2.7 -c Bio/trie.c -o build/temp.linux-i686-2.7/Bio/trie.o
gcc -pthread -shared -Wl,-z,relro -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now build/temp.linux-i686-2.7/Bio/triemodule.o build/temp.linux-i686-2.7/Bio/trie.o -L/usr/lib -lpython2.7 -o build/lib.linux-i686-2.7/Bio/trie.so
building 'Bio.Nexus.cnexus' extension
creating build/temp.linux-i686-2.7/Bio/Nexus
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now -fPIC -I/usr/include/python2.7 -c Bio/Nexus/cnexus.c -o build/temp.linux-i686-2.7/Bio/Nexus/cnexus.o
gcc -pthread -shared -Wl,-z,relro -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now build/temp.linux-i686-2.7/Bio/Nexus/cnexus.o -L/usr/lib -lpython2.7 -o build/lib.linux-i686-2.7/Bio/Nexus/cnexus.so
building 'Bio.Cluster.cluster' extension
creating build/temp.linux-i686-2.7/Bio/Cluster
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now -fPIC -I/usr/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/Cluster/clustermodule.c -o build/temp.linux-i686-2.7/Bio/Cluster/clustermodule.o
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now -fPIC -I/usr/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/Cluster/cluster.c -o build/temp.linux-i686-2.7/Bio/Cluster/cluster.o
gcc -pthread -shared -Wl,-z,relro -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now build/temp.linux-i686-2.7/Bio/Cluster/clustermodule.o build/temp.linux-i686-2.7/Bio/Cluster/cluster.o -L/usr/lib -lpython2.7 -o build/lib.linux-i686-2.7/Bio/Cluster/cluster.so
building 'Bio.KDTree._CKDTree' extension
creating build/temp.linux-i686-2.7/Bio/KDTree
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now -fPIC -I/usr/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/KDTree/KDTree.c -o build/temp.linux-i686-2.7/Bio/KDTree/KDTree.o
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now -fPIC -I/usr/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/KDTree/KDTreemodule.c -o build/temp.linux-i686-2.7/Bio/KDTree/KDTreemodule.o
gcc -pthread -shared -Wl,-z,relro -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now build/temp.linux-i686-2.7/Bio/KDTree/KDTree.o build/temp.linux-i686-2.7/Bio/KDTree/KDTreemodule.o -L/usr/lib -lpython2.7 -o build/lib.linux-i686-2.7/Bio/KDTree/_CKDTree.so
building 'Bio.Motif._pwm' extension
creating build/temp.linux-i686-2.7/Bio/Motif
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now -fPIC -I/usr/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/Motif/_pwm.c -o build/temp.linux-i686-2.7/Bio/Motif/_pwm.o
gcc -pthread -shared -Wl,-z,relro -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now build/temp.linux-i686-2.7/Bio/Motif/_pwm.o -L/usr/lib -lpython2.7 -o build/lib.linux-i686-2.7/Bio/Motif/_pwm.so
building 'Bio.motifs._pwm' extension
creating build/temp.linux-i686-2.7/Bio/motifs
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now -fPIC -I/usr/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/motifs/_pwm.c -o build/temp.linux-i686-2.7/Bio/motifs/_pwm.o
gcc -pthread -shared -Wl,-z,relro -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now build/temp.linux-i686-2.7/Bio/motifs/_pwm.o -L/usr/lib -lpython2.7 -o build/lib.linux-i686-2.7/Bio/motifs/_pwm.so
building 'Bio.PDB.QCPSuperimposer.qcprotmodule' extension
creating build/temp.linux-i686-2.7/Bio/PDB
creating build/temp.linux-i686-2.7/Bio/PDB/QCPSuperimposer
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now -fPIC -I/usr/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c Bio/PDB/QCPSuperimposer/qcprotmodule.c -o build/temp.linux-i686-2.7/Bio/PDB/QCPSuperimposer/qcprotmodule.o
In file included from /usr/include/python2.7/pyconfig.h:4:0,
                 from /usr/include/python2.7/Python.h:8,
                 from Bio/PDB/QCPSuperimposer/qcprotmodule.c:43:
/usr/include/python2.7/pyconfig-32.h:1182:0: warning: "_POSIX_C_SOURCE" redefined [enabled by default]
 #define _POSIX_C_SOURCE 200112L
 ^
In file included from /usr/include/stdio.h:27:0,
                 from Bio/PDB/QCPSuperimposer/qcprotmodule.c:40:
/usr/include/features.h:168:0: note: this is the location of the previous definition
 # define _POSIX_C_SOURCE 200809L
 ^
In file included from /usr/include/python2.7/pyconfig.h:4:0,
                 from /usr/include/python2.7/Python.h:8,
                 from Bio/PDB/QCPSuperimposer/qcprotmodule.c:43:
/usr/include/python2.7/pyconfig-32.h:1204:0: warning: "_XOPEN_SOURCE" redefined [enabled by default]
 #define _XOPEN_SOURCE 600
 ^
In file included from /usr/include/stdio.h:27:0,
                 from Bio/PDB/QCPSuperimposer/qcprotmodule.c:40:
/usr/include/features.h:170:0: note: this is the location of the previous definition
 # define _XOPEN_SOURCE 700
 ^
gcc -pthread -shared -Wl,-z,relro -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m32 -march=x86-64 -mtune=generic -mfpmath=sse -fasynchronous-unwind-tables -Wl,-z,relro -Wl,-z,now build/temp.linux-i686-2.7/Bio/PDB/QCPSuperimposer/qcprotmodule.o -L/usr/lib -lpython2.7 -o build/lib.linux-i686-2.7/Bio/PDB/QCPSuperimposer/qcprotmodule.so
+ popd
+ exit 0
~/build/BUILD/python-biopython-1.66
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.nL6Geo
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386
++ dirname /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386
+ cd python-biopython-1.66
+ pushd python2
~/build/BUILD/python-biopython-1.66/python2 ~/build/BUILD/python-biopython-1.66
+ /usr/bin/python2 setup.py install -O1 --skip-build --root=/builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386 --install-data=/usr/share/python-biopython
running install
running install_lib
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
copying build/lib.linux-i686-2.7/Bio/pairwise2.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/CAPS
copying build/lib.linux-i686-2.7/Bio/CAPS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/CAPS
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Medline
copying build/lib.linux-i686-2.7/Bio/Medline/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Medline
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Geo
copying build/lib.linux-i686-2.7/Bio/Geo/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Geo
copying build/lib.linux-i686-2.7/Bio/Geo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Geo
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/HmmerIO/hmmer3_domtab.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/HmmerIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/HmmerIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/HmmerIO/hmmer3_text.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/HmmerIO/hmmer2_text.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/HmmerIO/hmmer3_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/BlatIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/BlastIO/blast_tab.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/BlastIO/blast_text.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/BlastIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/BlastIO/blast_xml.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/BlastIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/ExonerateIO/exonerate_cigar.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/ExonerateIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/ExonerateIO/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/ExonerateIO
copying build/lib.linux-i686-2.7/Bio/SearchIO/ExonerateIO/exonerate_text.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/ExonerateIO
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-i686-2.7/Bio/SearchIO/_model/hsp.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-i686-2.7/Bio/SearchIO/_model/hit.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-i686-2.7/Bio/SearchIO/_model/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-i686-2.7/Bio/SearchIO/_model/_base.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-i686-2.7/Bio/SearchIO/_model/query.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/_model
copying build/lib.linux-i686-2.7/Bio/SearchIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Crystal
copying build/lib.linux-i686-2.7/Bio/Crystal/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Crystal
copying build/lib.linux-i686-2.7/Bio/MaxEntropy.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Emboss
copying build/lib.linux-i686-2.7/Bio/Emboss/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Emboss
copying build/lib.linux-i686-2.7/Bio/Emboss/Primer3.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Emboss
copying build/lib.linux-i686-2.7/Bio/Emboss/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Emboss
copying build/lib.linux-i686-2.7/Bio/Emboss/PrimerSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Emboss
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Restriction
copying build/lib.linux-i686-2.7/Bio/Restriction/PrintFormat.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Restriction
copying build/lib.linux-i686-2.7/Bio/Restriction/Restriction.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Restriction
copying build/lib.linux-i686-2.7/Bio/Restriction/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Restriction
copying build/lib.linux-i686-2.7/Bio/Restriction/Restriction_Dictionary.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Restriction
copying build/lib.linux-i686-2.7/Bio/Restriction/RanaConfig.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Restriction
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Data
copying build/lib.linux-i686-2.7/Bio/Data/CodonTable.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Data
copying build/lib.linux-i686-2.7/Bio/Data/IUPACData.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Data
copying build/lib.linux-i686-2.7/Bio/Data/SCOPData.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Data
copying build/lib.linux-i686-2.7/Bio/Data/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Data
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram/_Colors.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram/_CircularDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram/_GraphSet.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram/_Feature.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram/_FeatureSet.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram/_Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram/_Track.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram/_CrossLink.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram/_LinearDrawer.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-2.7/Bio/Graphics/GenomeDiagram/_Diagram.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram
copying build/lib.linux-i686-2.7/Bio/Graphics/ColorSpiral.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics
copying build/lib.linux-i686-2.7/Bio/Graphics/BasicChromosome.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics
copying build/lib.linux-i686-2.7/Bio/Graphics/KGML_vis.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics
copying build/lib.linux-i686-2.7/Bio/Graphics/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics
copying build/lib.linux-i686-2.7/Bio/Graphics/Distribution.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics
copying build/lib.linux-i686-2.7/Bio/Graphics/Comparative.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics
copying build/lib.linux-i686-2.7/Bio/Graphics/DisplayRepresentation.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/_py3k
copying build/lib.linux-i686-2.7/Bio/_py3k/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/_py3k
copying build/lib.linux-i686-2.7/Bio/_py3k/_ordereddict.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/_py3k
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GenBank
copying build/lib.linux-i686-2.7/Bio/GenBank/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GenBank
copying build/lib.linux-i686-2.7/Bio/GenBank/utils.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GenBank
copying build/lib.linux-i686-2.7/Bio/GenBank/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GenBank
copying build/lib.linux-i686-2.7/Bio/GenBank/Scanner.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GenBank
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SubsMat
copying build/lib.linux-i686-2.7/Bio/SubsMat/MatrixInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SubsMat
copying build/lib.linux-i686-2.7/Bio/SubsMat/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SubsMat
copying build/lib.linux-i686-2.7/Bio/SubsMat/FreqTable.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SubsMat
copying build/lib.linux-i686-2.7/Bio/cpairwise2.so -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Wise
copying build/lib.linux-i686-2.7/Bio/Wise/dnal.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Wise
copying build/lib.linux-i686-2.7/Bio/Wise/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Wise
copying build/lib.linux-i686-2.7/Bio/Wise/psw.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Wise
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal
copying build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/Controller.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal
copying build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/Async.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data/split_island.par -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data/split_ssm_1d.par -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data/ssm_1d.par -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data/split_ssm_2d.par -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data/decline_split.par -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data/simple.par -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data/ssm_2d.par -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data/bottle.par -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data/island.par -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/data/decline_lambda.par -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal/data
copying build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal
copying build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/Cache.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal
copying build/lib.linux-i686-2.7/Bio/PopGen/SimCoal/Template.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/SimCoal
copying build/lib.linux-i686-2.7/Bio/PopGen/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/FDist
copying build/lib.linux-i686-2.7/Bio/PopGen/FDist/Controller.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/FDist
copying build/lib.linux-i686-2.7/Bio/PopGen/FDist/Async.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/FDist
copying build/lib.linux-i686-2.7/Bio/PopGen/FDist/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/FDist
copying build/lib.linux-i686-2.7/Bio/PopGen/FDist/Utils.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/FDist
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-2.7/Bio/PopGen/GenePop/Controller.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-2.7/Bio/PopGen/GenePop/LargeFileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-2.7/Bio/PopGen/GenePop/EasyController.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-2.7/Bio/PopGen/GenePop/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-2.7/Bio/PopGen/GenePop/FileParser.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop
copying build/lib.linux-i686-2.7/Bio/PopGen/GenePop/Utils.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/GenePop
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/Async
copying build/lib.linux-i686-2.7/Bio/PopGen/Async/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/Async
copying build/lib.linux-i686-2.7/Bio/PopGen/Async/Local.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PopGen/Async
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/UniProt
copying build/lib.linux-i686-2.7/Bio/UniProt/GOA.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/UniProt
copying build/lib.linux-i686-2.7/Bio/UniProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/UniProt
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/NMR
copying build/lib.linux-i686-2.7/Bio/NMR/NOEtools.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/NMR
copying build/lib.linux-i686-2.7/Bio/NMR/xpktools.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/NMR
copying build/lib.linux-i686-2.7/Bio/NMR/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/NMR
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Pathway
copying build/lib.linux-i686-2.7/Bio/Pathway/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Pathway
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Pathway/Rep
copying build/lib.linux-i686-2.7/Bio/Pathway/Rep/MultiGraph.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Pathway/Rep
copying build/lib.linux-i686-2.7/Bio/Pathway/Rep/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Pathway/Rep
copying build/lib.linux-i686-2.7/Bio/Pathway/Rep/Graph.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Pathway/Rep
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Nexus
copying build/lib.linux-i686-2.7/Bio/Nexus/Nexus.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Nexus
copying build/lib.linux-i686-2.7/Bio/Nexus/Nodes.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Nexus
copying build/lib.linux-i686-2.7/Bio/Nexus/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Nexus
copying build/lib.linux-i686-2.7/Bio/Nexus/Trees.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Nexus
copying build/lib.linux-i686-2.7/Bio/Nexus/cnexus.so -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Nexus
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/TogoWS
copying build/lib.linux-i686-2.7/Bio/TogoWS/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/TogoWS
copying build/lib.linux-i686-2.7/Bio/DocSQL.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Cluster
copying build/lib.linux-i686-2.7/Bio/Cluster/cluster.so -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Cluster
copying build/lib.linux-i686-2.7/Bio/Cluster/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Cluster
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SVDSuperimposer
copying build/lib.linux-i686-2.7/Bio/SVDSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SVDSuperimposer
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/UniGene
copying build/lib.linux-i686-2.7/Bio/UniGene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/UniGene
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez
copying build/lib.linux-i686-2.7/Bio/Entrez/Parser.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez
copying build/lib.linux-i686-2.7/Bio/Entrez/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmmedline_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Seq_split.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/MMDB.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_BlastOutput.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmcommon_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_ScoreMat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Seqloc.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isogrk1.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Protein.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_MedArchive.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/SP_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NSE.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Cdd.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isotech.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isobox.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_ID2Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Pub.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/articlemeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/mathmlsetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_PCSubstance.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Entrezgene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Remap.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_BlastDL.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Cdd.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isocyr1.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/eSpell.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/mathml2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isodia.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/Docsum_3_0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/MMDB_Structural_model.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Gene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isoamsn.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/pubmed_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/journalmeta.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isolat1.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NSE.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/format.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Seqalign.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/htmltable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/MMDB_Features.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isogrk3.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Organism.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Entrez2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmmedline_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmserials_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_FeatDef.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_PCAssay.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/SP_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/eLink_101123.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/INSD_INSDSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_PCSubstance.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isoamso.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Remap.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/pubmed_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Seqfeat.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Variation.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/section.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isoamsc.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isopub.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/backmatter.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/INSD_INSDSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/XHTMLtablesetup.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/pubmed_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/pubmed_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isocyr2.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/GenBank_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isonum.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/bookdoc_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlm-articleset-2.0.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_RNA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/link.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/notat.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_TxInit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Mim.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_GBSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Mime.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_PubMed.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Pub.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_ID1Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/pubmed_020114.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Submit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmcommon_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Seqres.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/HomoloGene.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/EMBL_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Project.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/bookdoc_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/OMSSA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isolat2.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/xmlspecchars.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/HomoloGene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isoamsa.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/Docsum_3_1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Seqloc.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Medline.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Rsite.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/Docsum_3_1.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Seqset.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/archivecustom-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/MMDB_Chemical_graph.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/pubmed_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/EMBL_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_120101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Cn3d.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_ObjPrt.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_PubMed.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_SeqCode.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/Docsum_3_2.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Sequence.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/einfo.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/pubmed_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Blast4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Protein.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/Docsum_3_3.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Rsite.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_FeatDef.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/pubmed_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Medline.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/taxon.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/pubmed_150101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/GenBank_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Sequence.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/MMDB_Structural_model.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isomopf.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_SeqTable.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isoamsr.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/elink_020122.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/mmlextra.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/PRF_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Submit.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Entity.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/Docsum_3_3.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_130501.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/PRF_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_all.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/eInfo_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_ScoreMat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isoamsb.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmmedlinecitation_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/MMDB_Chemical_graph.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/para.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/OMSSA.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/archivecustom-modules.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_SeqCode.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/bookdoc_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/eSearch_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_BioTree.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/Docsum_3_2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_BioSource.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_PCAssay.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/bookdoc_100301.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmmedlinecitation_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmsharedcatcit_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/pubmed_140101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/bookdoc_110101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/references.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/egquery.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/archivearticle.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Project.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/PDB_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_TSeq.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmcommon_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Biblio.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/display.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_SeqTable.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isomscr.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/pubmed_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Seqset.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Entrez2.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/eLink_090910.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isogrk2.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/phrase.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/default-classes.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/MMDB_Features.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/esearch.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_RNA.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/PDB_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmserials_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_TSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/ePost_020511.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/bookdoc_130101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Mime.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_ID1Access.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/PIR_General.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/math.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Medlars.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/mmlalias.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Cn3d.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/Docsum_3_0.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Organism.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/archivecustom-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/mathml2-qname-1.mod -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Seqfeat.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Blast4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Mim.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Medlars.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_GBSeq.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/list.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_ID2Access.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmmedline_011101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isogrk4.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Seqalign.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmmedlinecitationset_100101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/Docsum_3_4.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_ObjPrt.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/PIR_General.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/common.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_BioSource.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/isomfrk.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_TxInit.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Variation.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Seq_split.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/MMDB.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmsharedcatcit_090101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Gene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/chars.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/eSummary_041029.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_BioTree.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Seqres.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/pmc-1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/Docsum_3_4.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/archivecustom-models.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/esummary-v1.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Entrezgene.mod.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_Biblio.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_MedArchive.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/default-mixes.ent -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/nlmmedlinecitation_080101.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_BlastOutput.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/Entrez/DTDs/NCBI_BlastDL.dtd -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Entrez/DTDs
copying build/lib.linux-i686-2.7/Bio/bgzf.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
copying build/lib.linux-i686-2.7/Bio/triefind.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/KDTree
copying build/lib.linux-i686-2.7/Bio/KDTree/_CKDTree.so -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/KDTree
copying build/lib.linux-i686-2.7/Bio/KDTree/KDTree.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/KDTree
copying build/lib.linux-i686-2.7/Bio/KDTree/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/KDTree
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SCOP
copying build/lib.linux-i686-2.7/Bio/SCOP/Des.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SCOP
copying build/lib.linux-i686-2.7/Bio/SCOP/Residues.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SCOP
copying build/lib.linux-i686-2.7/Bio/SCOP/Hie.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SCOP
copying build/lib.linux-i686-2.7/Bio/SCOP/Cla.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SCOP
copying build/lib.linux-i686-2.7/Bio/SCOP/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SCOP
copying build/lib.linux-i686-2.7/Bio/SCOP/Raf.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SCOP
copying build/lib.linux-i686-2.7/Bio/SCOP/Dom.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SCOP
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/AlignIO
copying build/lib.linux-i686-2.7/Bio/AlignIO/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/AlignIO
copying build/lib.linux-i686-2.7/Bio/AlignIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/AlignIO
copying build/lib.linux-i686-2.7/Bio/AlignIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/AlignIO
copying build/lib.linux-i686-2.7/Bio/AlignIO/StockholmIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/AlignIO
copying build/lib.linux-i686-2.7/Bio/AlignIO/EmbossIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/AlignIO
copying build/lib.linux-i686-2.7/Bio/AlignIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/AlignIO
copying build/lib.linux-i686-2.7/Bio/AlignIO/ClustalIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/AlignIO
copying build/lib.linux-i686-2.7/Bio/AlignIO/PhylipIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/AlignIO
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SwissProt
copying build/lib.linux-i686-2.7/Bio/SwissProt/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SwissProt
copying build/lib.linux-i686-2.7/Bio/SwissProt/KeyWList.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SwissProt
copying build/lib.linux-i686-2.7/Bio/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Application
copying build/lib.linux-i686-2.7/Bio/Application/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Application
copying build/lib.linux-i686-2.7/Bio/LogisticRegression.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Compass
copying build/lib.linux-i686-2.7/Bio/Compass/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Compass
copying build/lib.linux-i686-2.7/Bio/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Blast
copying build/lib.linux-i686-2.7/Bio/Blast/Record.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Blast
copying build/lib.linux-i686-2.7/Bio/Blast/NCBIXML.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Blast
copying build/lib.linux-i686-2.7/Bio/Blast/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Blast
copying build/lib.linux-i686-2.7/Bio/Blast/NCBIStandalone.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Blast
copying build/lib.linux-i686-2.7/Bio/Blast/Applications.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Blast
copying build/lib.linux-i686-2.7/Bio/Blast/ParseBlastTable.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Blast
copying build/lib.linux-i686-2.7/Bio/Blast/NCBIWWW.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Blast
copying build/lib.linux-i686-2.7/Bio/Seq.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Sequencing
copying build/lib.linux-i686-2.7/Bio/Sequencing/Ace.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Sequencing
copying build/lib.linux-i686-2.7/Bio/Sequencing/Phd.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Sequencing
copying build/lib.linux-i686-2.7/Bio/Sequencing/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Sequencing
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-i686-2.7/Bio/Sequencing/Applications/_Novoalign.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-i686-2.7/Bio/Sequencing/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-i686-2.7/Bio/Sequencing/Applications/_bwa.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Sequencing/Applications
copying build/lib.linux-i686-2.7/Bio/Sequencing/Applications/_samtools.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Sequencing/Applications
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/NeuralNetwork
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/Gene
copying build/lib.linux-i686-2.7/Bio/NeuralNetwork/Gene/Motif.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/Gene
copying build/lib.linux-i686-2.7/Bio/NeuralNetwork/Gene/Signature.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/Gene
copying build/lib.linux-i686-2.7/Bio/NeuralNetwork/Gene/Schema.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/Gene
copying build/lib.linux-i686-2.7/Bio/NeuralNetwork/Gene/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/Gene
copying build/lib.linux-i686-2.7/Bio/NeuralNetwork/Gene/Pattern.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/Gene
copying build/lib.linux-i686-2.7/Bio/NeuralNetwork/StopTraining.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/NeuralNetwork
copying build/lib.linux-i686-2.7/Bio/NeuralNetwork/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/NeuralNetwork
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/BackPropagation
copying build/lib.linux-i686-2.7/Bio/NeuralNetwork/BackPropagation/Network.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/BackPropagation
copying build/lib.linux-i686-2.7/Bio/NeuralNetwork/BackPropagation/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/BackPropagation
copying build/lib.linux-i686-2.7/Bio/NeuralNetwork/BackPropagation/Layer.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/NeuralNetwork/BackPropagation
copying build/lib.linux-i686-2.7/Bio/NeuralNetwork/Training.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/NeuralNetwork
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Align
copying build/lib.linux-i686-2.7/Bio/Align/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Align
copying build/lib.linux-i686-2.7/Bio/Align/AlignInfo.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Align
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-2.7/Bio/Align/Applications/_MSAProbs.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-2.7/Bio/Align/Applications/_Probcons.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-2.7/Bio/Align/Applications/_Mafft.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-2.7/Bio/Align/Applications/_ClustalOmega.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-2.7/Bio/Align/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-2.7/Bio/Align/Applications/_Prank.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-2.7/Bio/Align/Applications/_Clustalw.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-2.7/Bio/Align/Applications/_Dialign.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-2.7/Bio/Align/Applications/_Muscle.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-2.7/Bio/Align/Applications/_TCoffee.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Align/Applications
copying build/lib.linux-i686-2.7/Bio/Align/Generic.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Align
copying build/lib.linux-i686-2.7/Bio/SeqRecord.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
copying build/lib.linux-i686-2.7/Bio/NaiveBayes.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Alphabet
copying build/lib.linux-i686-2.7/Bio/Alphabet/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Alphabet
copying build/lib.linux-i686-2.7/Bio/Alphabet/IUPAC.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Alphabet
copying build/lib.linux-i686-2.7/Bio/Alphabet/Reduced.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Alphabet
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Affy
copying build/lib.linux-i686-2.7/Bio/Affy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Affy
copying build/lib.linux-i686-2.7/Bio/Affy/CelFile.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Affy
copying build/lib.linux-i686-2.7/Bio/ParserSupport.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
copying build/lib.linux-i686-2.7/Bio/File.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-2.7/Bio/Phylo/NewickIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-2.7/Bio/Phylo/NexusIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-2.7/Bio/Phylo/BaseTree.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-2.7/Bio/Phylo/PAML/codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-2.7/Bio/Phylo/PAML/_paml.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-2.7/Bio/Phylo/PAML/yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-2.7/Bio/Phylo/PAML/baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-2.7/Bio/Phylo/PAML/chi2.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-2.7/Bio/Phylo/PAML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-2.7/Bio/Phylo/PAML/_parse_baseml.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-2.7/Bio/Phylo/PAML/_parse_yn00.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-2.7/Bio/Phylo/PAML/_parse_codeml.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo/PAML
copying build/lib.linux-i686-2.7/Bio/Phylo/PhyloXML.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-2.7/Bio/Phylo/_cdao_owl.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-2.7/Bio/Phylo/Consensus.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-2.7/Bio/Phylo/_io.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-2.7/Bio/Phylo/NeXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-2.7/Bio/Phylo/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-2.7/Bio/Phylo/_utils.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-2.7/Bio/Phylo/NeXML.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-2.7/Bio/Phylo/CDAOIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-2.7/Bio/Phylo/Newick.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-2.7/Bio/Phylo/CDAO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-i686-2.7/Bio/Phylo/Applications/_Raxml.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-i686-2.7/Bio/Phylo/Applications/_Phyml.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-i686-2.7/Bio/Phylo/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-i686-2.7/Bio/Phylo/Applications/_Fasttree.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo/Applications
copying build/lib.linux-i686-2.7/Bio/Phylo/TreeConstruction.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo
copying build/lib.linux-i686-2.7/Bio/Phylo/PhyloXMLIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Phylo
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/FSSP
copying build/lib.linux-i686-2.7/Bio/FSSP/fssp_rec.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/FSSP
copying build/lib.linux-i686-2.7/Bio/FSSP/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/FSSP
copying build/lib.linux-i686-2.7/Bio/FSSP/FSSPTools.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/FSSP
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Statistics
copying build/lib.linux-i686-2.7/Bio/Statistics/lowess.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Statistics
copying build/lib.linux-i686-2.7/Bio/Statistics/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Statistics
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/SeqIO/Interfaces.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/SeqIO/SwissIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/SeqIO/FastaIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/SeqIO/UniprotIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/SeqIO/SeqXmlIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/SeqIO/_convert.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/SeqIO/AbiIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/SeqIO/PdbIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/SeqIO/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/SeqIO/PhdIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/SeqIO/SffIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/SeqIO/TabIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/SeqIO/IgIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/SeqIO/PirIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/SeqIO/_index.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/SeqIO/AceIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/SeqIO/QualityIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/SeqIO/InsdcIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqIO
copying build/lib.linux-i686-2.7/Bio/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
copying build/lib.linux-i686-2.7/Bio/kNN.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/codonalign
copying build/lib.linux-i686-2.7/Bio/codonalign/codonseq.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/codonalign
copying build/lib.linux-i686-2.7/Bio/codonalign/codonalignment.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/codonalign
copying build/lib.linux-i686-2.7/Bio/codonalign/codonalphabet.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/codonalign
copying build/lib.linux-i686-2.7/Bio/codonalign/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/codonalign
copying build/lib.linux-i686-2.7/Bio/codonalign/chisq.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/codonalign
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/motifs
copying build/lib.linux-i686-2.7/Bio/motifs/thresholds.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/motifs
copying build/lib.linux-i686-2.7/Bio/motifs/alignace.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/motifs
copying build/lib.linux-i686-2.7/Bio/motifs/mast.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/motifs
copying build/lib.linux-i686-2.7/Bio/motifs/meme.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/motifs
copying build/lib.linux-i686-2.7/Bio/motifs/matrix.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/motifs
copying build/lib.linux-i686-2.7/Bio/motifs/_pwm.so -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/motifs
copying build/lib.linux-i686-2.7/Bio/motifs/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/motifs
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/motifs/jaspar
copying build/lib.linux-i686-2.7/Bio/motifs/jaspar/db.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/motifs/jaspar
copying build/lib.linux-i686-2.7/Bio/motifs/jaspar/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/motifs/jaspar
copying build/lib.linux-i686-2.7/Bio/motifs/transfac.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/motifs
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/motifs/applications
copying build/lib.linux-i686-2.7/Bio/motifs/applications/_xxmotif.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/motifs/applications
copying build/lib.linux-i686-2.7/Bio/motifs/applications/_alignace.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/motifs/applications
copying build/lib.linux-i686-2.7/Bio/motifs/applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/motifs/applications
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/HMM
copying build/lib.linux-i686-2.7/Bio/HMM/Trainer.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/HMM
copying build/lib.linux-i686-2.7/Bio/HMM/DynamicProgramming.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/HMM
copying build/lib.linux-i686-2.7/Bio/HMM/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/HMM
copying build/lib.linux-i686-2.7/Bio/HMM/MarkovModel.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/HMM
copying build/lib.linux-i686-2.7/Bio/HMM/Utilities.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/HMM
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/KEGG
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/KEGG/Compound
copying build/lib.linux-i686-2.7/Bio/KEGG/Compound/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/KEGG/Compound
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/KEGG/Map
copying build/lib.linux-i686-2.7/Bio/KEGG/Map/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/KEGG/Map
copying build/lib.linux-i686-2.7/Bio/KEGG/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/KEGG
copying build/lib.linux-i686-2.7/Bio/KEGG/REST.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/KEGG
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/KEGG/KGML
copying build/lib.linux-i686-2.7/Bio/KEGG/KGML/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/KEGG/KGML
copying build/lib.linux-i686-2.7/Bio/KEGG/KGML/KGML_parser.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/KEGG/KGML
copying build/lib.linux-i686-2.7/Bio/KEGG/KGML/KGML_pathway.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/KEGG/KGML
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/KEGG/Enzyme
copying build/lib.linux-i686-2.7/Bio/KEGG/Enzyme/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/KEGG/Enzyme
copying build/lib.linux-i686-2.7/Bio/Index.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-2.7/Bio/SeqUtils/ProtParamData.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-2.7/Bio/SeqUtils/CodonUsageIndices.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-2.7/Bio/SeqUtils/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-2.7/Bio/SeqUtils/MeltingTemp.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-2.7/Bio/SeqUtils/CodonUsage.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-2.7/Bio/SeqUtils/CheckSum.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-2.7/Bio/SeqUtils/lcc.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-2.7/Bio/SeqUtils/ProtParam.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-2.7/Bio/SeqUtils/IsoelectricPoint.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SeqUtils
copying build/lib.linux-i686-2.7/Bio/trie.so -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/Vector.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/StructureAlignment.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/ResidueDepth.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/AbstractPropertyMap.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/Dice.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/Residue.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/PSEA.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-i686-2.7/Bio/PDB/QCPSuperimposer/qcprotmodule.so -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-i686-2.7/Bio/PDB/QCPSuperimposer/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB/QCPSuperimposer
copying build/lib.linux-i686-2.7/Bio/PDB/MMCIF2Dict.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/NeighborSearch.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/PDBList.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/NACCESS.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/PDBExceptions.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/Superimposer.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/Chain.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/DSSP.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/Polypeptide.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/Structure.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/FragmentMapper.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/PDBIO.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/StructureBuilder.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/Atom.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/Entity.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/Model.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/MMCIFParser.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/Selection.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/parse_pdb_header.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/HSExposure.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
copying build/lib.linux-i686-2.7/Bio/PDB/PDBParser.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/ExPASy
copying build/lib.linux-i686-2.7/Bio/ExPASy/ScanProsite.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/ExPASy
copying build/lib.linux-i686-2.7/Bio/ExPASy/Prosite.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/ExPASy
copying build/lib.linux-i686-2.7/Bio/ExPASy/Enzyme.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/ExPASy
copying build/lib.linux-i686-2.7/Bio/ExPASy/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/ExPASy
copying build/lib.linux-i686-2.7/Bio/ExPASy/Prodoc.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/ExPASy
copying build/lib.linux-i686-2.7/Bio/SeqFeature.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA
copying build/lib.linux-i686-2.7/Bio/GA/Organism.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Mutation
copying build/lib.linux-i686-2.7/Bio/GA/Mutation/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Mutation
copying build/lib.linux-i686-2.7/Bio/GA/Mutation/General.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Mutation
copying build/lib.linux-i686-2.7/Bio/GA/Mutation/Simple.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Mutation
copying build/lib.linux-i686-2.7/Bio/GA/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Selection
copying build/lib.linux-i686-2.7/Bio/GA/Selection/Diversity.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Selection
copying build/lib.linux-i686-2.7/Bio/GA/Selection/Tournament.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Selection
copying build/lib.linux-i686-2.7/Bio/GA/Selection/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Selection
copying build/lib.linux-i686-2.7/Bio/GA/Selection/Abstract.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Selection
copying build/lib.linux-i686-2.7/Bio/GA/Selection/RouletteWheel.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Selection
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Crossover
copying build/lib.linux-i686-2.7/Bio/GA/Crossover/Point.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Crossover
copying build/lib.linux-i686-2.7/Bio/GA/Crossover/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Crossover
copying build/lib.linux-i686-2.7/Bio/GA/Crossover/General.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Crossover
copying build/lib.linux-i686-2.7/Bio/GA/Crossover/Uniform.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Crossover
copying build/lib.linux-i686-2.7/Bio/GA/Crossover/TwoPoint.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Crossover
copying build/lib.linux-i686-2.7/Bio/GA/Crossover/GeneralPoint.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Crossover
copying build/lib.linux-i686-2.7/Bio/GA/Evolver.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Repair
copying build/lib.linux-i686-2.7/Bio/GA/Repair/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Repair
copying build/lib.linux-i686-2.7/Bio/GA/Repair/Stabilizing.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/GA/Repair
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Motif
copying build/lib.linux-i686-2.7/Bio/Motif/Thresholds.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Motif
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Motif/Parsers
copying build/lib.linux-i686-2.7/Bio/Motif/Parsers/MEME.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Motif/Parsers
copying build/lib.linux-i686-2.7/Bio/Motif/Parsers/AlignAce.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Motif/Parsers
copying build/lib.linux-i686-2.7/Bio/Motif/Parsers/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Motif/Parsers
copying build/lib.linux-i686-2.7/Bio/Motif/Parsers/MAST.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Motif/Parsers
copying build/lib.linux-i686-2.7/Bio/Motif/_pwm.so -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Motif
copying build/lib.linux-i686-2.7/Bio/Motif/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Motif
copying build/lib.linux-i686-2.7/Bio/Motif/_Motif.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Motif
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Motif/Applications
copying build/lib.linux-i686-2.7/Bio/Motif/Applications/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Motif/Applications
creating /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/BioSQL
copying build/lib.linux-i686-2.7/BioSQL/DBUtils.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/BioSQL
copying build/lib.linux-i686-2.7/BioSQL/BioSeq.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/BioSQL
copying build/lib.linux-i686-2.7/BioSQL/Loader.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/BioSQL
copying build/lib.linux-i686-2.7/BioSQL/__init__.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/BioSQL
copying build/lib.linux-i686-2.7/BioSQL/BioSeqDatabase.py -> /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/BioSQL
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/pairwise2.py to pairwise2.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/CAPS/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Medline/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Geo/Record.py to Record.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Geo/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/FastaIO.py to FastaIO.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO/hmmer3_domtab.py to hmmer3_domtab.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO/_base.py to _base.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO/hmmer3_text.py to hmmer3_text.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO/hmmer2_text.py to hmmer2_text.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO/hmmer3_tab.py to hmmer3_tab.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/BlatIO.py to BlatIO.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/BlastIO/blast_tab.py to blast_tab.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/BlastIO/blast_text.py to blast_text.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/BlastIO/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/BlastIO/blast_xml.py to blast_xml.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/_utils.py to _utils.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/ExonerateIO/exonerate_vulgar.py to exonerate_vulgar.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/ExonerateIO/exonerate_cigar.py to exonerate_cigar.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/ExonerateIO/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/ExonerateIO/_base.py to _base.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/ExonerateIO/exonerate_text.py to exonerate_text.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/_model/hsp.py to hsp.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/_model/hit.py to hit.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/_model/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/_model/_base.py to _base.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/_model/query.py to query.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/SearchIO/_index.py to _index.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Crystal/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/MaxEntropy.py to MaxEntropy.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Emboss/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Emboss/Primer3.py to Primer3.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Emboss/Applications.py to Applications.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Emboss/PrimerSearch.py to PrimerSearch.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Restriction/PrintFormat.py to PrintFormat.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Restriction/Restriction.py to Restriction.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Restriction/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Restriction/Restriction_Dictionary.py to Restriction_Dictionary.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Restriction/RanaConfig.py to RanaConfig.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Data/CodonTable.py to CodonTable.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Data/IUPACData.py to IUPACData.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Data/SCOPData.py to SCOPData.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Data/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_Colors.py to _Colors.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_CircularDrawer.py to _CircularDrawer.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_GraphSet.py to _GraphSet.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_Feature.py to _Feature.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py to _AbstractDrawer.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_FeatureSet.py to _FeatureSet.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_Graph.py to _Graph.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_Track.py to _Track.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_CrossLink.py to _CrossLink.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/__init__.py to __init__.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_LinearDrawer.py to _LinearDrawer.pyc
byte-compiling /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Graphics/GenomeDiagram/_Diagram.py to _Diagram.pyc
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writing byte-compilation script '/tmp/tmpUAd6A2.py'
/usr/bin/python2 -O /tmp/tmpUAd6A2.py
removing /tmp/tmpUAd6A2.py
running install_egg_info
Writing /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/biopython-1.66-py2.7.egg-info
+ popd
~/build/BUILD/python-biopython-1.66
+ /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 /builddir/build/BUILD/python-biopython-1.66
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/cpairwise2.so
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extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Cluster/cluster.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/KDTree/_CKDTree.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/motifs/_pwm.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/trie.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/PDB/QCPSuperimposer/qcprotmodule.so
extracting debug info from /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7/site-packages/Bio/Motif/_pwm.so
/usr/lib/rpm/sepdebugcrcfix: Updated 8 CRC32s, 0 CRC32s did match.
750 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1
Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/python2.7 using /usr/bin/python2.7
Bytecompiling .py files below /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/lib/debug/usr/lib/python2.7 using /usr/bin/python2.7
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-java-repack-jars
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.u3U5Z0
+ umask 022
~/build/BUILD/python-biopython-1.66/python2/Tests ~/build/BUILD/python-biopython-1.66
+ cd /builddir/build/BUILD
+ cd python-biopython-1.66
+ pushd python2/Tests
+ find . -name run_tests.py
+ xargs sed -i '1s|^#!/usr/bin/env python|#!/usr/bin/python2|'
++ grep -v Tutorial
++ ls test_Ace.py test_AlignIO.py test_AlignIO_ClustalIO.py test_AlignIO_EmbossIO.py test_AlignIO_FastaIO.py test_AlignIO_PhylipIO.py test_AlignIO_convert.py test_Application.py test_BWA_tool.py test_BioSQL_MySQLdb.py test_BioSQL_mysql_connector.py test_BioSQL_psycopg2.py test_BioSQL_sqlite3.py test_CAPS.py test_CelFile.py test_Chi2.py test_ClustalOmega_tool.py test_Clustalw_tool.py test_Cluster.py test_CodonTable.py test_CodonUsage.py test_ColorSpiral.py test_Compass.py test_Consensus.py test_Crystal.py test_DSSP_tool.py test_Dialign_tool.py test_DocSQL.py test_EMBL_unittest.py test_Emboss.py test_EmbossPhylipNew.py test_EmbossPrimer.py test_Entrez.py test_Entrez_online.py test_Enzyme.py test_FSSP.py test_Fasttree_tool.py test_File.py test_GACrossover.py test_GAMutation.py test_GAOrganism.py test_GAQueens.py test_GARepair.py test_GASelection.py test_GenBank.py test_GenBank_unittest.py test_GenomeDiagram.py test_GraphicsBitmaps.py test_GraphicsChromosome.py test_GraphicsDistribution.py test_GraphicsGeneral.py test_HMMCasino.py test_HMMGeneral.py test_KDTree.py test_KEGG.py test_KEGG_online.py test_KGML_graphics.py test_KGML_graphics_online.py test_KGML_nographics.py test_KeyWList.py test_Location.py test_LogisticRegression.py test_MMCIF.py test_MSAProbs_tool.py test_Mafft_tool.py test_MarkovModel.py test_Medline.py test_Motif.py test_Muscle_tool.py test_NACCESS_tool.py test_NCBITextParser.py test_NCBIXML.py test_NCBI_BLAST_tools.py test_NCBI_qblast.py test_NNExclusiveOr.py test_NNGene.py test_NNGeneral.py test_Nexus.py test_PAML_baseml.py test_PAML_codeml.py test_PAML_tools.py test_PAML_yn00.py test_PDB.py test_PDB_KDTree.py test_ParserSupport.py test_Pathway.py test_Phd.py test_Phylo.py test_PhyloXML.py test_Phylo_CDAO.py test_Phylo_NeXML.py test_Phylo_depend.py test_PopGen_DFDist.py test_PopGen_FDist.py test_PopGen_FDist_nodepend.py test_PopGen_FastSimCoal.py test_PopGen_GenePop.py test_PopGen_GenePop_EasyController.py test_PopGen_GenePop_nodepend.py test_PopGen_SimCoal.py test_PopGen_SimCoal_nodepend.py test_Prank_tool.py test_Probcons_tool.py test_ProtParam.py test_QCPSuperimposer.py test_Restriction.py test_SCOP_Astral.py test_SCOP_Cla.py test_SCOP_Des.py test_SCOP_Dom.py test_SCOP_Hie.py test_SCOP_Raf.py test_SCOP_Residues.py test_SCOP_Scop.py test_SCOP_online.py test_SVDSuperimposer.py test_SearchIO_blast_tab.py test_SearchIO_blast_tab_index.py test_SearchIO_blast_text.py test_SearchIO_blast_xml.py test_SearchIO_blast_xml_index.py test_SearchIO_blat_psl.py test_SearchIO_blat_psl_index.py test_SearchIO_exonerate.py test_SearchIO_exonerate_text_index.py test_SearchIO_exonerate_vulgar_index.py test_SearchIO_fasta_m10.py test_SearchIO_fasta_m10_index.py test_SearchIO_hmmer2_text.py test_SearchIO_hmmer2_text_index.py test_SearchIO_hmmer3_domtab.py test_SearchIO_hmmer3_domtab_index.py test_SearchIO_hmmer3_tab.py test_SearchIO_hmmer3_tab_index.py test_SearchIO_hmmer3_text.py test_SearchIO_hmmer3_text_index.py test_SearchIO_model.py test_SearchIO_write.py test_SeqIO.py test_SeqIO_AbiIO.py test_SeqIO_FastaIO.py test_SeqIO_Insdc.py test_SeqIO_PdbIO.py test_SeqIO_QualityIO.py test_SeqIO_SeqXML.py test_SeqIO_convert.py test_SeqIO_features.py test_SeqIO_index.py test_SeqIO_online.py test_SeqIO_write.py test_SeqRecord.py test_SeqUtils.py test_Seq_objs.py test_SffIO.py test_SubsMat.py test_SwissProt.py test_TCoffee_tool.py test_TogoWS.py test_TreeConstruction.py test_Tutorial.py test_UniGene.py test_Uniprot.py test_Wise.py test_XXmotif_tool.py test_align.py test_bgzf.py test_codonalign.py test_geo.py test_kNN.py test_lowess.py test_motifs.py test_motifs_online.py test_pairwise2.py test_phyml_tool.py test_prodoc.py test_prosite1.py test_prosite2.py test_psw.py test_py3k.py test_raxml_tool.py test_samtools_tool.py test_seq.py test_translate.py test_trie.py
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Ace.py
test_Ace ... ok
test_check_ACEParser (test_Ace.AceTestOne)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestOne)
Test to check that contig parser parses each contig into a contig. ... ok
test_check_ACEParser (test_Ace.AceTestThree)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestThree)
Test to check that record parser parses each contig into a record. ... ok
test_check_ACEParser (test_Ace.AceTestTwo)
Test to check that ACEParser can parse the whole file into one record. ... ok
test_check_record_parser (test_Ace.AceTestTwo)
Test to check that record parser parses each contig into a record. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.087 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_AlignIO.py
test_AlignIO ... ok
runTest (__main__.ComparisonTestCase)
test_AlignIO ... ok
----------------------------------------------------------------------
Ran 1 test in 2.406 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_AlignIO_ClustalIO.py
test_AlignIO_ClustalIO ... ok
test_cat_one_two (test_AlignIO_ClustalIO.TestClustalIO) ... ok
test_empy (test_AlignIO_ClustalIO.TestClustalIO)
Checking empty file. ... ok
test_kalign_header (test_AlignIO_ClustalIO.TestClustalIO)
Make sure we can parse the Kalign header. ... ok
test_one (test_AlignIO_ClustalIO.TestClustalIO) ... ok
test_three (test_AlignIO_ClustalIO.TestClustalIO) ... ok
test_two (test_AlignIO_ClustalIO.TestClustalIO) ... ok
test_write_read (test_AlignIO_ClustalIO.TestClustalIO)
Checking write/read. ... ok
test_write_read_single (test_AlignIO_ClustalIO.TestClustalIO)
Testing write/read when there is only one sequence. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.087 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_AlignIO_EmbossIO.py
test_AlignIO_EmbossIO ... ok
test_pair_example (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
test_pair_example2 (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
test_pair_example3 (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
test_pair_plus_simple (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
test_simple_example (test_AlignIO_EmbossIO.TestEmbossIO) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.087 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_AlignIO_FastaIO.py
test_AlignIO_FastaIO ... ok
runTest (__main__.ComparisonTestCase)
test_AlignIO_FastaIO ... ok
----------------------------------------------------------------------
Ran 1 test in 0.146 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_AlignIO_PhylipIO.py
test_AlignIO_PhylipIO ... ok
test_concatenation (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
test_five (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
test_five_a (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
test_four (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
test_one (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
test_two_and_three (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
test_write_read (test_AlignIO_PhylipIO.TestPhylipIO) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.087 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_AlignIO_convert.py
test_AlignIO_convert ... ok
test_Clustalw_hedgehog_aln_clustal_to_clustal (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to clustal ... ok
test_Clustalw_hedgehog_aln_clustal_to_fasta (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to fasta ... ok
test_Clustalw_hedgehog_aln_clustal_to_nexus (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to nexus ... ok
test_Clustalw_hedgehog_aln_clustal_to_phylip (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to phylip ... ok
test_Clustalw_hedgehog_aln_clustal_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to phylip-relaxed ... ok
test_Clustalw_hedgehog_aln_clustal_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to phylip-sequential ... ok
test_Clustalw_hedgehog_aln_clustal_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert Clustalw/hedgehog.aln from clustal to stockholm ... ok
test_Fasta_output001_m10_fasta-m10_to_clustal (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to clustal ... ok
test_Fasta_output001_m10_fasta-m10_to_fasta (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to fasta ... ok
test_Fasta_output001_m10_fasta-m10_to_nexus (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to nexus ... ok
test_Fasta_output001_m10_fasta-m10_to_phylip (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to phylip ... ok
test_Fasta_output001_m10_fasta-m10_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to phylip-relaxed ... ok
test_Fasta_output001_m10_fasta-m10_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to phylip-sequential ... ok
test_Fasta_output001_m10_fasta-m10_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert Fasta/output001.m10 from fasta-m10 to stockholm ... ok
test_GFF_multi_fna_fasta_to_clustal (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to clustal ... ok
test_GFF_multi_fna_fasta_to_fasta (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to fasta ... ok
test_GFF_multi_fna_fasta_to_nexus (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to nexus ... ok
test_GFF_multi_fna_fasta_to_phylip (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to phylip ... ok
test_GFF_multi_fna_fasta_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to phylip-relaxed ... ok
test_GFF_multi_fna_fasta_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to phylip-sequential ... ok
test_GFF_multi_fna_fasta_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert GFF/multi.fna from fasta to stockholm ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_clustal (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to clustal ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_fasta (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to fasta ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_nexus (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to nexus ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_phylip (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to phylip ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to phylip-relaxed ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to phylip-sequential ... ok
test_IntelliGenetics_VIF_mase-pro_txt_ig_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert IntelliGenetics/VIF_mase-pro.txt from ig to stockholm ... ok
test_NBRF_clustalw_pir_pir_to_clustal (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to clustal ... ok
test_NBRF_clustalw_pir_pir_to_fasta (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to fasta ... ok
test_NBRF_clustalw_pir_pir_to_nexus (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to nexus ... ok
test_NBRF_clustalw_pir_pir_to_phylip (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to phylip ... ok
test_NBRF_clustalw_pir_pir_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to phylip-relaxed ... ok
test_NBRF_clustalw_pir_pir_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to phylip-sequential ... ok
test_NBRF_clustalw_pir_pir_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert NBRF/clustalw.pir from pir to stockholm ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_clustal (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to clustal ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_fasta (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to fasta ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_nexus (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to nexus ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_phylip (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to phylip ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to phylip-relaxed ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to phylip-sequential ... ok
test_Nexus_test_Nexus_input_nex_nexus_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert Nexus/test_Nexus_input.nex from nexus to stockholm ... ok
test_Quality_example_fastq_fastq-sanger_to_clustal (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to clustal ... ok
test_Quality_example_fastq_fastq-sanger_to_fasta (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to fasta ... ok
test_Quality_example_fastq_fastq-sanger_to_nexus (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to nexus ... ok
test_Quality_example_fastq_fastq-sanger_to_phylip (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to phylip ... ok
test_Quality_example_fastq_fastq-sanger_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to phylip-relaxed ... ok
test_Quality_example_fastq_fastq-sanger_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to phylip-sequential ... ok
test_Quality_example_fastq_fastq-sanger_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to stockholm ... ok
test_Quality_example_fastq_fastq_to_clustal (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to clustal ... ok
test_Quality_example_fastq_fastq_to_fasta (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to fasta ... ok
test_Quality_example_fastq_fastq_to_nexus (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to nexus ... ok
test_Quality_example_fastq_fastq_to_phylip (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to phylip ... ok
test_Quality_example_fastq_fastq_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to phylip-relaxed ... ok
test_Quality_example_fastq_fastq_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to phylip-sequential ... ok
test_Quality_example_fastq_fastq_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to stockholm ... ok
test_Stockholm_simple_sth_stockholm_to_clustal (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to clustal ... ok
test_Stockholm_simple_sth_stockholm_to_fasta (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to fasta ... ok
test_Stockholm_simple_sth_stockholm_to_nexus (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to nexus ... ok
test_Stockholm_simple_sth_stockholm_to_phylip (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to phylip ... ok
test_Stockholm_simple_sth_stockholm_to_phylip-relaxed (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to phylip-relaxed ... ok
test_Stockholm_simple_sth_stockholm_to_phylip-sequential (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to phylip-sequential ... ok
test_Stockholm_simple_sth_stockholm_to_stockholm (test_AlignIO_convert.ConvertTests)
Convert Stockholm/simple.sth from stockholm to stockholm ... ok
----------------------------------------------------------------------
Ran 1 test in 0.379 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Application.py
test_Application ... ok
test_echo (test_Application.TestApp) ... ok
test_echo_capture_both (test_Application.TestApp) ... ok
test_echo_capture_neither (test_Application.TestApp) ... ok
test_echo_capture_stderr (test_Application.TestApp) ... ok
test_echo_capture_stdout (test_Application.TestApp) ... ok
test_echo_file_both (test_Application.TestApp) ... ok
test_echo_file_same (test_Application.TestApp) ... ok
test_echo_file_stderr (test_Application.TestApp) ... ok
test_echo_file_stdout (test_Application.TestApp) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.050 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_BWA_tool.py
test_BWA_tool ... skipping. Install bwa and correctly set the file path to the program if you want to use it from Biopython
----------------------------------------------------------------------
Ran 1 test in 0.042 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_BioSQL_MySQLdb.py
test_BioSQL_MySQLdb ... skipping. Connection failed, check settings if you plan to use BioSQL: (2002, "Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2)")
----------------------------------------------------------------------
Ran 1 test in 0.166 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_BioSQL_mysql_connector.py
test_BioSQL_mysql_connector ... skipping. Install mysql.connector if you want to use mysql with BioSQL 
----------------------------------------------------------------------
Ran 1 test in 0.119 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_BioSQL_psycopg2.py
test_BioSQL_psycopg2 ... skipping. Connection failed, check settings if you plan to use BioSQL: could not connect to server: Connection refused
	Is the server running on host "localhost" (::1) and accepting
	TCP/IP connections on port 5432?
could not connect to server: Connection refused
	Is the server running on host "localhost" (127.0.0.1) and accepting
	TCP/IP connections on port 5432?
----------------------------------------------------------------------
Ran 1 test in 0.141 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_BioSQL_sqlite3.py
test_BioSQL_sqlite3 ... ok
test_SeqIO_loading (common_BioSQL.AutoSeqIOTests) ... ok
test_backwards_compatibility (test_BioSQL_sqlite3.BackwardsCompatibilityTest)
Check can re-use an old BioSQL SQLite3 database. ... ok
test_NC_000932 (common_BioSQL.ClosedLoopTest)
GenBank file to BioSQL and back to a GenBank file, NC_000932. ... ok
test_NC_005816 (common_BioSQL.ClosedLoopTest)
GenBank file to BioSQL and back to a GenBank file, NC_005816. ... ok
test_NT_019265 (common_BioSQL.ClosedLoopTest)
GenBank file to BioSQL and back to a GenBank file, NT_019265. ... ok
test_arab1 (common_BioSQL.ClosedLoopTest)
GenBank file to BioSQL and back to a GenBank file, arab1. ... ok
test_cor6_6 (common_BioSQL.ClosedLoopTest)
GenBank file to BioSQL and back to a GenBank file, cor6_6. ... ok
test_no_ref (common_BioSQL.ClosedLoopTest)
GenBank file to BioSQL and back to a GenBank file, noref. ... ok
test_one_of (common_BioSQL.ClosedLoopTest)
GenBank file to BioSQL and back to a GenBank file, one_of. ... ok
test_protein_refseq2 (common_BioSQL.ClosedLoopTest)
GenBank file to BioSQL and back to a GenBank file, protein_refseq2. ... ok
test_duplicate_id_load (common_BioSQL.DupLoadTest)
Make sure can't import records with same ID (in one go). ... ok
test_duplicate_load (common_BioSQL.DupLoadTest)
Make sure can't import a single record twice (in one go). ... ok
test_duplicate_load2 (common_BioSQL.DupLoadTest)
Make sure can't import a single record twice (in steps). ... ok
test_record_loading (common_BioSQL.InDepthLoadTest)
Make sure all records are correctly loaded. ... ok
test_reload (common_BioSQL.InDepthLoadTest)
Make sure can't reimport existing records. ... ok
test_seq_feature (common_BioSQL.InDepthLoadTest)
In depth check that SeqFeatures are transmitted through the db. ... ok
test_transfer (common_BioSQL.InDepthLoadTest)
Make sure can load record into another namespace. ... ok
test_load_database (common_BioSQL.LoaderTest)
Load SeqRecord objects into a BioSQL database. ... ok
test_get_db_items (common_BioSQL.ReadTest)
Check list, keys, length etc ... ok
test_lookup_items (common_BioSQL.ReadTest)
Test retrieval of items using various ids. ... ok
test_server (common_BioSQL.ReadTest)
Check BioSeqDatabase methods ... ok
test_addition (common_BioSQL.SeqInterfaceTest)
Check can add DBSeq objects together. ... ok
test_convert (common_BioSQL.SeqInterfaceTest)
Check can turn a DBSeq object into a Seq or MutableSeq. ... ok
test_seq (common_BioSQL.SeqInterfaceTest)
Make sure Seqs from BioSQL implement the right interface. ... ok
test_seq_features (common_BioSQL.SeqInterfaceTest)
Check SeqFeatures of a sequence. ... ok
test_seq_record (common_BioSQL.SeqInterfaceTest)
Make sure SeqRecords from BioSQL implement the right interface. ... ok
test_seq_slicing (common_BioSQL.SeqInterfaceTest)
Check that slices of sequences are retrieved properly. ... ok
test_NC_000932 (common_BioSQL.TransferTest)
GenBank file to BioSQL, then again to a new namespace, NC_000932. ... ok
test_NC_005816 (common_BioSQL.TransferTest)
GenBank file to BioSQL, then again to a new namespace, NC_005816. ... ok
test_NT_019265 (common_BioSQL.TransferTest)
GenBank file to BioSQL, then again to a new namespace, NT_019265. ... ok
test_arab1 (common_BioSQL.TransferTest)
GenBank file to BioSQL, then again to a new namespace, arab1. ... ok
test_cor6_6 (common_BioSQL.TransferTest)
GenBank file to BioSQL, then again to a new namespace, cor6_6. ... ok
test_no_ref (common_BioSQL.TransferTest)
GenBank file to BioSQL, then again to a new namespace, noref. ... ok
test_one_of (common_BioSQL.TransferTest)
GenBank file to BioSQL, then again to a new namespace, one_of. ... ok
test_protein_refseq2 (common_BioSQL.TransferTest)
GenBank file to BioSQL, then again to a new namespace, protein_refseq2. ... ok
----------------------------------------------------------------------
Ran 1 test in 11.576 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_CAPS.py
test_CAPS ... ok
test (test_CAPS.TestCAPS) ... ok
testNoCAPS (test_CAPS.TestCAPS) ... ok
test_trivial (test_CAPS.TestCAPS) ... ok
test_uneven (test_CAPS.TestCAPS) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.443 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_CelFile.py
test_CelFile ... ok
test_read (test_CelFile.testCelFile) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.008 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Chi2.py
test_Chi2 ... ok
testCdfChi2 (test_Chi2.ModTest) ... ok
testIncompleteGamma (test_Chi2.ModTest) ... ok
testLnGamma (test_Chi2.ModTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.175 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_ClustalOmega_tool.py
test_ClustalOmega_tool ... skipping. Install clustalo if you want to use Clustal Omega from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.139 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Clustalw_tool.py
test_Clustalw_tool ... skipping. Install clustalw or clustalw2 if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.133 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Cluster.py
test_Cluster ... ok
test_clusterdistance (test_Cluster.TestCluster) ... ok
test_distancematrix_kmedoids (test_Cluster.TestCluster) ... ok
test_kcluster (test_Cluster.TestCluster) ... ok
test_matrix_parse (test_Cluster.TestCluster) ... ok
test_median_mean (test_Cluster.TestCluster) ... ok
test_pca (test_Cluster.TestCluster) ... ok
test_somcluster (test_Cluster.TestCluster) ... ok
test_treecluster (test_Cluster.TestCluster) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.027 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_CodonTable.py
test_CodonTable ... ok
runTest (__main__.ComparisonTestCase)
test_CodonTable ... ok
----------------------------------------------------------------------
Ran 1 test in 0.066 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_CodonUsage.py
test_CodonUsage ... ok
runTest (__main__.ComparisonTestCase)
test_CodonUsage ... ok
----------------------------------------------------------------------
Ran 1 test in 0.139 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_ColorSpiral.py
test_ColorSpiral ... ok
test_dict (test_ColorSpiral.DictTest)
get_color_dict() for classes A-D, no jitter. ... ok
test_colorlist (test_ColorSpiral.SpiralTest)
Get set of eight colours, no jitter, using ColorSpiral. ... ok
test_colorspiral (test_ColorSpiral.SpiralTest)
Get set of 16 colours, no jitter, using ColorSpiral. ... ok
test_colorspiral (test_ColorSpiral.SquareTest)
Set of 625 colours, with jitter, using get_colors(). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.064 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Compass.py
test_Compass ... ok
testAlignmentParsingOne (test_Compass.CompassTest) ... ok
testAlignmentParsingTwo (test_Compass.CompassTest) ... ok
testCompassIteratorEasy (test_Compass.CompassTest) ... ok
testCompassIteratorHard (test_Compass.CompassTest) ... ok
testCompassParser (test_Compass.CompassTest) ... ok
testCompassScanAndConsume (test_Compass.CompassTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Consensus.py
test_Consensus ... ok
test_bitstring (test_Consensus.BitStringTest) ... ok
test_bootstrap (test_Consensus.BootstrapTest) ... ok
test_bootstrap_consensus (test_Consensus.BootstrapTest) ... ok
test_bootstrap_trees (test_Consensus.BootstrapTest) ... ok
test_adam_consensus (test_Consensus.ConsensusTest) ... ok
test_count_clades (test_Consensus.ConsensusTest) ... ok
test_get_support (test_Consensus.ConsensusTest) ... ok
test_majority_consensus (test_Consensus.ConsensusTest) ... ok
test_strict_consensus (test_Consensus.ConsensusTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 2.757 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Crystal.py
test_Crystal ... ok
testAdd (test_Crystal.ChainTestCase) ... ok
testAppend (test_Crystal.ChainTestCase) ... ok
testContains (test_Crystal.ChainTestCase) ... ok
testCount (test_Crystal.ChainTestCase) ... ok
testDelItem (test_Crystal.ChainTestCase) ... ok
testDelSlice (test_Crystal.ChainTestCase) ... ok
testEquals (test_Crystal.ChainTestCase) ... ok
testGetItem (test_Crystal.ChainTestCase) ... ok
testGetSlice (test_Crystal.ChainTestCase) ... ok
testIndex (test_Crystal.ChainTestCase) ... ok
testInsert (test_Crystal.ChainTestCase) ... ok
testLen (test_Crystal.ChainTestCase) ... ok
testRemove (test_Crystal.ChainTestCase) ... ok
testSetItem (test_Crystal.ChainTestCase) ... ok
testSetSlice (test_Crystal.ChainTestCase) ... ok
testClear (test_Crystal.CrystalTestCase) ... ok
testDelItem (test_Crystal.CrystalTestCase) ... ok
testGetItem (test_Crystal.CrystalTestCase) ... ok
testHasKey (test_Crystal.CrystalTestCase) ... ok
testItems (test_Crystal.CrystalTestCase) ... ok
testKeys (test_Crystal.CrystalTestCase) ... ok
testLen (test_Crystal.CrystalTestCase) ... ok
testSetItem (test_Crystal.CrystalTestCase) ... ok
testValues (test_Crystal.CrystalTestCase) ... ok
testEquals (test_Crystal.HeteroTestCase) ... ok
testInit (test_Crystal.HeteroTestCase) ... ok
testLen (test_Crystal.HeteroTestCase) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.042 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_DSSP_tool.py
test_DSSP_tool ... skipping. Install dssp if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.131 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Dialign_tool.py
test_Dialign_tool ... skipping. Install DIALIGN2-2 if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.088 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_DocSQL.py
test_DocSQL ... ok
runTest (__main__.ComparisonTestCase)
test_DocSQL ... ok
----------------------------------------------------------------------
Ran 1 test in 0.009 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_EMBL_unittest.py
test_EMBL_unittest ... ok
test_embl_content_after_co (test_EMBL_unittest.EMBLTests)
Test an AssertionError is thrown by content after a CO line ... ok
----------------------------------------------------------------------
Ran 1 test in 0.114 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Emboss.py
test_Emboss ... skipping. Install EMBOSS if you want to use Bio.Emboss.
----------------------------------------------------------------------
Ran 1 test in 0.146 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_EmbossPhylipNew.py
test_EmbossPhylipNew ... skipping. Install the Emboss package 'PhylipNew' if you want to use the Bio.Emboss.Applications wrappers for phylogenetic tools.
----------------------------------------------------------------------
Ran 1 test in 0.107 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_EmbossPrimer.py
test_EmbossPrimer ... ok
test_in_depth_single_parse (test_EmbossPrimer.Primer3ParseTest)
Make sure we get info right from a single primer find. ... ok
test_indepth_regular_parse (test_EmbossPrimer.Primer3ParseTest)
Make sure we get the data from normal primer3 files okay. ... ok
test_internal_oligo_single_parse (test_EmbossPrimer.Primer3ParseTest)
Make sure we can parse an internal oligo file correctly ... ok
test_mutli_record_full (test_EmbossPrimer.Primer3ParseTest)
Test parsing multiple primer sets (NirK full) ... ok
test_mutli_record_fwd (test_EmbossPrimer.Primer3ParseTest)
Test parsing multiple primer sets (NirK forward) ... ok
test_simple_parse (test_EmbossPrimer.Primer3ParseTest)
Make sure that we can use all single target primer3 files. ... ok
test_primer_representation (test_EmbossPrimer.PrimerSearchInputTest)
Make sure we can output primer information correctly. ... ok
test_in_depth_normal_parse (test_EmbossPrimer.PrimersearchParseTest)
Make sure the output from a simple primersearch file is correct. ... ok
test_simple_parse (test_EmbossPrimer.PrimersearchParseTest)
Make sure that we can parse all primersearch files. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.018 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Entrez.py
test_Entrez ... ok
test_fasta (test_Entrez.EFetchTest)
Test error handling when presented with Fasta non-XML data ... ok
test_genbank (test_Entrez.EFetchTest)
Test error handling when presented with GenBank non-XML data ... ok
test_nucleotide1 (test_Entrez.EFetchTest)
Test parsing XML returned by EFetch, Nucleotide database (first test) ... ok
test_nucleotide2 (test_Entrez.EFetchTest)
Test parsing XML returned by EFetch, Protein database ... ok
test_omim (test_Entrez.EFetchTest)
Test parsing XML returned by EFetch, OMIM database ... ok
test_pubmed1 (test_Entrez.EFetchTest)
Test parsing XML returned by EFetch, PubMed database (first test) ... ok
test_pubmed2 (test_Entrez.EFetchTest)
Test parsing XML returned by EFetch, PubMed database (second test) ... ok
test_pubmed_html (test_Entrez.EFetchTest)
Test error handling when presented with HTML (so XML-like) data ... ok
test_taxonomy (test_Entrez.EFetchTest)
Test parsing XML returned by EFetch, Taxonomy database ... ok
test_truncated_xml (test_Entrez.EFetchTest)
Test error handling for a truncated XML declaration ... ok
test_xml_without_declaration (test_Entrez.EFetchTest)
Test error handling for a missing XML declaration ... ok
test_egquery1 (test_Entrez.EGQueryTest)
Test parsing XML output returned by EGQuery (first test) ... ok
test_egquery2 (test_Entrez.EGQueryTest)
Test parsing XML output returned by EGQuery (second test) ... ok
test_corrupted (test_Entrez.EInfoTest)
Test if corrupted XML is handled correctly ... ok
test_list (test_Entrez.EInfoTest)
Test parsing database list returned by EInfo ... ok
test_pubmed1 (test_Entrez.EInfoTest)
Test parsing database info returned by EInfo ... ok
test_pubmed2 (test_Entrez.EInfoTest)
Test validating the XML against the DTD ... ok
test_pubmed3 (test_Entrez.EInfoTest)
Test non-validating parser on XML with an inconsistent DTD ... ok
test_medline (test_Entrez.ELinkTest)
Test parsing medline indexed articles returned by ELink ... ok
test_nucleotide (test_Entrez.ELinkTest)
Test parsing Nucleotide to Protein links returned by ELink ... ok
test_pubmed1 (test_Entrez.ELinkTest)
Test parsing pubmed links returned by ELink (first test) ... ok
test_pubmed2 (test_Entrez.ELinkTest)
Test parsing pubmed links returned by ELink (second test) ... ok
test_pubmed3 (test_Entrez.ELinkTest)
Test parsing pubmed link returned by ELink (third test) ... ok
test_pubmed4 (test_Entrez.ELinkTest)
Test parsing pubmed links returned by ELink (fourth test) ... ok
test_pubmed5 (test_Entrez.ELinkTest)
Test parsing pubmed links returned by ELink (fifth test) ... ok
test_pubmed6 (test_Entrez.ELinkTest)
Test parsing pubmed links returned by ELink (sixth test) ... ok
test_epost (test_Entrez.EPostTest)
Test parsing XML returned by EPost ... ok
test_invalid (test_Entrez.EPostTest)
Test parsing XML returned by EPost with an invalid id (overflow tag) ... ok
test_wrong (test_Entrez.EPostTest)
Test parsing XML returned by EPost with incorrect arguments ... ok
test_journals (test_Entrez.ESearchTest)
Test parsing XML returned by ESearch from the Journals database ... ok
test_notfound (test_Entrez.ESearchTest)
Test parsing XML returned by ESearch when no items were found ... ok
test_nucleotide (test_Entrez.ESearchTest)
Test parsing XML returned by ESearch from the Nucleotide database ... ok
test_pmc (test_Entrez.ESearchTest)
Test parsing XML returned by ESearch from PubMed Central ... ok
test_protein (test_Entrez.ESearchTest)
Test parsing XML returned by ESearch from the Protein database ... ok
test_pubmed1 (test_Entrez.ESearchTest)
Test parsing XML returned by ESearch from PubMed (first test) ... ok
test_pubmed2 (test_Entrez.ESearchTest)
Test parsing XML returned by ESearch from PubMed (second test) ... ok
test_pubmed3 (test_Entrez.ESearchTest)
Test parsing XML returned by ESearch from PubMed (third test) ... ok
test_espell (test_Entrez.ESpellTest)
Test parsing XML output returned by ESpell ... ok
test_journals (test_Entrez.ESummaryTest)
Test parsing XML returned by ESummary from the Journals database ... ok
test_nucleotide (test_Entrez.ESummaryTest)
Test parsing XML returned by ESummary from the Nucleotide database ... ok
test_protein (test_Entrez.ESummaryTest)
Test parsing XML returned by ESummary from the Protein database ... ok
test_pubmed (test_Entrez.ESummaryTest)
Test parsing XML returned by ESummary from PubMed ... ok
test_structure (test_Entrez.ESummaryTest)
Test parsing XML returned by ESummary from the Structure database ... ok
test_taxonomy (test_Entrez.ESummaryTest)
Test parsing XML returned by ESummary from the Taxonomy database ... ok
test_unists (test_Entrez.ESummaryTest)
Test parsing XML returned by ESummary from the UniSTS database ... ok
test_wrong (test_Entrez.ESummaryTest)
Test parsing XML returned by ESummary with incorrect arguments ... ok
test_closed_handle (test_Entrez.GeneralTests)
Test parsing closed handle fails gracefully ... ok
----------------------------------------------------------------------
Ran 1 test in 0.305 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Entrez_online.py
test_Entrez_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.005 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Enzyme.py
test_Enzyme ... ok
test_lactate (test_Enzyme.TestEnzyme)
Parsing ENZYME record for lactate racemase (5.1.2.1) ... ok
test_lipoprotein (test_Enzyme.TestEnzyme)
Parsing ENZYME record for lipoprotein lipase (3.1.1.34) ... ok
test_proline (test_Enzyme.TestEnzyme)
Parsing ENZYME record for proline racemase (5.1.1.4) ... ok
test_valine (test_Enzyme.TestEnzyme)
Parsing ENZYME record for valine decarboxylase (4.1.1.14) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.026 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_FSSP.py
test_FSSP ... ok
runTest (__main__.ComparisonTestCase)
test_FSSP ... ok
----------------------------------------------------------------------
Ran 1 test in 2.878 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Fasttree_tool.py
test_Fasttree_tool ... skipping. Install FastTree and correctly set the file path to the program if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.172 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_File.py
test_File ... ok
test_handle (test_File.AsHandleTestCase)
Test as_handle with a file-like object argument ... ok
test_path (test_File.AsHandleTestCase)
Test as_handle with a path argument ... ok
test_stringio (test_File.AsHandleTestCase) ... ok
test_one (test_File.UndoHandleTests) ... ok
test_read (test_File.UndoHandleTests)
test read method ... ok
test_undohandle_read_block (test_File.UndoHandleTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.024 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GACrossover.py
test_GACrossover ... ok
test_basic_asym_crossover (test_GACrossover.FourPointTest)
Test basic asymmetric 2-point crossover functionality. ... ok
test_basic_crossover (test_GACrossover.FourPointTest)
Test basic 4-point crossover functionality. ... ok
test_prop_sym_crossover (test_GACrossover.FourPointTest)
Test properties of symmetric 4-point crossover. ... ok
test_basic_crossover (test_GACrossover.InterleaveTest)
Test basic interleave crossover functionality. ... ok
test_prop_asym_crossover (test_GACrossover.InterleaveTest)
Test basic interleave crossover with asymmetric genomes. ... ok
test_prop_sym_crossover (test_GACrossover.InterleaveTest)
Test properties of interleave point crossover. ... ok
test_keep_higher (test_GACrossover.SafeFitnessTest)
Make sure we always keep higher fitness when specified. ... ok
test_keep_lower (test_GACrossover.SafeFitnessTest)
Make sure we do normal crossover functionality when specified. ... ok
test_basic_crossover (test_GACrossover.SinglePointTest)
Test basic point crossover functionality. ... ok
test_basic_asym_crossover (test_GACrossover.TwoPointTest)
Test basic asymmetric 2-point crossover functionality. ... ok
test_basic_crossover (test_GACrossover.UniformTest)
Test basic uniform crossover functionality. ... ok
test_ds_prop_uniform_crossover (test_GACrossover.UniformTest)
Test properties of differing genome length, uniform crossovers. ... ok
test_ss_prop_uniform_crossover (test_GACrossover.UniformTest)
Test properties of equal genome length, uniform crossovers. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.089 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GAMutation.py
test_GAMutation ... ok
test_always_mutate (test_GAMutation.ConversionTest)
Test ability to cause mutations. ... ok
test_never_mutate (test_GAMutation.ConversionTest)
Make sure we do not mutate at unexpected times. ... ok
test_keep_higher (test_GAMutation.SafeFitnessTest)
Make sure we always keep the higher fitness. ... ok
test_keep_new (test_GAMutation.SafeFitnessTest)
Make sure we always keep the new organism when specified. ... ok
test_always_mutate (test_GAMutation.SinglePositionTest)
Test ability to cause mutations. ... ok
test_never_mutate (test_GAMutation.SinglePositionTest)
Make sure we do not mutate at unexpected times. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.161 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GAOrganism.py
test_GAOrganism ... ok
test_function_population (test_GAOrganism.CreatePopulationTest)
Create a population using a function to generate genomes. ... ok
test_random_population (test_GAOrganism.CreatePopulationTest)
Create a population randomly from a alphabet. ... ok
test_random_population_types (test_GAOrganism.CreatePopulationTest)
Creating a random population with different types of alphabets. ... ok
test_organism_basic (test_GAOrganism.OrganismTest)
Exercise basic organism functionality. ... ok
test_organism_copy (test_GAOrganism.OrganismTest)
Test copying of organisms. ... ok
test_organism_fitness (test_GAOrganism.OrganismTest)
Test the ability to deal with the fitness of the genome. ... ok
test_provide_fitness (test_GAOrganism.OrganismTest)
Test that providing a pre-calculated fitness works. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.081 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GAQueens.py
test_GAQueens ... ok
test_queens (test_GAQueens.QueensTest)
Place five queens with a GA ... ok
----------------------------------------------------------------------
Ran 1 test in 0.380 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GARepair.py
test_GARepair ... ok
test_multiple_repair (test_GARepair.AmbiguousRepairTest)
Test repair of multiple ambiguous positions in a genome. ... ok
test_single_repair (test_GARepair.AmbiguousRepairTest)
Test repair of a single ambiguous position in a genome. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.087 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GASelection.py
test_GASelection ... ok
test_get_new_organism (test_GASelection.DiversitySelectionTest)
Getting a new organism not in the new population. ... ok
test_no_retrieve_organism (test_GASelection.DiversitySelectionTest)
Test not getting an organism already in the new population. ... ok
test_selection (test_GASelection.DiversitySelectionTest)
Test basic selection on a small population. ... ok
test_select_best (test_GASelection.RouletteWheelSelectionTest)
Ensure selection of a best organism in a population of 2. ... ok
test_selection (test_GASelection.RouletteWheelSelectionTest)
Test basic selection on a small population. ... ok
test_select_best (test_GASelection.TournamentSelectionTest)
Ensure selection of the best organism in a population of 2. ... ok
test_selection (test_GASelection.TournamentSelectionTest)
Test basic selection on a small population. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.105 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GenBank.py
test_GenBank ... ok
runTest (__main__.ComparisonTestCase)
test_GenBank ... ok
----------------------------------------------------------------------
Ran 1 test in 0.365 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GenBank_unittest.py
test_GenBank_unittest ... ok
test_000_genbank_bad_loc_wrap_warning (test_GenBank_unittest.GenBankTests) ... ok
test_001_negative_location_warning (test_GenBank_unittest.GenBankTests) ... ok
test_dot_lineage (test_GenBank_unittest.GenBankTests) ... ok
test_genbank_bad_loc_wrap_parsing (test_GenBank_unittest.GenBankTests) ... ok
test_genbank_read (test_GenBank_unittest.GenBankTests) ... ok
test_genbank_read_invalid (test_GenBank_unittest.GenBankTests) ... ok
test_genbank_read_multirecord (test_GenBank_unittest.GenBankTests) ... ok
test_genbank_read_no_origin_no_end (test_GenBank_unittest.GenBankTests) ... ok
test_invalid_product_line_raises_value_error (test_GenBank_unittest.GenBankTests)
Test GenBank parsing invalid product line raises ValueError ... ok
test_negative_location (test_GenBank_unittest.GenBankTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.163 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GenomeDiagram.py
test_GenomeDiagram ... Warn: Can't find .pfb for face 'Times-Roman'
ok
test_color_conversions (test_GenomeDiagram.ColorsTest)
Test color translations. ... ok
test_diagram_via_methods_pdf (test_GenomeDiagram.DiagramTest)
Construct and draw PDF using method approach. ... ok
test_diagram_via_object_pdf (test_GenomeDiagram.DiagramTest)
Construct and draw PDF using object approach. ... ok
test_partial_diagram (test_GenomeDiagram.DiagramTest)
construct and draw SVG and PDF for just part of a SeqRecord. ... ok
test_write_arguments (test_GenomeDiagram.DiagramTest)
Check how the write methods respond to output format arguments. ... ok
test_limits (test_GenomeDiagram.GraphTest)
Check line graphs. ... ok
test_slicing (test_GenomeDiagram.GraphTest)
Check GraphData slicing. ... ok
test_label_default (test_GenomeDiagram.LabelTest)
Feature labels - default. ... ok
test_all_sigils (test_GenomeDiagram.SigilsTest)
All sigils. ... ok
test_arrow_heads (test_GenomeDiagram.SigilsTest)
Feature arrow sigils, varying heads. ... ok
test_arrow_shafts (test_GenomeDiagram.SigilsTest)
Feature arrow sigils, varying shafts. ... ok
test_big_arrow_shafts (test_GenomeDiagram.SigilsTest)
Feature big-arrow sigils, varying shafts. ... ok
test_labels (test_GenomeDiagram.SigilsTest)
Feature labels. ... ok
test_long_arrow_heads (test_GenomeDiagram.SigilsTest)
Feature ARROW sigil heads within bounding box. ... ok
test_long_jaggy (test_GenomeDiagram.SigilsTest)
Feature JAGGY sigil heads within bounding box. ... ok
test_long_octo_heads (test_GenomeDiagram.SigilsTest)
Feature OCTO sigil heads within bounding box. ... ok
test_small_arrow_heads (test_GenomeDiagram.SigilsTest)
Feature arrow sigil heads within bounding box. ... ok
----------------------------------------------------------------------
Ran 1 test in 4.797 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GraphicsBitmaps.py
test_GraphicsBitmaps ... Warn: Can't find .pfb for face 'Times-Roman'
skipping. Check the fonts needed by ReportLab if you want bitmaps from Bio.Graphics
Can't setFont(Times-Roman) missing the T1 files?
Originally <type 'exceptions.TypeError'>: makeT1Font() argument 2 must be string, not None
----------------------------------------------------------------------
Ran 1 test in 0.089 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GraphicsChromosome.py
test_GraphicsChromosome ... ok
test_add_count (test_GraphicsChromosome.ChromosomeCountTest)
Add counts to specific chromosome segments. ... ok
test_add_label (test_GraphicsChromosome.ChromosomeCountTest)
Add labels to chromosome segments. ... ok
test_color_from_count (test_GraphicsChromosome.ChromosomeCountTest)
Retrieve a color from a count number with the default color scheme. ... ok
test_fill_chromosome (test_GraphicsChromosome.ChromosomeCountTest)
Test filling out the information on a chromosome. ... ok
test_get_segment_info (test_GraphicsChromosome.ChromosomeCountTest)
Test retrieval of segment information. ... ok
test_set_scale (test_GraphicsChromosome.ChromosomeCountTest)
Set the scale for a chromosome segment. ... ok
test_random_organism (test_GraphicsChromosome.OrganismGraphicTest)
Generate an organism with random chromosome info. ... ok
test_simple_organism (test_GraphicsChromosome.OrganismGraphicTest)
Test the basic functionality of drawing an organism. ... ok
test_simple_organism_pdf (test_GraphicsChromosome.OrganismGraphicTest)
Output a simple organism to a PDF file. ... ok
test_simple_organism_ps (test_GraphicsChromosome.OrganismGraphicTest)
Output a simple organism to a postscript file. ... ok
test_simple_organism_svg (test_GraphicsChromosome.OrganismGraphicTest)
Output a simple organism to an SVG file. ... ok
test_widget (test_GraphicsChromosome.OrganismGraphicTest)
Try widget derived functionality. ... ok
test_simple_tRNA_seqfeatures (test_GraphicsChromosome.OrganismSubAnnotationsTest)
Test sub-annotations (as SeqFeatures) on a genome segment, tRNA for Arabidopsis ... ok
test_simple_tRNA_tuples (test_GraphicsChromosome.OrganismSubAnnotationsTest)
Test sub-annotations (as tuples) on a genome segment, tRNA for Arabidopsis ... ok
----------------------------------------------------------------------
Ran 1 test in 2.190 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GraphicsDistribution.py
test_GraphicsDistribution ... ok
test_multi_page (test_GraphicsDistribution.BarChartTest)
Create a page with multiple distributions on it. ... ok
test_simple_page (test_GraphicsDistribution.BarChartTest)
Test displaying a page with single distribution. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.274 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_GraphicsGeneral.py
test_GraphicsGeneral ... ok
test_simple_scatter_plot (test_GraphicsGeneral.ComparativeTest)
Test creation of a simple ScatterPlot. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.694 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_HMMCasino.py
test_HMMCasino ... ok
runTest (__main__.ComparisonTestCase)
test_HMMCasino ... ok
----------------------------------------------------------------------
Ran 1 test in 1.728 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_HMMGeneral.py
test_HMMGeneral ... ok
test_log_likelihood (test_HMMGeneral.AbstractTrainerTest)
Calculate log likelihood. ... ok
test_ml_estimator (test_HMMGeneral.AbstractTrainerTest)
Test the maximum likelihood estimator for simple cases. ... ok
test_allow_transition (test_HMMGeneral.HiddenMarkovModelTest)
Testing allow_transition ... ok
test_non_ergodic (test_HMMGeneral.HiddenMarkovModelTest)
Test a non-ergodic model (meaning that some transitions are not ... ok
test_simple_hmm (test_HMMGeneral.HiddenMarkovModelTest)
Test a simple model with 2 states and 2 symbols. ... ok
test_transitions_from (test_HMMGeneral.HiddenMarkovModelTest)
Testing the calculation of transitions_from ... ok
test_transitions_to (test_HMMGeneral.HiddenMarkovModelTest)
Testing the calculation of transitions_to ... ok
test_allow_all_transitions (test_HMMGeneral.MarkovModelBuilderTest)
Testing allow_all_transitions. ... ok
test_set_equal_probabilities (test_HMMGeneral.MarkovModelBuilderTest) ... ok
test_set_initial_probabilities (test_HMMGeneral.MarkovModelBuilderTest) ... ok
test_set_random_probabilities (test_HMMGeneral.MarkovModelBuilderTest) ... ok
test_test_initialize (test_HMMGeneral.MarkovModelBuilderTest)
Making sure MarkovModelBuilder is initialized correctly. ... ok
test_calculate_s_value (test_HMMGeneral.ScaledDPAlgorithmsTest)
Testing the calculation of s values. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.085 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_KDTree.py
test_KDTree ... ok
test_KDTree (test_KDTree.KDTreeTest) ... ok
test_KDTree_neighbour (test_KDTree.KDTreeTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.272 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_KEGG.py
test_KEGG ... ok
runTest (__main__.ComparisonTestCase)
test_KEGG ... ok
----------------------------------------------------------------------
Ran 1 test in 0.027 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_KEGG_online.py
test_KEGG_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.005 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_KGML_graphics.py
test_KGML_graphics ... skipping. Install at least reportlab 2.7 for transparency support.
----------------------------------------------------------------------
Ran 1 test in 0.035 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_KGML_graphics_online.py
test_KGML_graphics_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.004 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_KGML_nographics.py
test_KGML_nographics ... ok
test_read_and_write_KGML_files (test_KGML_nographics.KGMLPathwayTest)
Read KGML from, and write KGML to, local files. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.868 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_KeyWList.py
test_KeyWList ... ok
test_parse (test_KeyWList.KeyWListTest)
Parsing keywlist.txt ... ok
test_parse2 (test_KeyWList.KeyWListTest)
Parsing keywlist2.txt (without header and footer) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.023 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Location.py
test_Location ... ok
runTest (__main__.ComparisonTestCase)
test_Location ... ok
----------------------------------------------------------------------
Ran 1 test in 0.078 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_LogisticRegression.py
test_LogisticRegression ... ok
test_calculate_model (test_LogisticRegression.TestLogisticRegression) ... ok
test_calculate_model_with_update_callback (test_LogisticRegression.TestLogisticRegression) ... ok
test_calculate_probability (test_LogisticRegression.TestLogisticRegression) ... ok
test_classify (test_LogisticRegression.TestLogisticRegression) ... ok
test_dimensionality_of_input_xs (test_LogisticRegression.TestLogisticRegression) ... ok
test_leave_one_out (test_LogisticRegression.TestLogisticRegression) ... ok
test_model_accuracy (test_LogisticRegression.TestLogisticRegression) ... ok
test_xs_and_ys_input_parameter_lengths (test_LogisticRegression.TestLogisticRegression) ... ok
test_ys_input_class_assignments (test_LogisticRegression.TestLogisticRegression) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.155 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_MMCIF.py
test_MMCIF ... ok
testModels (test_MMCIF.ParseReal)
Test file with multiple models ... ok
test_filehandle (test_MMCIF.ParseReal)
Test if the parser can handle file handle as well as filename ... ok
test_parser (test_MMCIF.ParseReal)
Extract polypeptides from 1A80. ... ok
----------------------------------------------------------------------
Ran 1 test in 4.086 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_MSAProbs_tool.py
test_MSAProbs_tool ... skipping. Install msaprobs if you want to use MSAProbs from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.124 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Mafft_tool.py
test_Mafft_tool ... skipping. Install MAFFT if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.090 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_MarkovModel.py
test_MarkovModel ... ok
test_baum_welch (test_MarkovModel.TestMarkovModel) ... ok
test_topcoder1 (test_MarkovModel.TestMarkovModel) ... ok
test_topcoder2 (test_MarkovModel.TestMarkovModel) ... ok
test_topcoder3 (test_MarkovModel.TestMarkovModel) ... ok
test_topcoder4 (test_MarkovModel.TestMarkovModel) ... ok
test_topcoder5 (test_MarkovModel.TestMarkovModel) ... ok
test_train_visible (test_MarkovModel.TestMarkovModel) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.020 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Medline.py
test_Medline ... ok
test_multiline_mesh (test_Medline.TestMedline) ... ok
test_parse (test_Medline.TestMedline) ... ok
test_read (test_Medline.TestMedline) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.008 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Motif.py
test_Motif ... ok
test_simple (test_Motif.MotifTestPWM)
Test if Motif PWM scoring works. ... ok
test_with_alt_alphabet (test_Motif.MotifTestPWM)
Test motif search using alternative instance of alphabet. ... ok
test_FAoutput (test_Motif.MotifTestsBasic)
Ensure that we can write proper FASTA output files. ... ok
test_TFoutput (test_Motif.MotifTestsBasic)
Ensure that we can write proper TransFac output files. ... ok
test_alignace_parsing (test_Motif.MotifTestsBasic)
Test if Motif can parse AlignAce output files. ... ok
test_pfm_output (test_Motif.MotifTestsBasic)
Ensure that we can write proper pfm output files. ... ok
test_pfm_parsing (test_Motif.MotifTestsBasic)
Test to be sure that Motif can parse pfm  files. ... ok
test_sites_parsing (test_Motif.MotifTestsBasic)
Test to be sure that Motif can parse sites files. ... ok
test_mast_parser_1 (test_Motif.TestMAST)
Test if Motif can parse MAST output files (first test) ... ok
test_mast_parser_2 (test_Motif.TestMAST)
Test if Motif can parse MAST output files (second test) ... ok
test_mast_parser_3 (test_Motif.TestMAST)
Test if Motif can parse MAST output files (third test) ... ok
test_meme_parser_1 (test_Motif.TestMEME)
Test if Motif can parse MEME output files (first test) ... ok
test_meme_parser_2 (test_Motif.TestMEME)
Test if Motif can parse MEME output files (second test) ... ok
test_meme_parser_3 (test_Motif.TestMEME)
Test if Motif can parse MEME output files (third test) ... ok
test_meme_parser_4 (test_Motif.TestMEME)
Test if Motif can parse MEME output files (fourth test) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.131 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Muscle_tool.py
test_Muscle_tool ... skipping. Install MUSCLE if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.126 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_NACCESS_tool.py
test_NACCESS_tool ... skipping. Install naccess if you want to use it from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.096 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_NCBITextParser.py
test_NCBITextParser ... ok
test_conversion (test_NCBITextParser.TestBlastRecord)
Test converting a Blast record multiple alignment ... ok
test_text_2010L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.10 output (text_2010L_blastn_001) ... ok
test_text_2010L_blastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.10 output without alignments (text_2010L_blastn_002) ... ok
test_text_2010L_blastn_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.10 output without descriptions (text_2010L_blastn_003) ... ok
test_text_2010L_blastn_004 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.10 output (text_2010L_blastn_004) ... ok
test_text_2010L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output (text_2010L_blastp_001) ... ok
test_text_2010L_blastp_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output without hits (text_2010L_blastp_002) ... ok
test_text_2010L_blastp_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output (text_2010L_blastp_003) ... ok
test_text_2010L_blastp_004 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output without descriptions (text_2010L_blastp_004) ... ok
test_text_2010L_blastp_005 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output without alignments (text_2010L_blastp_005) ... ok
test_text_2010L_blastp_006 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output (text_2010L_blastp_006) ... ok
test_text_2010L_blastp_007 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.10 output (text_2010L_blastp_007) ... ok
test_text_2010L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.0.10 output (text_2010L_blastx_001) ... ok
test_text_2010L_blastx_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.0.10 output without hits (text_2010L_blastx_002) ... ok
test_text_2010L_phiblast_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing PHI-BLAST, BLASTP 2.0.10 output, one round (text_2010L_phiblast_001) ... ok
test_text_2010L_phiblast_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing PHI-BLAST, BLASTP 2.0.10 output, three rounds (text_2010L_phiblast_002) ... ok
test_text_2010L_phiblast_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing PHI-BLAST, BLASTP 2.0.10 output, two rounds (text_2010L_phiblast_003) ... ok
test_text_2010L_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.0.10 output (text_2010L_tblastn_001) ... ok
test_text_2010L_tblastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.0.10 output without hits (text_2010L_tblastn_002) ... ok
test_text_2010L_tblastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTX 2.0.10 output (text_2010L_tblastx_001) ... ok
test_text_2011L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.11 output (text_2011L_blastn_001) ... ok
test_text_2011L_blastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.11 output without alignments (text_2011L_blastn_002) ... ok
test_text_2011L_blastn_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.11 output without descriptions (text_2011L_blastn_003) ... ok
test_text_2011L_blastn_004 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.11 output (text_2011L_blastn_004) ... ok
test_text_2011L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output (text_2011L_blastp_001) ... ok
test_text_2011L_blastp_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output without hits (text_2011L_blastp_002) ... ok
test_text_2011L_blastp_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output (text_2011L_blastp_003) ... ok
test_text_2011L_blastp_004 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output without descriptions (text_2011L_blastp_004) ... ok
test_text_2011L_blastp_005 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output without alignments (text_2011L_blastp_005) ... ok
test_text_2011L_blastp_006 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output (text_2011L_blastp_006) ... ok
test_text_2011L_blastp_007 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output (text_2011L_blastp_007) ... ok
test_text_2011L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.0.11 output (text_2011L_blastx_001) ... ok
test_text_2011L_blastx_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.0.11 output without hits (text_2011L_blastx_002) ... ok
test_text_2011L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_001) ... ok
test_text_2011L_psiblast_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing PHI-BLAST, BLASTP 2.0.11 output, two rounds (text_2011L_psiblast_002) ... ok
test_text_2011L_psiblast_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.11 output (text_2011L_psiblast_003) ... ok
test_text_2011L_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.0.11 output (text_2011L_tblastn_001) ... ok
test_text_2011L_tblastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.0.11 output without hits (text_2011L_tblastn_002) ... ok
test_text_2011L_tblastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTX 2.0.11 output (text_2011L_tblastx_001) ... ok
test_text_2012L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.12 output (text_2012L_psiblast_001) ... ok
test_text_2014L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.0.14 output (text_2014L_blastn_001) ... ok
test_text_2014L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.0.14 output (text_2014L_psiblast_001) ... ok
test_text_2201L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.1 output (text_2201L_blastx_001) ... ok
test_text_2202L_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.2.2 output with error messages (text_2202L_blastn_001) ... ok
test_text_2202L_blastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.2.2 output with missing error messages (text_2202L_blastn_002) ... ok
test_text_2202L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.2 output with multiple records (text_2202L_blastp_001) ... ok
test_text_2208L_psiblast_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.8 output (text_2208L_psiblast_001) ... ok
test_text_2215L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.15 output with no hits (text_2215L_blastx_001) ... ok
test_text_2216L_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.2.16 output (text_2216L_tblastn_001) ... ok
test_text_2220L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.20 output (text_2220L_blastx_001) ... ok
test_text_2220L_blastx_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.20 output with multiple queries (text_2220L_blastx_002) ... ok
test_text_2221L_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.21 output with multiple queries (text_2221L_blastp_001) ... ok
test_text_2222L_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.22 output with multiple queries (text_2222L_blastx_001) ... ok
test_text_2222_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.22+ output with multiple queries (text_2222_blastx_001) ... ok
test_text_2226_blastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.2.26+ output with no results. ... ok
test_text_2226_blastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.2.26+ output with single hsp results. ... ok
test_text_2226_blastn_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTN 2.2.26+ output with multiple hsp results present. ... ok
test_text_2226_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.26+ with no results. ... ok
test_text_2226_blastp_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.26+ with single hsp results. ... ok
test_text_2226_blastp_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok
test_text_2226_blastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.26+ with no results. ... ok
test_text_2226_blastx_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTX 2.2.26+ with single hsp results. ... ok
test_text_2226_blastx_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.26+ with multiple hsp results present. ... ok
test_text_2226_tblastn_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.2.26+ output with no results. ... ok
test_text_2226_tblastn_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.2.26+ output with single hsp results. ... ok
test_text_2226_tblastn_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTN 2.2.26+ output with multiple hsp results present. ... ok
test_text_2226_tblastx_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTX 2.2.26+ output with no results. ... ok
test_text_2226_tblastx_002 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTX 2.2.26+ output with single hsp results. ... ok
test_text_2226_tblastx_003 (test_NCBITextParser.TestNCBITextParser)
Test parsing TBLASTX 2.2.26+ output with multiple hsp results present. ... ok
test_text_2230_blastp_001 (test_NCBITextParser.TestNCBITextParser)
Test parsing BLASTP 2.2.30+ output with line of dashes. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.806 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_NCBIXML.py
test_NCBIXML ... ok
test_xml_2212L_blastn_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTN 2.2.12, gi|1348916|gb|G26684.1|G26684 (xml_2212L_blastn_001) ... ok
test_xml_2212L_blastp_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTP 2.2.12, gi|49176427|ref|NP_418280.3| (xml_2212L_blastp_001) ... ok
test_xml_2212L_blastx_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTX 2.2.12, gi|1347369|gb|G25137.1|G25137 (xml_2212L_blastx_001) ... ok
test_xml_2212L_tblastn_001 (test_NCBIXML.TestNCBIXML)
Parsing TBLASTN 2.2.12, gi|729325|sp|P39483|DHG2_BACME (xml_2212L_tblastn_001) ... ok
test_xml_2212L_tblastx_001 (test_NCBIXML.TestNCBIXML)
Parsing TBLASTX 2.2.12, gi|1348853|gb|G26621.1|G26621, BLOSUM80 (xml_2212L_tblastx_001) ... ok
test_xml_2218L_blastp_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTP 2.2.18, Fake query (xml_2218L_blastp_001) ... ok
test_xml_2218L_rpsblast_001 (test_NCBIXML.TestNCBIXML)
Parsing PSI-BLASTP 2.2.18, single query which converges in 3 iterations (xml_2218L_rpsblast_001) ... ok
test_xml_2218_blastp_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTP 2.2.18+, gi|160837788|ref|NP_075631.2| (xml_2218_blastp_001) ... ok
test_xml_2218_blastp_002 (test_NCBIXML.TestNCBIXML)
Parsing BLASTP 2.2.18+, SwissProt Q08386 and P07175, no hits (xml_2218_blastp_002) ... ok
test_xml_2222_blastp_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTP 2.2.22+, multiple queries against NR (xml_2222_blastp_001) ... ok
test_xml_2222_blastx_001 (test_NCBIXML.TestNCBIXML)
Parsing BLASTX 2.2.22+, multiple queries against NR (xml_2222_blastx_001) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.269 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_NCBI_BLAST_tools.py
test_NCBI_BLAST_tools ... skipping. Install the NCBI BLAST+ command line tools if you want to use the Bio.Blast.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.033 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_NCBI_qblast.py
test_NCBI_qblast ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.021 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_NNExclusiveOr.py
test_NNExclusiveOr ... ok
runTest (__main__.ComparisonTestCase)
test_NNExclusiveOr ... ok
----------------------------------------------------------------------
Ran 1 test in 0.601 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_NNGene.py
test_NNGene ... ok
test_representation (test_NNGene.MotifCoderTest)
Convert a sequence into its motif representation. ... ok
test_find (test_NNGene.MotifFinderTest)
Find all motifs in a set of sequences. ... ok
test_find_differences (test_NNGene.MotifFinderTest)
Find the difference in motif counts between two sets of sequences. ... ok
test_motif (test_NNGene.PatternIOTest)
Reading and writing motifs to a file ... ok
test_schema (test_NNGene.PatternIOTest)
Reading and writing schemas to a file. ... ok
test_signature (test_NNGene.PatternIOTest)
Reading and writing signatures to a file. ... ok
test_count (test_NNGene.PatternRepositoryTest)
Retrieve counts for particular patterns in the repository. ... ok
test_get_all (test_NNGene.PatternRepositoryTest)
Retrieve all patterns from a repository. ... ok
test_get_differing (test_NNGene.PatternRepositoryTest)
Retrieve patterns from both sides of the list (top and bottom). ... ok
test_get_random (test_NNGene.PatternRepositoryTest)
Retrieve random patterns from the repository. ... ok
test_get_top (test_NNGene.PatternRepositoryTest)
Retrieve a certain number of the top patterns. ... ok
test_get_top_percentage (test_NNGene.PatternRepositoryTest)
Retrieve the top percentge of patterns from the repository. ... ok
test_remove_polyA (test_NNGene.PatternRepositoryTest)
Test the ability to remove A rich patterns from the repository. ... ok
test_representation (test_NNGene.SchemaCoderTest)
Convert a string into a representation of motifs. ... ok
test_easy_from_motifs (test_NNGene.SchemaFactoryTest)
Generating schema from a simple list of motifs. ... ok
test_hard_from_motifs (test_NNGene.SchemaFactoryTest)
Generating schema from a real life set of motifs. ... ok
test_schema_representation (test_NNGene.SchemaFactoryTest)
Convert sequences into schema representations. ... ok
test_find (test_NNGene.SchemaFinderTest)
Find schemas from sequence inputs. ... ok
test_find_differences (test_NNGene.SchemaFinderTest)
Find schemas that differentiate between two sets of sequences. ... ok
runTest (test_NNGene.SchemaMatchingTest)
SchemaMatchingTest:Matching schema to strings works correctly.
     ... ok
test_all_unambiguous (test_NNGene.SchemaTest)
Return all unambiguous characters that can be in a motif. ... ok
test_find_ambiguous (test_NNGene.SchemaTest)
Find the positions of ambiguous items in a sequence. ... ok
test_find_matches (test_NNGene.SchemaTest)
Find all matches in a sequence. ... ok
test_motif_cache (test_NNGene.SchemaTest)
Make sure motif compiled regular expressions are cached properly. ... ok
test_num_ambiguous (test_NNGene.SchemaTest)
Find the number of ambiguous items in a sequence. ... ok
test_num_matches (test_NNGene.SchemaTest)
Find how many matches are present in a sequence. ... ok
test_representation (test_NNGene.SignatureCoderTest)
Convert a sequence into its signature representation. ... ok
test_find (test_NNGene.SignatureFinderTest)
Find signatures from sequence inputs. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.353 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_NNGeneral.py
test_NNGeneral ... ok
test_adding_examples (test_NNGeneral.ExampleManagerTest)
Make sure test examples are added properly. ... ok
test_partioning_examples (test_NNGeneral.ExampleManagerTest)
Test that we can change how to partition the test examples. ... ok
test_validation_increase_stop (test_NNGeneral.StopTrainingTest)
Stop training when the ValidationExamples increase. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.019 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Nexus.py
test_Nexus ... ok
test_NexusTest1 (test_Nexus.NexusTest1)
Test Nexus module ... ok
test_TreeTest1 (test_Nexus.NexusTest1)
Test Tree module. ... ok
test_WriteToFileName (test_Nexus.NexusTest1)
Test writing to a given filename. ... ok
test_internal_node_labels (test_Nexus.NexusTest1)
Handle text labels on internal nodes. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.130 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PAML_baseml.py
test_PAML_baseml ... ok
testAlignmentExists (test_PAML_baseml.ModTest) ... ok
testAlignmentFileIsValid (test_PAML_baseml.ModTest) ... ok
testAlignmentSpecified (test_PAML_baseml.ModTest) ... ok
testCtlFileExistsOnRead (test_PAML_baseml.ModTest) ... ok
testCtlFileExistsOnRun (test_PAML_baseml.ModTest) ... ok
testCtlFileValidOnRead (test_PAML_baseml.ModTest) ... ok
testCtlFileValidOnRun (test_PAML_baseml.ModTest) ... ok
testOptionExists (test_PAML_baseml.ModTest) ... ok
testOutputFileSpecified (test_PAML_baseml.ModTest) ... ok
testOutputFileValid (test_PAML_baseml.ModTest) ... ok
testPamlErrorsCaught (test_PAML_baseml.ModTest) ... ok
testParseAllVersions (test_PAML_baseml.ModTest) ... ok
testParseAlpha1Rho1 (test_PAML_baseml.ModTest) ... ok
testParseModel (test_PAML_baseml.ModTest) ... ok
testParseNhomo (test_PAML_baseml.ModTest) ... ok
testParseSEs (test_PAML_baseml.ModTest) ... ok
testResultsExist (test_PAML_baseml.ModTest) ... ok
testResultsParsable (test_PAML_baseml.ModTest) ... ok
testResultsValid (test_PAML_baseml.ModTest) ... ok
testTreeExists (test_PAML_baseml.ModTest) ... ok
testTreeFileValid (test_PAML_baseml.ModTest) ... ok
testTreeSpecified (test_PAML_baseml.ModTest) ... ok
testWorkingDirValid (test_PAML_baseml.ModTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.295 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PAML_codeml.py
test_PAML_codeml ... ok
testAlignmentExists (test_PAML_codeml.ModTest) ... ok
testAlignmentFileIsValid (test_PAML_codeml.ModTest) ... ok
testAlignmentSpecified (test_PAML_codeml.ModTest) ... ok
testCtlFileExistsOnRead (test_PAML_codeml.ModTest) ... ok
testCtlFileExistsOnRun (test_PAML_codeml.ModTest) ... ok
testCtlFileValidOnRead (test_PAML_codeml.ModTest) ... ok
testCtlFileValidOnRun (test_PAML_codeml.ModTest) ... ok
testOptionExists (test_PAML_codeml.ModTest) ... ok
testOutputFileSpecified (test_PAML_codeml.ModTest) ... ok
testOutputFileValid (test_PAML_codeml.ModTest) ... ok
testPamlErrorsCaught (test_PAML_codeml.ModTest) ... ok
testParseAA (test_PAML_codeml.ModTest) ... ok
testParseAAPairwise (test_PAML_codeml.ModTest) ... ok
testParseAllNSsites (test_PAML_codeml.ModTest) ... ok
testParseBranchSiteA (test_PAML_codeml.ModTest) ... ok
testParseCladeModelC (test_PAML_codeml.ModTest) ... ok
testParseFreeRatio (test_PAML_codeml.ModTest) ... ok
testParseNSsite3 (test_PAML_codeml.ModTest) ... ok
testParseNgene2Mgene02 (test_PAML_codeml.ModTest) ... ok
testParseNgene2Mgene1 (test_PAML_codeml.ModTest) ... ok
testParseNgene2Mgene34 (test_PAML_codeml.ModTest) ... ok
testParsePairwise (test_PAML_codeml.ModTest) ... ok
testParseSEs (test_PAML_codeml.ModTest) ... ok
testResultsExist (test_PAML_codeml.ModTest) ... ok
testResultsParsable (test_PAML_codeml.ModTest) ... ok
testResultsValid (test_PAML_codeml.ModTest) ... ok
testTreeExists (test_PAML_codeml.ModTest) ... ok
testTreeFileValid (test_PAML_codeml.ModTest) ... ok
testTreeParseVersatility (test_PAML_codeml.ModTest)
Test finding trees in the results, in response to bug #453, where ... ok
testTreeSpecified (test_PAML_codeml.ModTest) ... ok
testWorkingDirValid (test_PAML_codeml.ModTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.640 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PAML_tools.py
test_PAML_tools ... skipping. Install PAML if you want to use the Bio.Phylo.PAML wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.146 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PAML_yn00.py
test_PAML_yn00 ... ok
testAlignmentExists (test_PAML_yn00.ModTest) ... ok
testAlignmentFileIsValid (test_PAML_yn00.ModTest) ... ok
testAlignmentSpecified (test_PAML_yn00.ModTest) ... ok
testCtlFileExistsOnRead (test_PAML_yn00.ModTest) ... ok
testCtlFileExistsOnRun (test_PAML_yn00.ModTest) ... ok
testCtlFileValidOnRead (test_PAML_yn00.ModTest) ... ok
testCtlFileValidOnRun (test_PAML_yn00.ModTest) ... ok
testOptionExists (test_PAML_yn00.ModTest) ... ok
testOutputFileSpecified (test_PAML_yn00.ModTest) ... ok
testOutputFileValid (test_PAML_yn00.ModTest) ... ok
testParseAllVersions (test_PAML_yn00.ModTest) ... ok
testResultsExist (test_PAML_yn00.ModTest) ... ok
testResultsParsable (test_PAML_yn00.ModTest) ... ok
testResultsValid (test_PAML_yn00.ModTest) ... ok
testWorkingDirValid (test_PAML_yn00.ModTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.152 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PDB.py
test_PDB ... ok
test_1_warnings (test_PDB.A_ExceptionTest)
Check warnings: Parse a flawed PDB file in permissive mode. ... ok
test_2_strict (test_PDB.A_ExceptionTest)
Check error: Parse a flawed PDB file in strict mode. ... ok
test_3_bad_xyz (test_PDB.A_ExceptionTest)
Check error: Parse an entry with bad x,y,z value. ... ok
test_4_occupancy (test_PDB.A_ExceptionTest)
Parse file with missing occupancy ... ok
test_AtomElement (test_PDB.Atom_Element)
Atom Element ... ok
test_hydrogens (test_PDB.Atom_Element) ... ok
test_ions (test_PDB.Atom_Element)
Element for magnesium is assigned correctly. ... ok
test_atom_copy (test_PDB.CopyTests) ... ok
test_entitity_copy (test_PDB.CopyTests)
Make a copy of a residue. ... ok
test_DSSP_file (test_PDB.DsspTests)
Test parsing of pregenerated DSSP ... ok
test_DSSP_hbonds (test_PDB.DsspTests)
Test parsing of DSSP hydrogen bond information. ... ok
test_DSSP_noheader_file (test_PDB.DsspTests)
Test parsing of pregenerated DSSP missing header information ... ok
test_ExposureCN (test_PDB.Exposure)
HSExposureCN. ... ok
test_HSExposureCA (test_PDB.Exposure)
HSExposureCA. ... ok
test_HSExposureCB (test_PDB.Exposure)
HSExposureCB. ... ok
test_capsid (test_PDB.HeaderTests)
Parse the header of a known PDB file (1A8O). ... ok
test_fibril (test_PDB.HeaderTests)
Parse the header of another PDB file (2BEG). ... ok
test_get_atoms (test_PDB.IterationTests)
Yields all atoms from the structure, excluding duplicates and ALTLOCs which are not parsed. ... ok
test_get_chains (test_PDB.IterationTests)
Yields chains from different models separately. ... ok
test_get_residues (test_PDB.IterationTests)
Yields all residues from all models. ... ok
test_NACCESS_asa_file (test_PDB.NACCESSTests)
Test parsing of pregenerated asa NACCESS file ... ok
test_NACCESS_rsa_file (test_PDB.NACCESSTests)
Test parsing of pregenerated rsa NACCESS file ... ok
test_c_n (test_PDB.ParseReal)
Extract polypeptides from 1A80. ... ok
test_empty (test_PDB.ParseReal)
Parse an empty file. ... ok
test_model_numbering (test_PDB.ParseReal)
Preserve model serial numbers during I/O. ... ok
test_strict (test_PDB.ParseReal)
Parse 1A8O.pdb file in strict mode. ... ok
test_c_n (test_PDB.ParseTest)
Extract polypeptides using C-N. ... ok
test_ca_ca (test_PDB.ParseTest)
Extract polypeptides using CA-CA. ... ok
test_details (test_PDB.ParseTest)
Verify details of the parsed example PDB file. ... ok
test_structure (test_PDB.ParseTest)
Verify the structure of the parsed example PDB file. ... ok
test_transform (test_PDB.TransformTests)
Transform entities (rotation and translation). ... ok
test_pdbio_missing_occupancy (test_PDB.WriteTest)
Write PDB file with missing occupancy ... ok
test_pdbio_select (test_PDB.WriteTest)
Write a selection of the structure using a Select subclass ... ok
test_pdbio_write_custom_residue (test_PDB.WriteTest)
Write a chainless residue using PDBIO ... ok
test_pdbio_write_residue (test_PDB.WriteTest)
Write a single residue using PDBIO ... ok
test_pdbio_write_structure (test_PDB.WriteTest)
Write a full structure using PDBIO ... ok
----------------------------------------------------------------------
Ran 1 test in 3.098 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PDB_KDTree.py
test_PDB_KDTree ... ok
test_neighbor_search (test_PDB_KDTree.NeighborTest)
NeighborSearch: Find nearby randomly generated coordinates. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.110 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_ParserSupport.py
test_ParserSupport ... ok
runTest (__main__.ComparisonTestCase)
test_ParserSupport ... ok
----------------------------------------------------------------------
Ran 1 test in 0.024 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Pathway.py
test_Pathway ... ok
testEdges (test_Pathway.GraphTestCase) ... ok
testEquals (test_Pathway.GraphTestCase) ... ok
testNodes (test_Pathway.GraphTestCase) ... ok
testRemoveNode (test_Pathway.GraphTestCase) ... ok
testEdges (test_Pathway.MultiGraphTestCase) ... ok
testEquals (test_Pathway.MultiGraphTestCase) ... ok
testNodes (test_Pathway.MultiGraphTestCase) ... ok
testRemoveNode (test_Pathway.MultiGraphTestCase) ... ok
testEq (test_Pathway.ReactionTestCase) ... ok
testRev (test_Pathway.ReactionTestCase) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.009 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Phd.py
test_Phd ... ok
test_check_SeqIO (test_Phd.PhdTest454)
Test phd_454 using parser via SeqIO. ... ok
test_check_SeqIO (test_Phd.PhdTestOne)
Test phd1 using parser via SeqIO. ... ok
test_check_record_parser (test_Phd.PhdTestOne)
Test phd1 file in detail. ... ok
test_check_SeqIO (test_Phd.PhdTestSolexa)
Test phd2 using parser via SeqIO. ... ok
test_check_SeqIO (test_Phd.PhdTestTwo)
Test phd2 using parser via SeqIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.136 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Phylo.py
test_Phylo ... ok
test_convert (test_Phylo.IOTests)
Convert a tree between all supported formats. ... ok
test_convert_phyloxml_binary (test_Phylo.IOTests)
Try writing phyloxml to a binary handle; fail on Py3. ... ok
test_convert_phyloxml_filename (test_Phylo.IOTests)
Write phyloxml to a given filename. ... ok
test_convert_phyloxml_text (test_Phylo.IOTests)
Write phyloxml to a text handle. ... ok
test_format_branch_length (test_Phylo.IOTests)
Custom format string for Newick branch length serialization. ... ok
test_int_labels (test_Phylo.IOTests)
Read newick formatted tree with numeric labels. ... ok
test_newick_read_multiple (test_Phylo.IOTests)
Parse a Nexus file with multiple trees. ... ok
test_newick_read_scinot (test_Phylo.IOTests)
Parse Newick branch lengths in scientific notation. ... ok
test_newick_read_single1 (test_Phylo.IOTests)
Read first Newick file with one tree. ... ok
test_newick_read_single2 (test_Phylo.IOTests)
Read second Newick file with one tree. ... ok
test_newick_read_single3 (test_Phylo.IOTests)
Read Nexus file with one tree. ... ok
test_newick_write (test_Phylo.IOTests)
Parse a Nexus file with multiple trees. ... ok
test_unicode_exception (test_Phylo.IOTests)
Read a Newick file with a unicode byte order mark (BOM). ... ok
test_collapse (test_Phylo.MixinTests)
TreeMixin: collapse() method. ... ok
test_collapse_all (test_Phylo.MixinTests)
TreeMixin: collapse_all() method. ... ok
test_common_ancestor (test_Phylo.MixinTests)
TreeMixin: common_ancestor() method. ... ok
test_depths (test_Phylo.MixinTests)
TreeMixin: depths() method. ... ok
test_distance (test_Phylo.MixinTests)
TreeMixin: distance() method. ... ok
test_find_clades (test_Phylo.MixinTests)
TreeMixin: find_clades() method. ... ok
test_find_elements (test_Phylo.MixinTests)
TreeMixin: find_elements() method. ... ok
test_find_terminal (test_Phylo.MixinTests)
TreeMixin: find_elements() with terminal argument. ... ok
test_get_path (test_Phylo.MixinTests)
TreeMixin: get_path() method. ... ok
test_is_bifurcating (test_Phylo.MixinTests)
TreeMixin: is_bifurcating() method. ... ok
test_is_monophyletic (test_Phylo.MixinTests)
TreeMixin: is_monophyletic() method. ... ok
test_ladderize (test_Phylo.MixinTests)
TreeMixin: ladderize() method. ... ok
test_prune (test_Phylo.MixinTests)
TreeMixin: prune() method. ... ok
test_split (test_Phylo.MixinTests)
TreeMixin: split() method. ... ok
test_total_branch_length (test_Phylo.MixinTests)
TreeMixin: total_branch_length() method. ... ok
test_trace (test_Phylo.MixinTests)
TreeMixin: trace() method. ... ok
test_randomized (test_Phylo.TreeTests)
Tree.randomized: generate a new randomized tree. ... ok
test_root_at_midpoint (test_Phylo.TreeTests)
Tree.root_at_midpoint: reroot at the tree's midpoint. ... ok
test_root_with_outgroup (test_Phylo.TreeTests)
Tree.root_with_outgroup: reroot at a given clade. ... ok
test_str (test_Phylo.TreeTests)
Tree.__str__: pretty-print to a string. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.815 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PhyloXML.py
test_PhyloXML ... ok
test_clade_getitem (test_PhyloXML.MethodTests)
Clade.__getitem__: get sub-clades by extended indexing. ... ok
test_clade_to_phylogeny (test_PhyloXML.MethodTests)
Convert a Clade object to a new Phylogeny. ... ok
test_color_hex (test_PhyloXML.MethodTests)
BranchColor: to_hex() method. ... ok
test_events (test_PhyloXML.MethodTests)
Events: Mapping-type behavior. ... ok
test_phylogeny_to_phyloxml (test_PhyloXML.MethodTests)
Convert a Phylogeny object to a new Phyloxml. ... ok
test_phyloxml_getitem (test_PhyloXML.MethodTests)
Phyloxml.__getitem__: get phylogenies by name or index. ... ok
test_sequence_conversion (test_PhyloXML.MethodTests) ... ok
test_singlular (test_PhyloXML.MethodTests)
Clade, Phylogeny: Singular properties for plural attributes. ... ok
test_to_alignment (test_PhyloXML.MethodTests) ... ok
test_parse_apaf (test_PhyloXML.ParseTests)
Parse the phylogenies in apaf.xml. ... ok
test_parse_bcl2 (test_PhyloXML.ParseTests)
Parse the phylogenies in bcl_2.xml. ... ok
test_parse_dollo (test_PhyloXML.ParseTests)
Parse the phylogenies in o_tol_332_d_dollo.xml. ... ok
test_parse_made (test_PhyloXML.ParseTests)
Parse the phylogenies in made_up.xml. ... ok
test_parse_phylo (test_PhyloXML.ParseTests)
Parse the phylogenies in phyloxml_examples.xml. ... ok
test_read_apaf (test_PhyloXML.ParseTests)
Read apaf.xml to produce a phyloXML object. ... ok
test_read_bcl2 (test_PhyloXML.ParseTests)
Read bcl_2.xml to produce a phyloXML object. ... ok
test_read_dollo (test_PhyloXML.ParseTests)
Read o_tol_332_d_dollo.xml to produce a phyloXML object. ... ok
test_read_made (test_PhyloXML.ParseTests)
Read made_up.xml to produce a phyloXML object. ... ok
test_read_phylo (test_PhyloXML.ParseTests)
Read phyloxml_examples.xml to produce a phyloXML object. ... ok
test_shape_apaf (test_PhyloXML.ParseTests)
Check the branching structure of apaf.xml. ... ok
test_shape_bcl2 (test_PhyloXML.ParseTests)
Check the branching structure of bcl_2.xml. ... ok
test_shape_dollo (test_PhyloXML.ParseTests)
Check the branching structure of o_tol_332_d_dollo.xml. ... ok
test_shape_phylo (test_PhyloXML.ParseTests)
Check the branching structure of phyloxml_examples.xml. ... ok
test_Annotation (test_PhyloXML.TreeTests)
Instantiation of Annotation objects. ... ok
test_BinaryCharacters (test_PhyloXML.TreeTests)
Instantiation of BinaryCharacters objects. ... ok
test_Clade (test_PhyloXML.TreeTests)
Instantiation of Clade objects. ... ok
test_CladeRelation (test_PhyloXML.TreeTests)
Instantiation of CladeRelation objects. ... ok
test_Confidence (test_PhyloXML.TreeTests)
Instantiation of Confidence objects. ... ok
test_Date (test_PhyloXML.TreeTests)
Instantiation of Date objects. ... ok
test_Distribution (test_PhyloXML.TreeTests)
Instantiation of Distribution objects. ... ok
test_DomainArchitecture (test_PhyloXML.TreeTests)
Instantiation of DomainArchitecture objects. ... ok
test_Events (test_PhyloXML.TreeTests)
Instantiation of Events objects. ... ok
test_Other (test_PhyloXML.TreeTests)
Instantiation of Other objects. ... ok
test_Phylogeny (test_PhyloXML.TreeTests)
Instantiation of Phylogeny objects. ... ok
test_Phyloxml (test_PhyloXML.TreeTests)
Instantiation of Phyloxml objects. ... ok
test_Polygon (test_PhyloXML.TreeTests)
Instantiation of Polygon objects. ... ok
test_Property (test_PhyloXML.TreeTests)
Instantiation of Property objects. ... ok
test_Reference (test_PhyloXML.TreeTests)
Instantiation of Reference objects. ... ok
test_Sequence (test_PhyloXML.TreeTests)
Instantiation of Sequence objects. ... ok
test_SequenceRelation (test_PhyloXML.TreeTests)
Instantiation of SequenceRelation objects. ... ok
test_Taxonomy (test_PhyloXML.TreeTests)
Instantiation of Taxonomy objects. ... ok
test_Uri (test_PhyloXML.TreeTests)
Instantiation of Uri objects. ... ok
test_apaf (test_PhyloXML.WriterTests)
Round-trip parsing and serialization of apaf.xml. ... ok
test_bcl2 (test_PhyloXML.WriterTests)
Round-trip parsing and serialization of bcl_2.xml. ... ok
test_dollo (test_PhyloXML.WriterTests)
Round-trip parsing and serialization of o_tol_332_d_dollo.xml. ... ok
test_made (test_PhyloXML.WriterTests)
Round-trip parsing and serialization of made_up.xml. ... ok
test_phylo (test_PhyloXML.WriterTests)
Round-trip parsing and serialization of phyloxml_examples.xml. ... ok
----------------------------------------------------------------------
Ran 1 test in 1.130 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Phylo_CDAO.py
test_Phylo_CDAO ... skipping. Install RDFlib if you want to use the CDAO tree format.
----------------------------------------------------------------------
Ran 1 test in 0.132 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Phylo_NeXML.py
test_Phylo_NeXML ... ok
test_parse_0 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in characters.xml. ... ok
test_parse_1 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in edgelabels.xml. ... ok
test_parse_10 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in treebase-record.xml. ... ok
test_parse_11 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in trees-uris.xml. ... ok
test_parse_12 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in trees.xml. ... ok
test_parse_2 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in meta_taxa.xml. ... ok
test_parse_3 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in meta_types.xml. ... ok
test_parse_4 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in nexml.xml. ... ok
test_parse_5 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in phenoscape.xml. ... ok
test_parse_6 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in sets.xml. ... ok
test_parse_7 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in taxa.xml. ... ok
test_parse_8 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in timetree.xml. ... ok
test_parse_9 (test_Phylo_NeXML.ParseTests)
Parse the phylogenies in tolweb.xml. ... ok
test_write_1 (test_Phylo_NeXML.WriterTests)
Write and re-parse the phylogenies in edgelabels.xml. ... ok
test_write_10 (test_Phylo_NeXML.WriterTests)
Write and re-parse the phylogenies in treebase-record.xml. ... ok
test_write_11 (test_Phylo_NeXML.WriterTests)
Write and re-parse the phylogenies in trees-uris.xml. ... ok
test_write_12 (test_Phylo_NeXML.WriterTests)
Write and re-parse the phylogenies in trees.xml. ... ok
test_write_6 (test_Phylo_NeXML.WriterTests)
Write and re-parse the phylogenies in sets.xml. ... ok
test_write_8 (test_Phylo_NeXML.WriterTests)
Write and re-parse the phylogenies in timetree.xml. ... ok
test_write_9 (test_Phylo_NeXML.WriterTests)
Write and re-parse the phylogenies in tolweb.xml. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.262 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Phylo_depend.py
test_Phylo_depend ... skipping. Install matplotlib if you want to use Bio.Phylo._utils.
----------------------------------------------------------------------
Ran 1 test in 0.004 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PopGen_DFDist.py
test_PopGen_DFDist ... skipping. Install Dfdist, Ddatacal, pv2 and cplot2 if you want to use DFDist with Bio.PopGen.FDist.
----------------------------------------------------------------------
Ran 1 test in 0.015 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PopGen_FDist.py
test_PopGen_FDist ... skipping. Install fdist2, datacal, pv and cplot if you want to use FDist2 with Bio.PopGen.FDist.
----------------------------------------------------------------------
Ran 1 test in 0.011 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PopGen_FDist_nodepend.py
test_PopGen_FDist_nodepend ... ok
test_convert (test_PopGen_FDist_nodepend.ConversionTest)
Basic conversion test. ... ok
test_convert_big (test_PopGen_FDist_nodepend.ConversionTest)
Big interface conversion test. ... ok
test_record_parser (test_PopGen_FDist_nodepend.ParserTest)
Basic operation of the Record Parser. ... ok
test_record_basic (test_PopGen_FDist_nodepend.RecordTest)
Basic test on Record ... ok
----------------------------------------------------------------------
Ran 1 test in 0.013 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PopGen_FastSimCoal.py
test_PopGen_FastSimCoal ... skipping. Install fastsimcoal if you want to use Bio.PopGen.SimCoal.Controller.FastSimCoalController.
----------------------------------------------------------------------
Ran 1 test in 0.028 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PopGen_GenePop.py
test_PopGen_GenePop ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
----------------------------------------------------------------------
Ran 1 test in 0.034 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PopGen_GenePop_EasyController.py
test_PopGen_GenePop_EasyController ... skipping. Install GenePop if you want to use Bio.PopGen.GenePop.
----------------------------------------------------------------------
Ran 1 test in 0.028 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PopGen_GenePop_nodepend.py
test_PopGen_GenePop_nodepend ... ok
test_file_record_parser (test_PopGen_GenePop_nodepend.FileParserTest)
Basic operation of the File Record Parser. ... ok
test_wrong_file_parser (test_PopGen_GenePop_nodepend.FileParserTest)
Testing the ability to deal with wrongly formatted files ... ok
test_record_parser (test_PopGen_GenePop_nodepend.ParserTest)
Basic operation of the Record Parser. ... ok
test_wrong_file_parser (test_PopGen_GenePop_nodepend.ParserTest)
Testing the ability to deal with wrongly formatted files ... ok
test_record_basic (test_PopGen_GenePop_nodepend.RecordTest)
Basic test on Record ... ok
test_utils (test_PopGen_GenePop_nodepend.UtilsTest)
Basic operation of GenePop Utils. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.009 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PopGen_SimCoal.py
test_PopGen_SimCoal ... skipping. Install SIMCOAL2 if you want to use Bio.PopGen.SimCoal.
----------------------------------------------------------------------
Ran 1 test in 0.026 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_PopGen_SimCoal_nodepend.py
test_PopGen_SimCoal_nodepend ... ok
test_template_full (test_PopGen_SimCoal_nodepend.TemplateTest)
Full template creation test ... ok
----------------------------------------------------------------------
Ran 1 test in 0.024 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Prank_tool.py
test_Prank_tool ... skipping. Install PRANK if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.124 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Probcons_tool.py
test_Probcons_tool ... skipping. Install PROBCONS if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.126 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_ProtParam.py
test_ProtParam ... ok
test_aromaticity (test_ProtParam.ProtParamTest)
Test calculating protein aromaticity ... ok
test_count_amino_acids (test_ProtParam.ProtParamTest)
Test getting amino acid counts ... ok
test_flexibility (test_ProtParam.ProtParamTest)
Test calculating protein flexibility ... ok
test_get_amino_acids_percent (test_ProtParam.ProtParamTest)
Test getting amino acid percentage ... ok
test_get_molecular_weight (test_ProtParam.ProtParamTest)
Test calculating protein molecular weight ... ok
test_get_molecular_weight_identical (test_ProtParam.ProtParamTest)
Test calculating the protein molecular weight agrees with calculation from Bio.SeqUtils ... ok
test_get_monoisotopic_molecular_weight (test_ProtParam.ProtParamTest)
Test calculating the monoisotopic molecular weight ... ok
test_get_monoisotopic_molecular_weight_identical (test_ProtParam.ProtParamTest)
Test calculating the protein molecular weight agrees with calculation from Bio.SeqUtils ... ok
test_gravy (test_ProtParam.ProtParamTest)
Test calculating gravy ... ok
test_instability_index (test_ProtParam.ProtParamTest)
Test calculating protein instability index ... ok
test_isoelectric_point (test_ProtParam.ProtParamTest)
Test calculating the isoelectric point ... ok
test_protein_scale (test_ProtParam.ProtParamTest)
Test calculating the Kite Doolittle scale ... ok
test_secondary_structure_fraction (test_ProtParam.ProtParamTest)
Test calculating secondary structure fractions ... ok
----------------------------------------------------------------------
Ran 1 test in 0.092 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_QCPSuperimposer.py
test_QCPSuperimposer ... /builddir/build/BUILD/python-biopython-1.66/python2/build/lib.linux-i686-2.7/Bio/PDB/QCPSuperimposer/__init__.py:22: BiopythonExperimentalWarning: Bio.PDB.QCPSuperimposer is an experimental submodule which may undergo significant changes prior to its future official release.
  BiopythonExperimentalWarning)
ok
runTest (__main__.ComparisonTestCase)
test_QCPSuperimposer ... ok
----------------------------------------------------------------------
Ran 1 test in 0.090 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Restriction.py
test_Restriction ... ok
test_basic_isochizomers (test_Restriction.EnzymeComparison)
Test to be sure isochizomer and neoschizomers are as expected. ... ok
test_comparisons (test_Restriction.EnzymeComparison)
Comparison operators between iso and neoschizomers. ... ok
test_make_format_map1 (test_Restriction.RestrictionBatchPrintTest)
Make sure print_as('map'); print_that() does not error on wrap round with no markers. ... ok
test_make_format_map2 (test_Restriction.RestrictionBatchPrintTest)
Make sure print_as('map'); print_that() does not error on wrap round with marker. ... ok
test_make_format_map3 (test_Restriction.RestrictionBatchPrintTest)
Make sure print_as('map'); print_that() does not error on wrap round with marker restricted. ... ok
test_batch_analysis (test_Restriction.RestrictionBatches)
Sequence analysis with a restriction batch. ... ok
test_creating_batch (test_Restriction.RestrictionBatches)
Creating and modifying a restriction batch. ... ok
test_circular_sequences (test_Restriction.SimpleEnzyme)
Deal with cutting circular sequences. ... ok
test_eco_cutting (test_Restriction.SimpleEnzyme)
Test basic cutting with EcoRI. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.307 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SCOP_Astral.py
test_SCOP_Astral ... ok
testConstructWithCustomFile (test_SCOP_Astral.AstralTests) ... ok
testGetDomainsClustered (test_SCOP_Astral.AstralTests) ... ok
testGetDomainsFromFile (test_SCOP_Astral.AstralTests) ... ok
testGetSeq (test_SCOP_Astral.AstralTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.132 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SCOP_Cla.py
test_SCOP_Cla ... ok
testError (test_SCOP_Cla.ClaTests)
Test if a corrupt record raises the appropriate exception ... ok
testIndex (test_SCOP_Cla.ClaTests)
Test CLA file indexing ... ok
testParse (test_SCOP_Cla.ClaTests)
Test if all records in a CLA file are being read ... ok
testRecord (test_SCOP_Cla.ClaTests)
Test one record in detail ... ok
testStr (test_SCOP_Cla.ClaTests)
Test if we can convert each record to a string correctly ... ok
----------------------------------------------------------------------
Ran 1 test in 0.115 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SCOP_Des.py
test_SCOP_Des ... ok
testError (test_SCOP_Des.DesTests)
Test if a corrupt record raises the appropriate exception ... ok
testParse (test_SCOP_Des.DesTests)
Test if all records in a DES file are being read ... ok
testRecord (test_SCOP_Des.DesTests)
Test one record in detail ... ok
testStr (test_SCOP_Des.DesTests)
Test if we can convert each record to a string correctly ... ok
----------------------------------------------------------------------
Ran 1 test in 0.113 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SCOP_Dom.py
test_SCOP_Dom ... ok
testError (test_SCOP_Dom.DomTests)
Test if a corrupt record raises the appropriate exception ... ok
testParse (test_SCOP_Dom.DomTests)
Test if all records in a DOM file are being read ... ok
testRecord (test_SCOP_Dom.DomTests)
Test one record in detail ... ok
testStr (test_SCOP_Dom.DomTests)
Test if we can convert each record to a string correctly ... ok
----------------------------------------------------------------------
Ran 1 test in 0.114 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SCOP_Hie.py
test_SCOP_Hie ... ok
testError (test_SCOP_Hie.HieTests)
Test if a corrupt record raises the appropriate exception ... ok
testParse (test_SCOP_Hie.HieTests)
Test if all records in a HIE file are being read ... ok
testStr (test_SCOP_Hie.HieTests)
Test if we can convert each record to a string correctly ... ok
----------------------------------------------------------------------
Ran 1 test in 0.112 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SCOP_Raf.py
test_SCOP_Raf ... ok
testParse (test_SCOP_Raf.RafTests)
Can we parse a RAF record? ... ok
testSeqMapAdd (test_SCOP_Raf.RafTests) ... ok
testSeqMapIndex (test_SCOP_Raf.RafTests) ... ok
testSeqMapSlice (test_SCOP_Raf.RafTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.121 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SCOP_Residues.py
test_SCOP_Residues ... ok
testAstralParse (test_SCOP_Residues.ResiduesTests)
Test if we can parse residue subsets enclosed in brackets ... ok
testJustPdbId (test_SCOP_Residues.ResiduesTests) ... ok
testParse (test_SCOP_Residues.ResiduesTests) ... ok
testParseError (test_SCOP_Residues.ResiduesTests) ... ok
testPdbId (test_SCOP_Residues.ResiduesTests) ... ok
testStr (test_SCOP_Residues.ResiduesTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.114 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SCOP_Scop.py
test_SCOP_Scop ... ok
testConstructFromDirectory (test_SCOP_Scop.ScopTests) ... ok
testGetAscendent (test_SCOP_Scop.ScopTests) ... ok
testParse (test_SCOP_Scop.ScopTests) ... ok
testParseDomain (test_SCOP_Scop.ScopTests) ... ok
testSccsOrder (test_SCOP_Scop.ScopTests) ... ok
test_get_descendents (test_SCOP_Scop.ScopTests)
Test getDescendents method ... ok
----------------------------------------------------------------------
Ran 1 test in 0.119 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SCOP_online.py
test_SCOP_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.003 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SVDSuperimposer.py
test_SVDSuperimposer ... ok
runTest (__main__.ComparisonTestCase)
test_SVDSuperimposer ... ok
----------------------------------------------------------------------
Ran 1 test in 0.006 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_blast_tab.py
test_SearchIO_blast_tab ... ok
test_tab_2226_tblastn_001 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_001) ... ok
test_tab_2226_tblastn_002 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_002) ... ok
test_tab_2226_tblastn_003 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_003) ... ok
test_tab_2226_tblastn_004 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_004) ... ok
test_tab_2226_tblastn_005 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_005) ... ok
test_tab_2226_tblastn_006 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_006) ... ok
test_tab_2226_tblastn_007 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_007) ... ok
test_tab_2226_tblastn_008 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_008) ... ok
test_tab_2226_tblastn_009 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_009) ... ok
test_tab_2226_tblastn_010 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_010) ... ok
test_tab_2226_tblastn_011 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_011) ... ok
test_tab_2226_tblastn_012 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output with comments (tab_2226_tblastn_012) ... ok
test_tab_2226_tblastn_013 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.26+ tabular output (tab_2226_tblastn_013) ... ok
test_tab_2228_tblastn_001 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTN 2.2.28+ tabular output (tab_2228_tblastn_001) ... ok
test_tab_2228_tblastx_001 (test_SearchIO_blast_tab.BlastTabCases)
Test parsing TBLASTX 2.2.28+ tabular output (tab_2228_tblastx_001) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.270 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_blast_tab_index.py
test_SearchIO_blast_tab_index ... ok
test_blasttab_2226_tblastn_001 (test_SearchIO_blast_tab_index.BlastTabIndexCases)
Test blast-tab indexing, BLAST 2.2.26+, multiple queries ... ok
test_blasttab_2226_tblastn_002 (test_SearchIO_blast_tab_index.BlastTabIndexCases)
Test blast-tab indexing, BLAST 2.2.26+, single query, no hits ... ok
test_blasttab_2226_tblastn_004 (test_SearchIO_blast_tab_index.BlastTabIndexCases)
Test blast-tab indexing, BLAST 2.2.26+, single query, multiple hits ... ok
test_blasttab_2226_tblastn_005 (test_SearchIO_blast_tab_index.BlastTabIndexCases)
Test blast-tab indexing, BLAST 2.2.26+, multiple queries, commented ... ok
test_blasttab_2226_tblastn_006 (test_SearchIO_blast_tab_index.BlastTabIndexCases)
Test blast-tab indexing, BLAST 2.2.26+, single query, no hits, commented ... ok
test_blasttab_2226_tblastn_009 (test_SearchIO_blast_tab_index.BlastTabIndexCases)
Test blast-tab indexing, BLAST 2.2.26+, custom columns ... ok
test_blasttab_2226_tblastn_010 (test_SearchIO_blast_tab_index.BlastTabIndexCases)
Test blast-tab indexing, BLAST 2.2.26+, custom columns, commented ... ok
test_blasttab_2226_tblastn_011 (test_SearchIO_blast_tab_index.BlastTabIndexCases)
Test blast-tab indexing, BLAST 2.2.26+, all columns, commented ... ok
test_blasttab_comment_sing (test_SearchIO_blast_tab_index.BlastTabIndexCases)
Test blast-tab indexing, BLAST 2.2.26+, single query, multiple hits, commented ... ok
test_blasttab_2226_multiple_first (test_SearchIO_blast_tab_index.BlastTabRawCases)
Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, first (tab_2226_tblastn_001.txt) ... ok
test_blasttab_2226_multiple_first_commented (test_SearchIO_blast_tab_index.BlastTabRawCases)
Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, first, commented (tab_2226_tblastn_005.txt) ... ok
test_blasttab_2226_multiple_last (test_SearchIO_blast_tab_index.BlastTabRawCases)
Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, last (tab_2226_tblastn_001.txt) ... ok
test_blasttab_2226_multiple_last_commented (test_SearchIO_blast_tab_index.BlastTabRawCases)
Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, last, commented (tab_2226_tblastn_005.txt) ... ok
test_blasttab_2226_multiple_middle_commented (test_SearchIO_blast_tab_index.BlastTabRawCases)
Test blast-tab raw string retrieval, BLAST 2.2.26+, multiple queries, middle, commented (tab_2226_tblastn_005.txt) ... ok
test_blasttab_2226_single (test_SearchIO_blast_tab_index.BlastTabRawCases)
Test blast-tab raw string retrieval, BLAST 2.2.26+, single query (tab_2226_tblastn_004.txt) ... ok
test_blasttab_2226_single_commented (test_SearchIO_blast_tab_index.BlastTabRawCases)
Test blast-tab raw string retrieval, BLAST 2.2.26+, single query, commented (tab_2226_tblastn_008.txt) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.197 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_blast_text.py
test_SearchIO_blast_text ... ok
test_text_2226_blastn_001 (test_SearchIO_blast_text.BlastnCases)
Test parsing blastn output (text_2226_blastn_001.txt) ... ok
test_text_2226_blastn_002 (test_SearchIO_blast_text.BlastnCases)
Test parsing blastn output (text_2226_blastn_002.txt) ... ok
test_text_2226_blastn_003 (test_SearchIO_blast_text.BlastnCases)
Test parsing blastn output (text_2226_blastn_003.txt) ... ok
test_text_2226_blastn_004 (test_SearchIO_blast_text.BlastnCases)
Test parsing blastn output (text_2226_blastn_004.txt) ... ok
test_text_2226_blastp_001 (test_SearchIO_blast_text.BlastpCases)
Test parsing blastp output (text_2226_blastp_001.txt) ... ok
test_text_2226_blastp_002 (test_SearchIO_blast_text.BlastpCases)
Test parsing blastp output (text_2226_blastp_002.txt) ... ok
test_text_2226_blastp_003 (test_SearchIO_blast_text.BlastpCases)
Test parsing blastp output (text_2226_blastp_003.txt) ... ok
test_text_2226_blastp_004 (test_SearchIO_blast_text.BlastpCases)
Test parsing blastp output (text_2226_blastp_004.txt) ... ok
test_text_2226_blastx_001 (test_SearchIO_blast_text.BlastxCases)
Test parsing blastx output (text_2226_blastx_001.txt) ... ok
test_text_2226_blastx_002 (test_SearchIO_blast_text.BlastxCases)
Test parsing blastx output (text_2226_blastx_002.txt) ... ok
test_text_2226_blastx_003 (test_SearchIO_blast_text.BlastxCases)
Test parsing blastx output (text_2226_blastx_003.txt) ... ok
test_text_2226_blastx_004 (test_SearchIO_blast_text.BlastxCases)
Test parsing blastx output (text_2226_blastx_004.txt) ... ok
test_text_2226_tblastn_001 (test_SearchIO_blast_text.TblastnCases)
Test parsing tblastn output (text_2226_tblastn_001.txt) ... ok
test_text_2226_tblastn_002 (test_SearchIO_blast_text.TblastnCases)
Test parsing tblastn output (text_2226_tblastn_002.txt) ... ok
test_text_2226_tblastn_003 (test_SearchIO_blast_text.TblastnCases)
Test parsing tblastn output (text_2226_tblastn_003.txt) ... ok
test_text_2226_tblastn_004 (test_SearchIO_blast_text.TblastnCases)
Test parsing tblastn output (text_2226_tblastn_004.txt) ... ok
test_text_2226_tblastx_001 (test_SearchIO_blast_text.TblastxCases)
Test parsing tblastx output (text_2226_tblastx_001.txt) ... ok
test_text_2226_tblastx_002 (test_SearchIO_blast_text.TblastxCases)
Test parsing tblastx output (text_2226_tblastx_002.txt) ... ok
test_text_2226_tblastx_003 (test_SearchIO_blast_text.TblastxCases)
Test parsing tblastx output (text_2226_tblastx_003.txt) ... ok
test_text_2226_tblastx_004 (test_SearchIO_blast_text.TblastxCases)
Test parsing tblastx output (text_2226_tblastx_004.txt) ... ok
test_text_2230_blastp_001 (test_SearchIO_blast_text.TblastxCases)
Test parsing blastp output (text_2230_blastp_001.txt) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.293 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_blast_xml.py
test_SearchIO_blast_xml ... ok
test_xml_2226_blastn_006 (test_SearchIO_blast_xml.BlastXmlSpecialCases) ... ok
test_xml_2212L_blastn_001 (test_SearchIO_blast_xml.BlastnXmlCases) ... ok
test_xml_2226_blastn_001 (test_SearchIO_blast_xml.BlastnXmlCases) ... ok
test_xml_2226_blastn_002 (test_SearchIO_blast_xml.BlastnXmlCases) ... ok
test_xml_2226_blastn_003 (test_SearchIO_blast_xml.BlastnXmlCases) ... ok
test_xml_2226_blastn_004 (test_SearchIO_blast_xml.BlastnXmlCases) ... ok
test_xml_2226_blastn_005 (test_SearchIO_blast_xml.BlastnXmlCases) ... ok
test_xml_2212L_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2218L_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2218_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2218_blastp_002 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2222_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2226_blastp_001 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2226_blastp_002 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2226_blastp_003 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2226_blastp_004 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2226_blastp_005 (test_SearchIO_blast_xml.BlastpXmlCases) ... ok
test_xml_2212L_blastx_001 (test_SearchIO_blast_xml.BlastxXmlCases) ... ok
test_xml_2222_blastx_001 (test_SearchIO_blast_xml.BlastxXmlCases) ... ok
test_xml_2226_blastx_001 (test_SearchIO_blast_xml.BlastxXmlCases) ... ok
test_xml_2226_blastx_002 (test_SearchIO_blast_xml.BlastxXmlCases) ... ok
test_xml_2226_blastx_003 (test_SearchIO_blast_xml.BlastxXmlCases) ... ok
test_xml_2226_blastx_004 (test_SearchIO_blast_xml.BlastxXmlCases) ... ok
test_xml_2212L_tblastn_001 (test_SearchIO_blast_xml.TblastnXmlCases) ... ok
test_xml_2226_tblastn_001 (test_SearchIO_blast_xml.TblastnXmlCases) ... ok
test_xml_2226_tblastn_002 (test_SearchIO_blast_xml.TblastnXmlCases) ... ok
test_xml_2226_tblastn_003 (test_SearchIO_blast_xml.TblastnXmlCases) ... ok
test_xml_2226_tblastn_004 (test_SearchIO_blast_xml.TblastnXmlCases) ... ok
test_xml_2226_tblastn_005 (test_SearchIO_blast_xml.TblastnXmlCases) ... ok
test_xml_2212L_tblastx_001 (test_SearchIO_blast_xml.TblastxXmlCases) ... ok
test_xml_2226_tblastx_001 (test_SearchIO_blast_xml.TblastxXmlCases) ... ok
test_xml_2226_tblastx_002 (test_SearchIO_blast_xml.TblastxXmlCases) ... ok
test_xml_2226_tblastx_003 (test_SearchIO_blast_xml.TblastxXmlCases) ... ok
test_xml_2226_tblastx_004 (test_SearchIO_blast_xml.TblastxXmlCases) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.486 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_blast_xml_index.py
test_SearchIO_blast_xml_index ... ok
test_blastxml_2212L_blastp_001 (test_SearchIO_blast_xml_index.BlastXmlIndexCases)
Test blast-xml indexing, BLAST 2.2.12 ... ok
test_blastxml_2218_blastp_001 (test_SearchIO_blast_xml_index.BlastXmlIndexCases)
Test blast-xml indexing, BLAST 2.2.18+ ... ok
test_blastxml_2222_blastx_001 (test_SearchIO_blast_xml_index.BlastXmlIndexCases)
Test blast-xml indexing, BLAST 2.2.22+ ... ok
test_blastxml_2226_tblastn_001 (test_SearchIO_blast_xml_index.BlastXmlIndexCases)
Test blast-xml indexing, BLAST 2.2.26+, multiple queries ... ok
test_blastxml_2226_tblastn_002 (test_SearchIO_blast_xml_index.BlastXmlIndexCases)
Test blast-xml indexing, BlAST 2.2.26+, single query, no hits ... ok
test_blastxml_2226_tblastn_004 (test_SearchIO_blast_xml_index.BlastXmlIndexCases)
Test blast-xml indexing, BLAST 2.2.26+, single query, multiple hits ... ok
test_blastxml_2226_multiple_first (test_SearchIO_blast_xml_index.BlastXmlRawCases)
Test blast-xml raw string retrieval, BLAST 2.2.26+, multiple queries, first (xml_2226_blastp_001.xml) ... ok
test_blastxml_2226_multiple_last (test_SearchIO_blast_xml_index.BlastXmlRawCases)
Test blast-xml raw string retrieval, BLAST 2.2.26+, multiple queries, last (xml_2226_blastp_001.xml) ... ok
test_blastxml_2226_multiple_middle (test_SearchIO_blast_xml_index.BlastXmlRawCases)
Test blast-xml raw string retrieval, BLAST 2.2.26+, multiple queries, middle (xml_2226_blastp_001.xml) ... ok
test_blastxml_2226_single (test_SearchIO_blast_xml_index.BlastXmlRawCases)
Test blast-xml raw string retrieval, BLAST 2.2.26+, single query (xml_2226_blastp_004.xml) ... ok
----------------------------------------------------------------------
Ran 1 test in 1.995 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_blat_psl.py
test_SearchIO_blat_psl ... ok
test_psl_34_001 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_34_001.psl) ... ok
test_psl_34_002 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_34_001.psl) ... ok
test_psl_34_003 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_34_003.psl) ... ok
test_psl_34_004 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_34_004.psl) ... ok
test_psl_34_005 (test_SearchIO_blat_psl.BlatPslCases)
Test parsing blat output (psl_34_005.psl) ... ok
test_psl_34_001 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_34_001.psl) ... ok
test_psl_34_002 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_34_001.psl) ... ok
test_psl_34_003 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_34_003.psl) ... ok
test_psl_34_004 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_34_004.psl) ... ok
test_psl_34_005 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (psl_34_005.psl) ... ok
test_pslx_34_001 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (pslx_34_001.pslx) ... ok
test_pslx_34_002 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (pslx_34_002.pslx) ... ok
test_pslx_34_003 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (pslx_34_003.pslx) ... ok
test_pslx_34_004 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (pslx_34_004.pslx) ... ok
test_pslx_34_005 (test_SearchIO_blat_psl.BlatPslxCases)
Test parsing blat output (pslx_34_005.pslx) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.182 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_blat_psl_index.py
test_SearchIO_blat_psl_index ... ok
test_psl_34_001 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-psl indexing, multiple queries ... ok
test_psl_34_002 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-psl indexing, single query, no hits ... ok
test_psl_34_003 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-psl indexing, single query, single hit ... ok
test_psl_34_004 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-psl indexing, single query, multiple hits with multiple hsps ... ok
test_psl_34_005 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-psl indexing, multiple queries, no header ... ok
test_psl_34_006 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-pslx indexing, multiple queries ... ok
test_psl_34_007 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-pslx indexing, single query, no hits ... ok
test_psl_34_008 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-pslx indexing, single query, single hit ... ok
test_psl_34_009 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-pslx indexing, single query, multiple hits with multiple hsps ... ok
test_psl_34_010 (test_SearchIO_blat_psl_index.BlatPslIndexCases)
Test blat-pslx indexing, multiple queries, no header ... ok
----------------------------------------------------------------------
Ran 1 test in 0.256 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_exonerate.py
test_SearchIO_exonerate ... ok
test_exn_22_o_vulgar_cigar (test_SearchIO_exonerate.ExonerateCigarCases)
Test parsing exonerate output (exn_22_o_vulgar_cigar.exn) ... ok
test_vulgar_text_similar_c2c (test_SearchIO_exonerate.ExonerateSpcCases)
Compares vulgar-text coordinate parsing for the coding2coding model. ... ok
test_vulgar_text_similar_g2g (test_SearchIO_exonerate.ExonerateSpcCases)
Compares vulgar-text coordinate parsing for the genome2genome model. ... ok
test_vulgar_text_similar_p2d (test_SearchIO_exonerate.ExonerateSpcCases)
Compares vulgar-text coordinate parsing for the protein2dna model. ... ok
test_exn_22_m_affine_local (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_affine_local.exn) ... ok
test_exn_22_m_cdna2genome (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_cdna2genome.exn) ... ok
test_exn_22_m_coding2coding (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_coding2coding.exn) ... ok
test_exn_22_m_coding2coding_fshifts (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_coding2coding_fshifts.exn) ... ok
test_exn_22_m_coding2genome (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_coding2genome.exn) ... ok
test_exn_22_m_dna2protein (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_dna2protein.exn) ... ok
test_exn_22_m_est2genome (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_est2genome.exn) ... ok
test_exn_22_m_genome2genome (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_genome2genome.exn) ... ok
test_exn_22_m_ner (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_ner.exn) ... ok
test_exn_22_m_protein2dna_fshifts (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_protein2dna_fshifts.exn) ... ok
test_exn_22_m_ungapped (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_ungapped.exn) ... ok
test_exn_22_m_ungapped_trans (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_m_ungapped_trans.exn) ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_q_multiple.exn) ... ok
test_exn_22_q_none (test_SearchIO_exonerate.ExonerateTextCases)
Test parsing exonerate output (exn_22_q_none.exn) ... ok
test_exn_22_o_vulgar (test_SearchIO_exonerate.ExonerateVulgarCases)
Test parsing exonerate output (exn_22_o_vulgar.exn) ... ok
test_exn_22_o_vulgar_fshifts (test_SearchIO_exonerate.ExonerateVulgarCases)
Test parsing exonerate output (exn_22_o_vulgar_fshifts.exn) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.237 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_exonerate_text_index.py
test_SearchIO_exonerate_text_index ... ok
test_exn_22_m_est2genome (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases)
Test exonerate-text indexing, single ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate_text_index.ExonerateTextIndexCases)
Test exonerate-text indexing, single ... ok
----------------------------------------------------------------------
Ran 1 test in 0.138 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_exonerate_vulgar_index.py
test_SearchIO_exonerate_vulgar_index ... ok
test_exn_22_m_est2genome (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases)
Test exonerate-vulgar indexing, single ... ok
test_exn_22_q_multiple (test_SearchIO_exonerate_vulgar_index.ExonerateVulgarIndexCases)
Test exonerate-vulgar indexing, single ... ok
----------------------------------------------------------------------
Ran 1 test in 0.114 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_fasta_m10.py
test_SearchIO_fasta_m10 ... ok
test_output002 (test_SearchIO_fasta_m10.Fasta34Cases)
Test parsing fasta34 output (output002.m10) ... ok
test_output003 (test_SearchIO_fasta_m10.Fasta34Cases)
Test parsing fasta34 output (output003.m10) ... ok
test_output001 (test_SearchIO_fasta_m10.Fasta35Cases)
Test parsing fasta35 output (output001.m10) ... ok
test_output004 (test_SearchIO_fasta_m10.Fasta35Cases)
Test parsing fasta35 output (output004.m10) ... ok
test_output005 (test_SearchIO_fasta_m10.Fasta35Cases)
Test parsing ssearch35 output (output005.m10) ... ok
test_output006 (test_SearchIO_fasta_m10.Fasta35Cases)
Test parsing fasta35 output (output006.m10) ... ok
test_output007 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output007.m10) ... ok
test_output008 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing tfastx36 output (output008.m10) ... ok
test_output009 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output009.m10) ... ok
test_output010 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output010.m10) ... ok
test_output011 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output011.m10) ... ok
test_output012 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output012.m10) ... ok
test_output013 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output013.m10) ... ok
test_output014 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output014.m10) ... ok
test_output015 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output015.m10) ... ok
test_output016 (test_SearchIO_fasta_m10.Fasta36Cases)
Test parsing fasta36 output (output016.m10) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.202 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_fasta_m10_index.py
test_SearchIO_fasta_m10_index ... ok
test_output_001 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, fasta35, multiple queries ... ok
test_output_002 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, fasta34, multiple queries ... ok
test_output_005 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, ssearch35, multiple queries ... ok
test_output_008 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, tfastx36, multiple queries ... ok
test_output_009 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, fasta36, multiple queries ... ok
test_output_010 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, fasta36, single query, no hits ... ok
test_output_011 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, fasta36, single query, hits with single hsp ... ok
test_output_012 (test_SearchIO_fasta_m10_index.FastaM10IndexCases)
Test fasta-m10 indexing, fasta36, single query with multiple hsps ... ok
----------------------------------------------------------------------
Ran 1 test in 0.260 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_hmmer2_text.py
test_SearchIO_hmmer2_text ... ok
test_hmmpfam_21 (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.1 file (text_21_hmmpfam_001.out) ... ok
test_hmmpfam_22 (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.2 file (text_22_hmmpfam_001.out) ... ok
test_hmmpfam_23 (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.3 file (text_23_hmmpfam_001.out) ... ok
test_hmmpfam_23_missing_consensus (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.3 file (text_23_hmmpfam_003.out) ... ok
test_hmmpfam_23_no_match (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.3 file (text_23_hmmpfam_002.out) ... ok
test_hmmpfam_24 (test_SearchIO_hmmer2_text.HmmpfamTests)
Test parsing hmmpfam 2.4 file (text_24_hmmpfam_001.out) ... ok
test_hmmsearch_20 (test_SearchIO_hmmer2_text.HmmsearchTests)
Test parsing hmmsearch 2.0 file (text_20_hmmsearch_001.out) ... ok
test_hmmsearch_22 (test_SearchIO_hmmer2_text.HmmsearchTests)
Test parsing hmmsearch 2.2 file (text_22_hmmsearch_001.out) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.457 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_hmmer2_text_index.py
test_SearchIO_hmmer2_text_index ... ok
test_hmmertext_text_21_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
Test hmmer2-text indexing, HMMER 2.1 ... ok
test_hmmertext_text_22_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
Test hmmer2-text indexing, HMMER 2.2 ... ok
test_hmmertext_text_22_hmmsearch_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
Test hmmer2-text indexing, HMMER 2.2 ... ok
test_hmmertext_text_23_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
Test hmmer2-text indexing, HMMER 2.3 ... ok
test_hmmertext_text_24_hmmpfam_001 (test_SearchIO_hmmer2_text_index.Hmmer2TextIndexCases)
Test hmmer2-text indexing, HMMER 2.4 ... ok
test_hmmer2text_22_multiple_first_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
Test hmmer2-text raw string retrieval, multiple queries, hmmpfam ... ok
test_hmmer2text_22_multiple_last_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
Test hmmer2-text raw string retrieval, multiple queries, hmmpfam ... ok
test_hmmer2text_22_multiple_middle_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
Test hmmer2-text raw string retrieval, multiple queries, hmmpfam ... ok
test_hmmer2text_22_single_hmmpfam (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
Test hmmer2-text raw string retrieval, single query, hmmpfam ... ok
test_hmmer2text_22_single_hmmsearch (test_SearchIO_hmmer2_text_index.Hmmer2TextRawCases)
Test hmmer2-text raw string retrieval, single query, hmmsearch ... ok
----------------------------------------------------------------------
Ran 1 test in 0.254 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_hmmer3_domtab.py
test_SearchIO_hmmer3_domtab ... ok
test_domtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases)
Test parsing hmmsearch-domtab, hmmsearch 3.0, multiple queries (domtab_30_hmmsearch_001) ... ok
test_domtab_31b1_hmmsearch_001 (test_SearchIO_hmmer3_domtab.HmmersearchCases)
Test parsing hmmsearch-domtab, hmmsearch 3.1b1, single query (domtab_31b1_hmmsearch_001) ... ok
test_domtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Test parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_001) ... ok
test_domtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Test parsing hmmscan-domtab, hmmscan 3.0, single query, no hits (domtab_30_hmmscan_002) ... ok
test_domtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Test parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_003) ... ok
test_domtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Test parsing hmmscan-domtab, hmmscan 3.0, multiple queries (domtab_30_hmmscan_004) ... ok
test_domtab_31b1_hmmscan_001 (test_SearchIO_hmmer3_domtab.HmmscanCases)
Test parsing hmmscan-domtab, hmmscan 3.1b1, multiple queries (domtab_31b1_hmmscan_001) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.109 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_hmmer3_domtab_index.py
test_SearchIO_hmmer3_domtab_index ... ok
test_hmmerdomtab_30_hmmscan_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
Test hmmscan-domtab indexing, HMMER 3.0, multiple queries ... ok
test_hmmerdomtab_30_hmmscan_002 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
Test hmmscan-domtab indexing, HMMER 3.0, single query, no hits ... ok
test_hmmerdomtab_30_hmmscan_003 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
Test hmmscan-domtab indexing, HMMER 3.0, single query, multiple hits ... ok
test_hmmerdomtab_30_hmmscan_004 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
Test hmmscan-domtab indexing, HMMER 3.0, single query, no alignments ... ok
test_hmmerdomtab_30_hmmsearch_001 (test_SearchIO_hmmer3_domtab_index.HmmerDomtabIndexCases)
Test hmmsearch-domtab indexing, HMMER 3.0, single query, no alignments ... ok
test_hmmerdomtab_30_multiple_first (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, first (domtab_30_hmmscan_001.out) ... ok
test_hmmerdomtab_30_multiple_last (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, last (domtab_30_hmmscan_001.out) ... ok
test_hmmerdomtab_30_multiple_middle (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, multiple queries, middle (domtab_30_hmmscan_001.out) ... ok
test_hmmerdomtab_30_single (test_SearchIO_hmmer3_domtab_index.HmmerDomtabRawCases)
Test hmmscan-domtab raw string retrieval, HMMER 3.0, single query (domtab_30_hmmscan_004.out) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.132 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_hmmer3_tab.py
test_SearchIO_hmmer3_tab ... ok
test_30_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases)
Test parsing hmmer3-tab, hmmscan 3.0, multiple queries (tab_30_hmmscan_001) ... ok
test_30_hmmscan_002 (test_SearchIO_hmmer3_tab.HmmscanCases)
Test parsing hmmer3-tab, hmmscan 3.0, single query, no hits (tab_30_hmmscan_002) ... ok
test_30_hmmscan_003 (test_SearchIO_hmmer3_tab.HmmscanCases)
Test parsing hmmer3-tab, hmmscan 3.0, single query, single hit, single hsp (tab_30_hmmscan_003) ... ok
test_30_hmmscan_004 (test_SearchIO_hmmer3_tab.HmmscanCases)
Test parsing hmmer3-tab, hmmscan 3.0, single query, multiple hits (tab_30_hmmscan_004) ... ok
test_31b1_hmmscan_001 (test_SearchIO_hmmer3_tab.HmmscanCases)
Test parsing hmmer3-tab, hmmscan 3.1b1, multiple queries (tab_31b1_hmmscan_001) ... ok
test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_tab.HmmsearchCases)
Test parsing hmmer3-tab, hmmsearch 3.1b1, multiple queries (tab_31b1_hmmscan_001) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.100 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_hmmer3_tab_index.py
test_SearchIO_hmmer3_tab_index ... ok
test_hmmer3tab_30_hmmscan_001 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases)
Test hmmer3-tab indexing, HMMER 3.0, multiple queries ... ok
test_hmmer3tab_30_hmmscan_002 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases)
Test hmmer3-tab indexing, HMMER 3.0, single query, no hits ... ok
test_hmmer3tab_30_hmmscan_003 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases)
Test hmmer3-tab indexing, HMMER 3.0, single query, multiple hits ... ok
test_hmmer3tab_30_hmmscan_004 (test_SearchIO_hmmer3_tab_index.Hmmer3TabIndexCases)
Test hmmer3-tab indexing, HMMER 3.0, single query, no alignments ... ok
test_hmmer3tab_30_multiple_first (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases)
Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, first (tab_30_hmmscan_001.out) ... ok
test_hmmer3tab_30_multiple_last (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases)
Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, last (tab_30_hmmscan_001.out) ... ok
test_hmmer3tab_30_multiple_middle (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases)
Test hmmer3-tab raw string retrieval, HMMER 3.0, multiple queries, middle (tab_30_hmmscan_001.out) ... ok
test_hmmer3tab_30_single (test_SearchIO_hmmer3_tab_index.Hmmer3TabRawCases)
Test hmmer3-tab raw string retrieval, HMMER 3.0, single query (tab_30_hmmscan_004.out) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.113 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_hmmer3_text.py
test_SearchIO_hmmer3_text ... ok
test_30_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmersearch 3.0 (text_30_hmmsearch_001) ... ok
test_30_hmmsearch_002 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmersearch 3.0 (text_30_hmmsearch_002) ... ok
test_30_hmmsearch_003 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmersearch 3.0 (text_30_hmmsearch_003) ... ok
test_30_hmmsearch_004 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmersearch 3.0 (text_30_hmmsearch_004) ... ok
test_30_hmmsearch_005 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmersearch 3.0 (text_30_hmmsearch_005) ... ok
test_31b1_hmmsearch_001 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmsearch 3.1b1 (text_31b1_hmmsearch_001) ... ok
test_31b2_hmmscan_001 (test_SearchIO_hmmer3_text.HmmersearchCases)
Test parsing hmmscan 3.1b2 (text_31b2_hmmscan_001) ... ok
test_30_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_001) ... ok
test_30_hmmscan_002 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_002) ... ok
test_30_hmmscan_003 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_003) ... ok
test_30_hmmscan_004 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_004) ... ok
test_30_hmmscan_005 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_005) ... ok
test_30_hmmscan_006 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_006) ... ok
test_30_hmmscan_007 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_007) ... ok
test_30_hmmscan_008 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_008) ... ok
test_30_hmmscan_009 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_009) ... ok
test_30_hmmscan_010 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.0 (text_30_hmmscan_010) ... ok
test_31b1_hmmscan_001 (test_SearchIO_hmmer3_text.HmmscanCases)
Test parsing hmmscan 3.1b1 (text_31b1_hmmscan_001) ... ok
test_31b2_phmmer_001 (test_SearchIO_hmmer3_text.PhmmerCases)
Test parsing phmmer 3.1b2 (text_31b2_phmmer_001) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.312 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_hmmer3_text_index.py
test_SearchIO_hmmer3_text_index ... ok
test_hmmertext_text_30_hmmscan_001 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
Test hmmer3-text indexing, HMMER 3.0, multiple queries ... ok
test_hmmertext_text_30_hmmscan_002 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
Test hmmer3-text indexing, HMMER 3.0, single query, no hits ... ok
test_hmmertext_text_30_hmmscan_006 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
Test hmmer3-text indexing, HMMER 3.0, single query, multiple hits ... ok
test_hmmertext_text_30_hmmscan_007 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
Test hmmer3-text indexing, HMMER 3.0, single query, no alignments ... ok
test_hmmertext_text_30_hmmscan_008 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
Test hmmer3-text indexing, HMMER 3.0, single query, no alignment width ... ok
test_hmmertext_text_30_hmmsearch_005 (test_SearchIO_hmmer3_text_index.Hmmer3TextIndexCases)
Test hmmer3-text indexing, HMMER 3.0, multiple queries ... ok
test_hmmer3text_30_multiple_first (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases)
Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, first (text_30_hmmscan_001.out) ... ok
test_hmmer3text_30_multiple_last (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases)
Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, last (text_30_hmmscan_001.out) ... ok
test_hmmer3text_30_multiple_middle (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases)
Test hmmer3-text raw string retrieval, HMMER 3.0, multiple queries, middle (text_30_hmmscan_001.out) ... ok
test_hmmer3text_30_single (test_SearchIO_hmmer3_text_index.Hmmer3TextRawCases)
Test hmmer3-text raw string retrieval, HMMER 3.0, single query (text_30_hmmscan_003.out) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.187 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_model.py
test_SearchIO_model ... ok
test_alphabet_no_seq (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment alphabet property, query and hit sequences not present ... ok
test_alphabet_with_seq (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment alphabet property, query or hit sequences present ... ok
test_coords_setters_getters (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit coordinate-related setters and getters ... ok
test_coords_setters_readonly (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit coordinate-related read-only getters ... ok
test_default_attrs (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment attributes' default values ... ok
test_frame_set_error (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit frame setters, invalid values ... ok
test_frame_set_ok (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit frame setters ... ok
test_getitem (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__getitem__ ... ok
test_getitem_alignment_annot (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__getitem__, with alignment annotation ... ok
test_getitem_attrs (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__getitem__, with attributes ... ok
test_id_desc_set (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit id and description setters ... ok
test_init_with_seqrecord (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__init__, with SeqRecord ... ok
test_init_wrong_seqtypes (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__init__, wrong sequence argument types ... ok
test_len (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__len__ ... ok
test_repr (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment.__repr__ ... ok
test_seq_unequal_hit_query_len (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment sequence setter with unequal hit and query lengths ... ok
test_seqmodel (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment sequence attribute types and default values ... ok
test_strand_set_error (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit strand setters, invalid values ... ok
test_strand_set_from_minus_frame (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit strand getters, from minus frame ... ok
test_strand_set_from_plus_frame (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit strand getters, from plus frame ... ok
test_strand_set_from_zero_frame (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit strand getters, from zero frame ... ok
test_strand_set_ok (test_SearchIO_model.HSPFragmentCases)
Test HSPFragment query and hit strand setters ... ok
test_getitem (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment.__getitem__, no alignments ... ok
test_getitem_only_hit (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment.__getitem__, only hit ... ok
test_getitem_only_query (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment.__getitem__, only query ... ok
test_init (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment.__init__ attributes ... ok
test_iter (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSP.__iter__, no alignments ... ok
test_len (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment.__len__, no alignments ... ok
test_repr (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment.__repr__, no alignments ... ok
test_seqmodel (test_SearchIO_model.HSPFragmentWithoutSeqCases)
Test HSPFragment sequence attributes, no alignments ... ok
test_alphabet (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.alphabet getter ... ok
test_alphabet_set (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.alphabet setter ... ok
test_contains (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.__contains__ ... ok
test_delitem (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.__delitem__ ... ok
test_fragments (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.fragments property ... ok
test_getitem (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.__getitem__ ... ok
test_id_desc_set (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP query and hit id and description setters ... ok
test_is_fragmented (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.is_fragmented property ... ok
test_len (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.__len__ ... ok
test_range (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP range properties ... ok
test_ranges (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP ranges properties ... ok
test_seqs (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP sequence properties ... ok
test_setitem_multiple (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.__setitem__, multiple items ... ok
test_setitem_single (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP.__setitem___, single item ... ok
test_setters_readonly (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP read-only properties ... ok
test_span (test_SearchIO_model.HSPMultipleFragmentCases)
Test HSP span properties ... ok
test_alignment (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP.alignment property ... ok
test_aln_span (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP.aln_span property ... ok
test_fragment (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP.fragment property ... ok
test_init_no_fragment (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP.__init__ without fragments ... ok
test_is_fragmented (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP.is_fragmented property ... ok
test_len (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP.__len__ ... ok
test_range (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP range properties ... ok
test_seq (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP sequence properties ... ok
test_setters_readonly (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP read-only properties ... ok
test_span (test_SearchIO_model.HSPSingleFragmentCases)
Test HSP span properties ... ok
test_append (test_SearchIO_model.HitCases)
Test Hit.append ... ok
test_delitem (test_SearchIO_model.HitCases)
Test Hit.__delitem__ ... ok
test_desc_set (test_SearchIO_model.HitCases)
Test Hit.description setter ... ok
test_desc_set_no_seqrecord (test_SearchIO_model.HitCases)
Test Hit.description setter, without HSP SeqRecords ... ok
test_filter (test_SearchIO_model.HitCases)
Test Hit.filter ... ok
test_filter_no_filtered (test_SearchIO_model.HitCases)
Test Hit.hit_filter, all hits filtered out ... ok
test_filter_no_func (test_SearchIO_model.HitCases)
Test Hit.filter, without arguments ... ok
test_fragments (test_SearchIO_model.HitCases)
Test Hit.fragments ... ok
test_getitem_multiple (test_SearchIO_model.HitCases)
Test Hit.__getitem__, multiple items ... ok
test_getitem_single (test_SearchIO_model.HitCases)
Test Hit.__getitem__, single item ... ok
test_hsp_map_no_func (test_SearchIO_model.HitCases)
Test Hit.map, without arguments ... ok
test_hsps (test_SearchIO_model.HitCases)
Test Hit.hsps ... ok
test_id_set (test_SearchIO_model.HitCases)
Test Hit.id setter ... ok
test_index (test_SearchIO_model.HitCases)
Test Hit.index ... ok
test_index_not_present (test_SearchIO_model.HitCases)
Test Hit.index, when index is not present ... ok
test_init_hsps_only (test_SearchIO_model.HitCases)
Test Hit.__init__, with hsps only ... ok
test_init_id_only (test_SearchIO_model.HitCases)
Test Hit.__init__, with ID only ... ok
test_init_none (test_SearchIO_model.HitCases)
Test Hit.__init__, no arguments ... ok
test_item_multiple (test_SearchIO_model.HitCases)
Test Hit.__setitem__, multiple items ... ok
test_iter (test_SearchIO_model.HitCases)
Test Hit.__iter__ ... ok
test_len (test_SearchIO_model.HitCases)
Test Hit.__len__ ... ok
test_map (test_SearchIO_model.HitCases)
Test Hit.hsp_map ... ok
test_nonzero (test_SearchIO_model.HitCases)
Test Hit.__nonzero__ ... ok
test_pop (test_SearchIO_model.HitCases)
Test Hit.pop ... ok
test_repr (test_SearchIO_model.HitCases)
Test Hit.__repr__ ... ok
test_setitem_single (test_SearchIO_model.HitCases)
Test Hit.__setitem__, single item ... ok
test_sort (test_SearchIO_model.HitCases)
Test Hit.sort ... ok
test_sort_not_in_place (test_SearchIO_model.HitCases)
Test Hit.sort, not in place ... ok
test_validate_hsp_ok (test_SearchIO_model.HitCases)
Test Hit._validate_hsp ... ok
test_validate_hsp_wrong_hit_id (test_SearchIO_model.HitCases)
Test Hit._validate_hsp, wrong hit ID ... ok
test_validate_hsp_wrong_query_id (test_SearchIO_model.HitCases)
Test Hit._validate_hsp, wrong query ID ... ok
test_validate_hsp_wrong_type (test_SearchIO_model.HitCases)
Test Hit._validate_hsp, wrong type ... ok
test_absorb_hit_does_not_exist (test_SearchIO_model.QueryResultCases)
Test QueryResult.absorb, hit does not exist ... ok
test_absorb_hit_exists (test_SearchIO_model.QueryResultCases)
Test QueryResult.absorb, hit with the same ID exists ... ok
test_append_alt_id_exists (test_SearchIO_model.QueryResultCases)
Test QueryResult.append, when alt ID exists ... ok
test_append_alt_id_exists_alt (test_SearchIO_model.QueryResultCases)
Test QueryResult.append, when alt ID exists as primary ... ok
test_append_custom_hit_key_function_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.append, with custom hit key function ... ok
test_append_id_exists (test_SearchIO_model.QueryResultCases)
Test QueryResult.append, when ID exists ... ok
test_append_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.append ... ok
test_contains (test_SearchIO_model.QueryResultCases)
Test QueryResult.__contains__ ... ok
test_contains_alt (test_SearchIO_model.QueryResultCases)
Test QueryResult.__contains__, with alternative IDs ... ok
test_delitem_alt_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__delitem__, with alt ID ... ok
test_delitem_int_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__delitem__ ... ok
test_delitem_slice_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__delitem__, with slice ... ok
test_delitem_string_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__getitem__, with string ... ok
test_description_set (test_SearchIO_model.QueryResultCases)
Test QueryResult.description setter ... ok
test_description_set_no_seqrecord (test_SearchIO_model.QueryResultCases)
Test QueryResult.description setter, without HSP SeqRecords ... ok
test_fragments (test_SearchIO_model.QueryResultCases)
Test QueryResult.fragments ... ok
test_getitem_alt_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__getitem__, single item with alternative ID ... ok
test_getitem_default_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__getitem__ ... ok
test_getitem_int_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__getitem__, with integer ... ok
test_getitem_slice_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__getitem__, with slice ... ok
test_getitm_slice_alt_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__getitem__, with slice and alt IDs ... ok
test_hit_filter (test_SearchIO_model.QueryResultCases)
Test QueryResult.hit_filter ... ok
test_hit_filter_no_filtered (test_SearchIO_model.QueryResultCases)
Test QueryResult.hit_filter, all hits filtered out ... ok
test_hit_filter_no_func (test_SearchIO_model.QueryResultCases)
Test QueryResult.hit_filter, without arguments ... ok
test_hit_keys (test_SearchIO_model.QueryResultCases)
Test QueryResult.hit_keys ... ok
test_hit_map (test_SearchIO_model.QueryResultCases)
Test QueryResult.hit_map ... ok
test_hit_map_no_func (test_SearchIO_model.QueryResultCases)
Test QueryResult.hit_map, without arguments ... ok
test_hits (test_SearchIO_model.QueryResultCases)
Test QueryResult.hits ... ok
test_hsp_filter (test_SearchIO_model.QueryResultCases)
Test QueryResult.hsp_filter ... ok
test_hsp_filter_no_filtered (test_SearchIO_model.QueryResultCases)
Test QueryResult.hsp_filter, all hits filtered out ... ok
test_hsp_filter_no_func (test_SearchIO_model.QueryResultCases)
Test QueryResult.hsp_filter, no arguments ... ok
test_hsp_map (test_SearchIO_model.QueryResultCases)
Test QueryResult.hsp_map ... ok
test_hsp_map_no_func (test_SearchIO_model.QueryResultCases)
Test QueryResult.hsp_map, without arguments ... ok
test_hsps (test_SearchIO_model.QueryResultCases)
Test QueryResult.hsps ... ok
test_id_set (test_SearchIO_model.QueryResultCases)
Test QueryResult.id setter ... ok
test_index (test_SearchIO_model.QueryResultCases)
Test QueryResult.index ... ok
test_index_alt (test_SearchIO_model.QueryResultCases)
Test QueryResult.index, with alt ID ... ok
test_index_not_present (test_SearchIO_model.QueryResultCases)
Test QueryResult.index, when index is not present ... ok
test_init_hits_only (test_SearchIO_model.QueryResultCases)
Test QueryResult.__init__, with hits only ... ok
test_init_id_only (test_SearchIO_model.QueryResultCases)
Test QueryResult.__init__, with ID only ... ok
test_init_none (test_SearchIO_model.QueryResultCases)
Test QueryResult.__init__, no arguments ... ok
test_items (test_SearchIO_model.QueryResultCases)
Test QueryResult.items ... ok
test_iter (test_SearchIO_model.QueryResultCases)
Test QueryResult.__iter__ ... ok
test_len (test_SearchIO_model.QueryResultCases)
Test QueryResult.__len__ ... ok
test_nonzero (test_SearchIO_model.QueryResultCases)
Test QueryResult.__nonzero__ ... ok
test_order (test_SearchIO_model.QueryResultCases) ... ok
test_pop_int_index_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.pop, with integer index ... ok
test_pop_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.pop ... ok
test_pop_string_alt_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.pop, with alternative ID ... ok
test_pop_string_index_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.pop, with string index ... ok
test_repr (test_SearchIO_model.QueryResultCases)
Test QueryResult.__repr__ ... ok
test_setitem_from_empty (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, from empty container ... ok
test_setitem_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__ ... ok
test_setitem_ok_alt (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, checking alt hit IDs ... ok
test_setitem_ok_alt_existing (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, existing key ... ok
test_setitem_ok_alt_ok_promote (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, previously alt ID ... ok
test_setitem_wrong_key_type (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, wrong key type ... ok
test_setitem_wrong_query_id (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, wrong query ID ... ok
test_setitem_wrong_type (test_SearchIO_model.QueryResultCases)
Test QueryResult.__setitem__, wrong type ... ok
test_sort_key_not_in_place_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.sort, with custom key, not in place ... ok
test_sort_key_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.sort, with custom key ... ok
test_sort_not_in_place_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.sort, not in place ... ok
test_sort_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.sort ... ok
test_sort_reverse_not_in_place_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.sort, reverse, not in place ... ok
test_sort_reverse_ok (test_SearchIO_model.QueryResultCases)
Test QueryResult.sort, reverse ... ok
----------------------------------------------------------------------
Ran 1 test in 0.178 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SearchIO_write.py
test_SearchIO_write ... ok
test_write_multiple_from_blasttab (test_SearchIO_write.BlastTabWriteCases)
Test blast-tab writing from blast-tab, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_001.txt) ... ok
test_write_multiple_from_blasttabc (test_SearchIO_write.BlastTabWriteCases)
Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, multiple queries (tab_2226_tblastn_005.txt) ... ok
test_write_multiple_from_blasttabc_allfields (test_SearchIO_write.BlastTabWriteCases)
Test blast-tabc writing from blast-tabc, BLAST 2.2.28+, multiple queries (tab_2228_tblastx_001.txt) ... ok
test_write_single_from_blasttab (test_SearchIO_write.BlastTabWriteCases)
Test blast-tab writing from blast-tab, BLAST 2.2.26+, single query (tab_2226_tblastn_004.txt) ... ok
test_write_single_from_blasttabc (test_SearchIO_write.BlastTabWriteCases)
Test blast-tabc writing from blast-tabc, BLAST 2.2.26+, single query (tab_2226_tblastn_008.txt) ... ok
test_write_multiple_from_blastxml (test_SearchIO_write.BlastXmlWriteCases)
Test blast-xml writing from blast-xml, BLAST 2.2.26+, multiple queries (xml_2226_blastp_001.xml) ... ok
test_write_single_from_blastxml (test_SearchIO_write.BlastXmlWriteCases)
Test blast-xml writing from blast-xml, BLAST 2.2.26+, single query (xml_2226_blastp_004.xml) ... ok
test_write_multiple_from_blatpsl (test_SearchIO_write.BlatPslWriteCases)
Test blat-psl writing from blat-psl, multiple queries (psl_34_001.psl) ... ok
test_write_multiple_from_blatpslx (test_SearchIO_write.BlatPslWriteCases)
Test blat-pslx writing from blat-pslx, multiple queries (pslx_34_001.pslx) ... ok
test_write_single_from_blatpsl (test_SearchIO_write.BlatPslWriteCases)
Test blat-psl writing from blat-psl, single query (psl_34_004.psl) ... ok
test_write_single_from_blatpslx (test_SearchIO_write.BlatPslWriteCases)
Test blat-pslx writing from blat-pslx, single query (pslx_34_004.pslx) ... ok
test_write_multiple_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases)
Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out) ... ok
test_write_single_from_hmmscandomtab (test_SearchIO_write.HmmerDomtabWriteCases)
Test hmmscan-domtab writing from hmmscan-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out) ... ok
test_write_single_from_hmmsearchdomtab (test_SearchIO_write.HmmerDomtabWriteCases)
Test hmmsearch-domtab writing from hmmsearch-domtab, HMMER 3.0, single query (tab_30_hmmscan_004.out) ... ok
test_write_multiple_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases)
Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, multiple queries (tab_30_hmmscan_001.out) ... ok
test_write_single_from_hmmertab (test_SearchIO_write.HmmerTabWriteCases)
Test hmmer3-tab writing from hmmer3-tab, HMMER 3.0, single query (tab_30_hmmscan_004.out) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.664 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqIO.py
test_SeqIO ... ok
runTest (__main__.ComparisonTestCase)
test_SeqIO ... ok
----------------------------------------------------------------------
Ran 1 test in 8.309 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqIO_AbiIO.py
test_SeqIO_AbiIO ... ok
test_file_type (test_SeqIO_AbiIO.TestAbi)
Test if filetype is ABIF. ... ok
test_raw (test_SeqIO_AbiIO.TestAbi)
Test access to raw ABIF tags. ... ok
test_seqrecord (test_SeqIO_AbiIO.TestAbi)
Test if the extracted seqrecords data are equal to expected values. ... ok
test_trim (test_SeqIO_AbiIO.TestAbi)
Test if trim works. ... ok
test_file_type (test_SeqIO_AbiIO.TestAbiFake)
Test if error is raised if filetype is not ABIF. ... ok
test_file_mode (test_SeqIO_AbiIO.TestAbiWrongMode)
Test if exception is raised if file is not opened in 'rb' mode. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.403 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqIO_FastaIO.py
test_SeqIO_FastaIO ... ok
test_mutli_dna_Quality/example (test_SeqIO_FastaIO.TitleFunctions)
Checking multi DNA file Quality/example.fasta ... ok
test_mutli_pro_Fasta/f002 (test_SeqIO_FastaIO.TitleFunctions)
Checking multi protein file Fasta/f002 ... ok
test_mutli_pro_Fasta/fa01 (test_SeqIO_FastaIO.TitleFunctions)
Checking multi protein file Fasta/fa01 ... ok
test_no_name (test_SeqIO_FastaIO.TitleFunctions)
Test FASTA record with no identifier. ... ok
test_nuc_Fasta/centaurea (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/centaurea.nu ... ok
test_nuc_Fasta/elderberry (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/elderberry.nu ... ok
test_nuc_Fasta/f001 (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/f001 ... ok
test_nuc_Fasta/lavender (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/lavender.nu ... ok
test_nuc_Fasta/lupine (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/lupine.nu ... ok
test_nuc_Fasta/phlox (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/phlox.nu ... ok
test_nuc_Fasta/sweetpea (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/sweetpea.nu ... ok
test_nuc_Fasta/wisteria (test_SeqIO_FastaIO.TitleFunctions)
Checking nucleotide file Fasta/wisteria.nu ... ok
test_pro_Fasta/aster (test_SeqIO_FastaIO.TitleFunctions)
Checking protein file Fasta/aster.pro ... ok
test_pro_Fasta/loveliesbleeding (test_SeqIO_FastaIO.TitleFunctions)
Checking protein file Fasta/loveliesbleeding.pro ... ok
test_pro_Fasta/rose (test_SeqIO_FastaIO.TitleFunctions)
Checking protein file Fasta/rose.pro ... ok
test_pro_Fasta/rosemary (test_SeqIO_FastaIO.TitleFunctions)
Checking protein file Fasta/rosemary.pro ... ok
----------------------------------------------------------------------
Ran 1 test in 0.119 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqIO_Insdc.py
test_SeqIO_Insdc ... ok
test_annotation1 (test_SeqIO_Insdc.TestEmbl)
Check parsing of annotation from EMBL files (1). ... ok
test_annotation2 (test_SeqIO_Insdc.TestEmbl)
Check parsing of annotation from EMBL files (2). ... ok
test_writing_empty_qualifiers (test_SeqIO_Insdc.TestEmbl) ... ok
test_annotation1 (test_SeqIO_Insdc.TestEmblRewrite)
Check writing-and-parsing EMBL file (1). ... ok
test_annotation2 (test_SeqIO_Insdc.TestEmblRewrite)
Check writing-and-parsing EMBL file (2). ... ok
test_annotation3 (test_SeqIO_Insdc.TestEmblRewrite)
Check writing-and-parsing EMBL file (3). ... ok
----------------------------------------------------------------------
Ran 1 test in 0.142 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqIO_PdbIO.py
test_SeqIO_PdbIO ... ok
test_atom_noheader (test_SeqIO_PdbIO.TestPdbAtom)
Parse a PDB with no HEADER line. ... ok
test_atom_parse (test_SeqIO_PdbIO.TestPdbAtom)
Parse a multi-chain PDB by ATOM entries. ... ok
test_atom_read (test_SeqIO_PdbIO.TestPdbAtom)
Read a single-chain PDB by ATOM entries. ... ok
test_seqres_missing (test_SeqIO_PdbIO.TestPdbSeqres)
Parse a PDB with no SEQRES entries. ... ok
test_seqres_parse (test_SeqIO_PdbIO.TestPdbSeqres)
Parse a multi-chain PDB by SEQRES entries. ... ok
test_seqres_read (test_SeqIO_PdbIO.TestPdbSeqres)
Read a single-chain PDB by SEQRES entries. ... ok
----------------------------------------------------------------------
Ran 1 test in 2.446 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqIO_QualityIO.py
test_SeqIO_QualityIO ... ok
test_illumina_to_sanger (test_SeqIO_QualityIO.MappingTests)
Mapping check for FASTQ Illumina (0 to 62) to Sanger (0 to 62) ... ok
test_phred_quality_from_solexa (test_SeqIO_QualityIO.MappingTests)
Mapping check for function phred_quality_from_solexa ... ok
test_sanger_to_illumina (test_SeqIO_QualityIO.MappingTests)
Mapping check for FASTQ Sanger (0 to 93) to Illumina (0 to 62) ... ok
test_sanger_to_solexa (test_SeqIO_QualityIO.MappingTests)
Mapping check for FASTQ Sanger (0 to 93) to Solexa (-5 to 62) ... ok
test_solexa_quality_from_phred (test_SeqIO_QualityIO.MappingTests)
Mapping check for function solexa_quality_from_phred ... ok
test_solexa_to_sanger (test_SeqIO_QualityIO.MappingTests)
Mapping check for FASTQ Solexa (-5 to 62) to Sanger (0 to 62) ... ok
test_diff_ids (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with diff ids ... ok
test_double_qual (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with double qual ... ok
test_double_seq (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with double seq ... ok
test_long_qual (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with long qual ... ok
test_no_qual (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with no qual ... ok
test_qual_del (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with del in quality ... ok
test_qual_escape (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with escape in quality ... ok
test_qual_null (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with null in quality ... ok
test_qual_space (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with space in quality ... ok
test_qual_tab (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with tab in quality ... ok
test_qual_unit_sep (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with unit sep in quality ... ok
test_qual_vtab (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with vtab in quality ... ok
test_short_qual (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with short qual ... ok
test_spaces (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with spaces ... ok
test_tabs (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with tabs ... ok
test_trunc_at_plus (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc at plus ... ok
test_trunc_at_qual (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc at qual ... ok
test_trunc_at_seq (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc at seq ... ok
test_trunc_in_plus (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc in plus ... ok
test_trunc_in_qual (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc in qual ... ok
test_trunc_in_seq (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc in seq ... ok
test_trunc_in_title (test_SeqIO_QualityIO.TestFastqErrors)
Reject FASTQ with trunc in title ... ok
test_fasta (test_SeqIO_QualityIO.TestQual)
Check FASTQ parsing matches FASTA parsing ... ok
test_fasta_out (test_SeqIO_QualityIO.TestQual)
Check FASTQ to FASTA output ... ok
test_paired (test_SeqIO_QualityIO.TestQual)
Check FASTQ parsing matches FASTA+QUAL parsing ... ok
test_qual (test_SeqIO_QualityIO.TestQual)
Check FASTQ parsing matches QUAL parsing ... ok
test_qual_negative (test_SeqIO_QualityIO.TestQual)
Check QUAL negative scores mapped to PHRED zero ... ok
test_qual_out (test_SeqIO_QualityIO.TestQual)
Check FASTQ to QUAL output ... ok
test_fastq_1000 (test_SeqIO_QualityIO.TestReadWrite)
Read and write back simple example with mixed case 1000bp read ... ok
test_fastq_2000 (test_SeqIO_QualityIO.TestReadWrite)
Read and write back simple example with upper case 2000bp read ... ok
test_fastq_dna (test_SeqIO_QualityIO.TestReadWrite)
Read and write back simple example with ambiguous DNA ... ok
test_fastq_rna (test_SeqIO_QualityIO.TestReadWrite)
Read and write back simple example with ambiguous RNA ... ok
test_illumina_full_range_illumina (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of illumina file illumina_full_range ... ok
test_longreads_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of sanger file longreads ... ok
test_misc_dna_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of sanger file misc_dna ... ok
test_misc_rna_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of sanger file misc_rna ... ok
test_sanger_full_range_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of sanger file sanger_full_range ... ok
test_solexa_full_range_solexa (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of solexa file solexa_full_range ... ok
test_wrapping_sanger (test_SeqIO_QualityIO.TestReferenceFastqConversions)
Reference conversions of sanger file wrapping ... ok
test_alt_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_alt_index_at_end into FASTA+QUAL ... ok
test_alt_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_alt_index_at_start into FASTA+QUAL ... ok
test_alt_index_in_middle (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_alt_index_in_middle into FASTA+QUAL ... ok
test_index_at_end (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_index_in_middle into FASTA+QUAL ... ok
test_index_at_start (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_index_at_start into FASTA+QUAL ... ok
test_no_manifest (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_no_manifest.sff into FASTA+QUAL ... ok
test_original (test_SeqIO_QualityIO.TestReferenceSffConversions)
Test converting E3MFGYR02_random_10_reads.sff into FASTA+QUAL ... ok
test_negative_clip (test_SeqIO_QualityIO.TestSFF) ... ok
test_overlapping_clip (test_SeqIO_QualityIO.TestSFF) ... ok
test_E3MFGYR02 (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_random_10_reads.sff ... ok
test_E3MFGYR02_alt_index_at_end (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_alt_index_at_end.sff ... ok
test_E3MFGYR02_alt_index_at_start (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_alt_index_at_start.sff ... ok
test_E3MFGYR02_alt_index_in_middle (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_alt_index_in_middle.sff ... ok
test_E3MFGYR02_index_at_start (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_index_at_start.sff ... ok
test_E3MFGYR02_index_in_middle (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_index_in_middle.sff ... ok
test_E3MFGYR02_no_manifest (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_no_manifest.sff ... ok
test_E3MFGYR02_trimmed (test_SeqIO_QualityIO.TestWriteRead)
Write and read back E3MFGYR02_random_10_reads.sff (trimmed) ... ok
test_example_fasta (test_SeqIO_QualityIO.TestWriteRead)
Write and read back example.fasta ... ok
test_example_fastq (test_SeqIO_QualityIO.TestWriteRead)
Write and read back example.fastq ... ok
test_example_qual (test_SeqIO_QualityIO.TestWriteRead)
Write and read back example.qual ... ok
test_generated (test_SeqIO_QualityIO.TestWriteRead)
Write and read back odd SeqRecord objects ... ok
test_greek_sff (test_SeqIO_QualityIO.TestWriteRead)
Write and read back greek.sff ... ok
test_illumina_faked (test_SeqIO_QualityIO.TestWriteRead)
Write and read back illumina_faked.fastq ... ok
test_paired_sff (test_SeqIO_QualityIO.TestWriteRead)
Write and read back paired.sff ... ok
test_sanger_93 (test_SeqIO_QualityIO.TestWriteRead)
Write and read back sanger_93.fastq ... ok
test_sanger_faked (test_SeqIO_QualityIO.TestWriteRead)
Write and read back sanger_faked.fastq ... ok
test_solexa_example (test_SeqIO_QualityIO.TestWriteRead)
Write and read back solexa_example.fastq ... ok
test_solexa_faked (test_SeqIO_QualityIO.TestWriteRead)
Write and read back solexa_faked.fastq ... ok
test_tricky (test_SeqIO_QualityIO.TestWriteRead)
Write and read back tricky.fastq ... ok
----------------------------------------------------------------------
Ran 1 test in 1.111 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqIO_SeqXML.py
test_SeqIO_SeqXML ... ok
test_duplicated_dbxref (test_SeqIO_SeqXML.TestDetailedRead)
Read multiple cross references to a single source ... ok
test_duplicated_property (test_SeqIO_SeqXML.TestDetailedRead)
Read property with multiple values ... ok
test_empty_description (test_SeqIO_SeqXML.TestDetailedRead)
Check empty description. ... ok
test_full_characters_set_read (test_SeqIO_SeqXML.TestDetailedRead)
Read full characters set for each type ... ok
test_global_species (test_SeqIO_SeqXML.TestDetailedRead)
Check global species. ... ok
test_local_source_definition (test_SeqIO_SeqXML.TestDetailedRead)
Check local source. ... ok
test_local_species (test_SeqIO_SeqXML.TestDetailedRead)
Check local species. ... ok
test_read_minimal_required (test_SeqIO_SeqXML.TestDetailedRead)
Check minimal record. ... ok
test_special_characters_desc (test_SeqIO_SeqXML.TestDetailedRead)
Read special XML characters in description. ... ok
test_unicode_characters_desc (test_SeqIO_SeqXML.TestDetailedRead)
Test special unicode characters in the description. ... ok
test_read_write_dna (test_SeqIO_SeqXML.TestReadAndWrite)
Read and write DNA. ... ok
test_read_write_globalSpecies (test_SeqIO_SeqXML.TestReadAndWrite)
Read and write global species. ... ok
test_read_write_protein (test_SeqIO_SeqXML.TestReadAndWrite)
Read and write protein. ... ok
test_read_write_rna (test_SeqIO_SeqXML.TestReadAndWrite)
Read and write RNA. ... ok
test_write_species (test_SeqIO_SeqXML.TestReadAndWrite)
Test writing species from annotation tags. ... ok
test_for_errors (test_SeqIO_SeqXML.TestReadCorruptFiles)
Handling of corrupt files. ... ok
test_check_SeqIO (test_SeqIO_SeqXML.TestSimpleRead)
Files readable using parser via SeqIO. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.236 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqIO_convert.py
test_SeqIO_convert ... /builddir/build/BUILD/python-biopython-1.66/python2/build/lib.linux-i686-2.7/Bio/SeqIO/QualityIO.py:699: BiopythonWarning: Data loss - max PHRED quality 62 in Illumina FASTQ
  BiopythonWarning)
/builddir/build/BUILD/python-biopython-1.66/python2/build/lib.linux-i686-2.7/Bio/SeqIO/QualityIO.py:793: BiopythonWarning: Data loss - max Solexa quality 62 in Solexa FASTQ
  BiopythonWarning)
ok
test_EMBL_TRBG361_embl_embl_to_fasta (test_SeqIO_convert.ConvertTests)
Convert EMBL/TRBG361.embl from embl to fasta ... ok
test_EMBL_U87107_embl_embl_to_fasta (test_SeqIO_convert.ConvertTests)
Convert EMBL/U87107.embl from embl to fasta ... ok
test_GenBank_NC_005816_gb_gb_to_fasta (test_SeqIO_convert.ConvertTests)
Convert GenBank/NC_005816.gb from gb to fasta ... ok
test_GenBank_cor6_6_gb_genbank_to_fasta (test_SeqIO_convert.ConvertTests)
Convert GenBank/cor6_6.gb from genbank to fasta ... ok
test_Quality_error_diff_ids_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to fasta ... ok
test_Quality_error_diff_ids_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to fastq ... ok
test_Quality_error_diff_ids_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to fastq-illumina ... ok
test_Quality_error_diff_ids_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to fastq-sanger ... ok
test_Quality_error_diff_ids_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to fastq-solexa ... ok
test_Quality_error_diff_ids_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to qual ... ok
test_Quality_error_diff_ids_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_diff_ids.fastq from fastq to tab ... ok
test_Quality_error_double_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to fasta ... ok
test_Quality_error_double_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to fastq ... ok
test_Quality_error_double_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to fastq-illumina ... ok
test_Quality_error_double_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to fastq-sanger ... ok
test_Quality_error_double_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to fastq-solexa ... ok
test_Quality_error_double_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to qual ... ok
test_Quality_error_double_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_qual.fastq from fastq to tab ... ok
test_Quality_error_double_seq_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to fasta ... ok
test_Quality_error_double_seq_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to fastq ... ok
test_Quality_error_double_seq_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to fastq-illumina ... ok
test_Quality_error_double_seq_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to fastq-sanger ... ok
test_Quality_error_double_seq_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to fastq-solexa ... ok
test_Quality_error_double_seq_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to qual ... ok
test_Quality_error_double_seq_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_double_seq.fastq from fastq to tab ... ok
test_Quality_error_long_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to fasta ... ok
test_Quality_error_long_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to fastq ... ok
test_Quality_error_long_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to fastq-illumina ... ok
test_Quality_error_long_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to fastq-sanger ... ok
test_Quality_error_long_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to fastq-solexa ... ok
test_Quality_error_long_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to qual ... ok
test_Quality_error_long_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_long_qual.fastq from fastq to tab ... ok
test_Quality_error_no_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to fasta ... ok
test_Quality_error_no_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to fastq ... ok
test_Quality_error_no_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to fastq-illumina ... ok
test_Quality_error_no_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to fastq-sanger ... ok
test_Quality_error_no_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to fastq-solexa ... ok
test_Quality_error_no_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to qual ... ok
test_Quality_error_no_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_no_qual.fastq from fastq to tab ... ok
test_Quality_error_qual_del_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_del.fastq from fastq to fastq ... ok
test_Quality_error_qual_del_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_del.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_del_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_del.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_del_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_del.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_del_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_del.fastq from fastq to qual ... ok
test_Quality_error_qual_escape_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_escape.fastq from fastq to fastq ... ok
test_Quality_error_qual_escape_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_escape.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_escape_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_escape.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_escape_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_escape.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_escape_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_escape.fastq from fastq to qual ... ok
test_Quality_error_qual_null_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_null.fastq from fastq to fastq ... ok
test_Quality_error_qual_null_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_null.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_null_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_null.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_null_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_null.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_null_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_null.fastq from fastq to qual ... ok
test_Quality_error_qual_space_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_space.fastq from fastq to fastq ... ok
test_Quality_error_qual_space_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_space.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_space_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_space.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_space_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_space.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_space_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_space.fastq from fastq to qual ... ok
test_Quality_error_qual_tab_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_tab.fastq from fastq to fastq ... ok
test_Quality_error_qual_tab_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_tab.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_tab_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_tab.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_tab_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_tab.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_tab_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_tab.fastq from fastq to qual ... ok
test_Quality_error_qual_unit_sep_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_unit_sep.fastq from fastq to fastq ... ok
test_Quality_error_qual_unit_sep_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_unit_sep.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_unit_sep_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_unit_sep.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_unit_sep_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_unit_sep.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_unit_sep_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_unit_sep.fastq from fastq to qual ... ok
test_Quality_error_qual_vtab_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_vtab.fastq from fastq to fastq ... ok
test_Quality_error_qual_vtab_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_vtab.fastq from fastq to fastq-illumina ... ok
test_Quality_error_qual_vtab_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_vtab.fastq from fastq to fastq-sanger ... ok
test_Quality_error_qual_vtab_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_vtab.fastq from fastq to fastq-solexa ... ok
test_Quality_error_qual_vtab_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_qual_vtab.fastq from fastq to qual ... ok
test_Quality_error_short_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to fasta ... ok
test_Quality_error_short_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to fastq ... ok
test_Quality_error_short_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to fastq-illumina ... ok
test_Quality_error_short_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to fastq-sanger ... ok
test_Quality_error_short_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to fastq-solexa ... ok
test_Quality_error_short_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to qual ... ok
test_Quality_error_short_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_short_qual.fastq from fastq to tab ... ok
test_Quality_error_spaces_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to fasta ... ok
test_Quality_error_spaces_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to fastq ... ok
test_Quality_error_spaces_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to fastq-illumina ... ok
test_Quality_error_spaces_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to fastq-sanger ... ok
test_Quality_error_spaces_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to fastq-solexa ... ok
test_Quality_error_spaces_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to qual ... ok
test_Quality_error_spaces_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_spaces.fastq from fastq to tab ... ok
test_Quality_error_tabs_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to fasta ... ok
test_Quality_error_tabs_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to fastq ... ok
test_Quality_error_tabs_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to fastq-illumina ... ok
test_Quality_error_tabs_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to fastq-sanger ... ok
test_Quality_error_tabs_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to fastq-solexa ... ok
test_Quality_error_tabs_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to qual ... ok
test_Quality_error_tabs_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_tabs.fastq from fastq to tab ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to fasta ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to fastq ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to qual ... ok
test_Quality_error_trunc_at_plus_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_plus.fastq from fastq to tab ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to fasta ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to fastq ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to qual ... ok
test_Quality_error_trunc_at_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_qual.fastq from fastq to tab ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to fasta ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to fastq ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to qual ... ok
test_Quality_error_trunc_at_seq_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_at_seq.fastq from fastq to tab ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to fasta ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to fastq ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to qual ... ok
test_Quality_error_trunc_in_plus_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_plus.fastq from fastq to tab ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to fasta ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to fastq ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to qual ... ok
test_Quality_error_trunc_in_qual_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_qual.fastq from fastq to tab ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to fasta ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to fastq ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to qual ... ok
test_Quality_error_trunc_in_seq_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_seq.fastq from fastq to tab ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to fasta ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to fastq ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to fastq-illumina ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to fastq-sanger ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to fastq-solexa ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to qual ... ok
test_Quality_error_trunc_in_title_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/error_trunc_in_title.fastq from fastq to tab ... ok
test_Quality_example_fastq_fastq-sanger_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to fasta ... ok
test_Quality_example_fastq_fastq-sanger_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to fastq ... ok
test_Quality_example_fastq_fastq-sanger_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to fastq-illumina ... ok
test_Quality_example_fastq_fastq-sanger_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to fastq-sanger ... ok
test_Quality_example_fastq_fastq-sanger_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to fastq-solexa ... ok
test_Quality_example_fastq_fastq-sanger_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to qual ... ok
test_Quality_example_fastq_fastq-sanger_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq-sanger to tab ... ok
test_Quality_example_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to fasta ... ok
test_Quality_example_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to fastq ... ok
test_Quality_example_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to fastq-illumina ... ok
test_Quality_example_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to fastq-sanger ... ok
test_Quality_example_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to fastq-solexa ... ok
test_Quality_example_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to qual ... ok
test_Quality_example_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/example.fastq from fastq to tab ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to fasta ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to fastq ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to fastq-illumina ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to fastq-sanger ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to fastq-solexa ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to qual ... ok
test_Quality_illumina_faked_fastq_fastq-illumina_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/illumina_faked.fastq from fastq-illumina to tab ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to fasta ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to fastq ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to fastq-illumina ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to fastq-sanger ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to fastq-solexa ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to qual ... ok
test_Quality_sanger_93_fastq_fastq-sanger_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_93.fastq from fastq-sanger to tab ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to fasta ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to fastq ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to fastq-illumina ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to fastq-sanger ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to fastq-solexa ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to qual ... ok
test_Quality_sanger_faked_fastq_fastq-sanger_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/sanger_faked.fastq from fastq-sanger to tab ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to fasta ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to fastq ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to fastq-illumina ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to fastq-sanger ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to fastq-solexa ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to qual ... ok
test_Quality_solexa_faked_fastq_fastq-solexa_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/solexa_faked.fastq from fastq-solexa to tab ... ok
test_Quality_tricky_fastq_fastq_to_fasta (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to fasta ... ok
test_Quality_tricky_fastq_fastq_to_fastq (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to fastq ... ok
test_Quality_tricky_fastq_fastq_to_fastq-illumina (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to fastq-illumina ... ok
test_Quality_tricky_fastq_fastq_to_fastq-sanger (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to fastq-sanger ... ok
test_Quality_tricky_fastq_fastq_to_fastq-solexa (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to fastq-solexa ... ok
test_Quality_tricky_fastq_fastq_to_qual (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to qual ... ok
test_Quality_tricky_fastq_fastq_to_tab (test_SeqIO_convert.ConvertTests)
Convert Quality/tricky.fastq from fastq to tab ... ok
----------------------------------------------------------------------
Ran 1 test in 0.242 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqIO_features.py
test_SeqIO_features ... ok
test_after (test_SeqIO_features.FeatureWriting)
Features: write/read simple after locations. ... ok
test_before (test_SeqIO_features.FeatureWriting)
Features: write/read simple before locations. ... ok
test_between (test_SeqIO_features.FeatureWriting)
GenBank/EMBL write/read simple between locations. ... ok
test_exact (test_SeqIO_features.FeatureWriting)
GenBank/EMBL write/read simple exact locations. ... ok
test_fuzzy_join (test_SeqIO_features.FeatureWriting)
Features: write/read fuzzy join locations. ... ok
test_join (test_SeqIO_features.FeatureWriting)
GenBank/EMBL write/read simple join locations. ... ok
test_oneof (test_SeqIO_features.FeatureWriting)
Features: write/read simple one-of locations. ... ok
test_within (test_SeqIO_features.FeatureWriting)
Features: write/read simple within locations. ... ok
test_mixed_strand (test_SeqIO_features.GenBankLocations) ... ok
test_rev_comp_styles (test_SeqIO_features.GenBankLocations) ... ok
test_CDS (test_SeqIO_features.NC_000932)
Checking GenBank CDS translations vs FASTA faa file. ... ok
test_CDS (test_SeqIO_features.NC_005816)
Checking GenBank CDS translations vs FASTA faa file. ... ok
test_Features (test_SeqIO_features.NC_005816)
Checking GenBank features sequences vs FASTA ffn file. ... ok
test_GenBank_vs_EMBL (test_SeqIO_features.NC_005816) ... ok
test_Genome (test_SeqIO_features.NC_005816)
Checking GenBank sequence vs FASTA fna file. ... ok
test_Translations (test_SeqIO_features.NC_005816)
Checking translation of FASTA features (faa vs ffn). ... ok
test_qualifiers (test_SeqIO_features.SeqFeatureCreation)
Pass in qualifiers to SeqFeatures. ... ok
test_mixed_strand_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (join, mixed strand) ... ok
test_mixed_strand_dna_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (multi-join, mixed strand) ... ok
test_protein_between (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on protein (between location, zero length) ... ok
test_protein_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on protein (join) ... ok
test_protein_join_fuzzy (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on protein (fuzzy join) ... ok
test_protein_multi_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on protein (multi-join) ... ok
test_protein_oneof (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on protein (one-of positions) ... ok
test_protein_simple (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on protein (simple) ... ok
test_simple_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (simple, default strand) ... ok
test_simple_dna_join (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (join, strand -1, before position) ... ok
test_simple_dna_join_after (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (join, strand -1, after position) ... ok
test_simple_dna_strand0 (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (simple, strand 0) ... ok
test_simple_dna_strand1 (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (simple, strand +1) ... ok
test_simple_dna_strand_minus (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (simple, strand -1) ... ok
test_simple_dna_strand_none (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (simple, strand None) ... ok
test_simple_rna (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on RNA (simple, default strand) ... ok
test_single_letter_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (single letter, default strand) ... ok
test_zero_len_dna (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (between location, zero length, default strand) ... ok
test_zero_len_dna_end (test_SeqIO_features.SeqFeatureExtractionWritingReading)
Feature on DNA (between location at end, zero length, default strand) ... ok
test_AAA03323 (test_SeqIO_features.TestWriteRead)
Write and read back AAA03323.embl ... ok
test_AE017046 (test_SeqIO_features.TestWriteRead)
Write and read back AE017046.embl ... ok
test_DD231055_edited (test_SeqIO_features.TestWriteRead)
Write and read back DD231055_edited.embl ... ok
test_Human_contigs (test_SeqIO_features.TestWriteRead)
Write and read back Human_contigs.embl ... ok
test_NC_000932 (test_SeqIO_features.TestWriteRead)
Write and read back NC_000932.gb ... ok
test_NC_005816 (test_SeqIO_features.TestWriteRead)
Write and read back NC_005816.gb ... ok
test_NT_019265 (test_SeqIO_features.TestWriteRead)
Write and read back NT_019265.gb ... ok
test_SC10H5 (test_SeqIO_features.TestWriteRead)
Write and read back SC10H5.embl ... ok
test_TRBG361 (test_SeqIO_features.TestWriteRead)
Write and read back TRBG361.embl ... ok
test_U87107 (test_SeqIO_features.TestWriteRead)
Write and read back U87107.embl ... ok
test_arab1 (test_SeqIO_features.TestWriteRead)
Write and read back arab1.gb ... ok
test_blank_seq (test_SeqIO_features.TestWriteRead)
Write and read back blank_seq.gb ... ok
test_cor6 (test_SeqIO_features.TestWriteRead)
Write and read back cor6_6.gb ... ok
test_dbsource_wrap (test_SeqIO_features.TestWriteRead)
Write and read back dbsource_wrap.gb ... ok
test_extra_keywords (test_SeqIO_features.TestWriteRead)
Write and read back extra_keywords.gb ... ok
test_gbvrl1_start (test_SeqIO_features.TestWriteRead)
Write and read back gbvrl1_start.seq ... ok
test_noref (test_SeqIO_features.TestWriteRead)
Write and read back noref.gb ... ok
test_one_of (test_SeqIO_features.TestWriteRead)
Write and read back of_one.gb ... ok
test_origin_line (test_SeqIO_features.TestWriteRead)
Write and read back origin_line.gb ... ok
test_pri1 (test_SeqIO_features.TestWriteRead)
Write and read back pri1.gb ... ok
test_protein_refseq (test_SeqIO_features.TestWriteRead)
Write and read back protein_refseq.gb ... ok
test_protein_refseq2 (test_SeqIO_features.TestWriteRead)
Write and read back protein_refseq2.gb ... ok
----------------------------------------------------------------------
Ran 1 test in 1.283 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqIO_index.py
test_SeqIO_index ... ok
test_ace_Ace_consed_sample_ace_get_raw (test_SeqIO_index.IndexDictTests)
Index ace file Ace/consed_sample.ace get_raw ... ok
test_ace_Ace_consed_sample_ace_keyf (test_SeqIO_index.IndexDictTests)
Index ace file Ace/consed_sample.ace with key function ... ok
test_ace_Ace_consed_sample_ace_simple (test_SeqIO_index.IndexDictTests)
Index ace file Ace/consed_sample.ace defaults ... ok
test_ace_Ace_contig1_ace_get_raw (test_SeqIO_index.IndexDictTests)
Index ace file Ace/contig1.ace get_raw ... ok
test_ace_Ace_contig1_ace_keyf (test_SeqIO_index.IndexDictTests)
Index ace file Ace/contig1.ace with key function ... ok
test_ace_Ace_contig1_ace_simple (test_SeqIO_index.IndexDictTests)
Index ace file Ace/contig1.ace defaults ... ok
test_ace_Ace_seq_cap_ace_get_raw (test_SeqIO_index.IndexDictTests)
Index ace file Ace/seq.cap.ace get_raw ... ok
test_ace_Ace_seq_cap_ace_keyf (test_SeqIO_index.IndexDictTests)
Index ace file Ace/seq.cap.ace with key function ... ok
test_ace_Ace_seq_cap_ace_simple (test_SeqIO_index.IndexDictTests)
Index ace file Ace/seq.cap.ace defaults ... ok
test_duplicates_index (test_SeqIO_index.IndexDictTests)
Index file with duplicate identifers with Bio.SeqIO.index() ... ok
test_duplicates_index_db (test_SeqIO_index.IndexDictTests)
Index file with duplicate identifers with Bio.SeqIO.index_db() ... ok
test_duplicates_to_dict (test_SeqIO_index.IndexDictTests)
Index file with duplicate identifers with Bio.SeqIO.to_dict() ... ok
test_embl_EMBL_A04195_imgt_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/A04195.imgt get_raw ... ok
test_embl_EMBL_A04195_imgt_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/A04195.imgt with key function ... ok
test_embl_EMBL_A04195_imgt_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/A04195.imgt defaults ... ok
test_embl_EMBL_AAA03323_embl_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/AAA03323.embl get_raw ... ok
test_embl_EMBL_AAA03323_embl_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/AAA03323.embl with key function ... ok
test_embl_EMBL_AAA03323_embl_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/AAA03323.embl defaults ... ok
test_embl_EMBL_TRBG361_embl_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/TRBG361.embl get_raw ... ok
test_embl_EMBL_TRBG361_embl_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/TRBG361.embl with key function ... ok
test_embl_EMBL_TRBG361_embl_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/TRBG361.embl defaults ... ok
test_embl_EMBL_U87107_embl_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/U87107.embl get_raw ... ok
test_embl_EMBL_U87107_embl_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/U87107.embl with key function ... ok
test_embl_EMBL_U87107_embl_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/U87107.embl defaults ... ok
test_embl_EMBL_epo_prt_selection_embl_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/epo_prt_selection.embl get_raw ... ok
test_embl_EMBL_epo_prt_selection_embl_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/epo_prt_selection.embl with key function ... ok
test_embl_EMBL_epo_prt_selection_embl_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/epo_prt_selection.embl defaults ... ok
test_embl_EMBL_patents_embl_get_raw (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/patents.embl get_raw ... ok
test_embl_EMBL_patents_embl_keyf (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/patents.embl with key function ... ok
test_embl_EMBL_patents_embl_simple (test_SeqIO_index.IndexDictTests)
Index embl file EMBL/patents.embl defaults ... ok
test_fasta_GenBank_NC_000932_faa_get_raw (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_000932.faa get_raw ... ok
test_fasta_GenBank_NC_000932_faa_keyf (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_000932.faa with key function ... ok
test_fasta_GenBank_NC_000932_faa_simple (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_000932.faa defaults ... ok
test_fasta_GenBank_NC_005816_faa_get_raw (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.faa get_raw ... ok
test_fasta_GenBank_NC_005816_faa_keyf (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.faa with key function ... ok
test_fasta_GenBank_NC_005816_faa_simple (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.faa defaults ... ok
test_fasta_GenBank_NC_005816_ffn_get_raw (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.ffn get_raw ... ok
test_fasta_GenBank_NC_005816_ffn_keyf (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.ffn with key function ... ok
test_fasta_GenBank_NC_005816_ffn_simple (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.ffn defaults ... ok
test_fasta_GenBank_NC_005816_fna_get_raw (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.fna get_raw ... ok
test_fasta_GenBank_NC_005816_fna_keyf (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.fna with key function ... ok
test_fasta_GenBank_NC_005816_fna_simple (test_SeqIO_index.IndexDictTests)
Index fasta file GenBank/NC_005816.fna defaults ... ok
test_fasta_SwissProt_multi_ex_fasta_get_raw (test_SeqIO_index.IndexDictTests)
Index fasta file SwissProt/multi_ex.fasta get_raw ... ok
test_fasta_SwissProt_multi_ex_fasta_keyf (test_SeqIO_index.IndexDictTests)
Index fasta file SwissProt/multi_ex.fasta with key function ... ok
test_fasta_SwissProt_multi_ex_fasta_simple (test_SeqIO_index.IndexDictTests)
Index fasta file SwissProt/multi_ex.fasta defaults ... ok
test_fastq-illumina_Quality_illumina_faked_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq-illumina file Quality/illumina_faked.fastq get_raw ... ok
test_fastq-illumina_Quality_illumina_faked_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq-illumina file Quality/illumina_faked.fastq with key function ... ok
test_fastq-illumina_Quality_illumina_faked_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq-illumina file Quality/illumina_faked.fastq defaults ... ok
test_fastq-sanger_Quality_example_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/example.fastq get_raw ... ok
test_fastq-sanger_Quality_example_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/example.fastq with key function ... ok
test_fastq-sanger_Quality_example_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/example.fastq defaults ... ok
test_fastq-sanger_Quality_sanger_faked_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/sanger_faked.fastq get_raw ... ok
test_fastq-sanger_Quality_sanger_faked_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/sanger_faked.fastq with key function ... ok
test_fastq-sanger_Quality_sanger_faked_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq-sanger file Quality/sanger_faked.fastq defaults ... ok
test_fastq-solexa_Quality_solexa_faked_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq-solexa file Quality/solexa_faked.fastq get_raw ... ok
test_fastq-solexa_Quality_solexa_faked_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq-solexa file Quality/solexa_faked.fastq with key function ... ok
test_fastq-solexa_Quality_solexa_faked_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq-solexa file Quality/solexa_faked.fastq defaults ... ok
test_fastq_Quality_example_dos_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example_dos.fastq get_raw ... ok
test_fastq_Quality_example_dos_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example_dos.fastq with key function ... ok
test_fastq_Quality_example_dos_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example_dos.fastq defaults ... ok
test_fastq_Quality_example_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example.fastq get_raw ... ok
test_fastq_Quality_example_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example.fastq with key function ... ok
test_fastq_Quality_example_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/example.fastq defaults ... ok
test_fastq_Quality_tricky_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/tricky.fastq get_raw ... ok
test_fastq_Quality_tricky_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/tricky.fastq with key function ... ok
test_fastq_Quality_tricky_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/tricky.fastq defaults ... ok
test_fastq_Quality_wrapping_original_sanger_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/wrapping_original_sanger.fastq get_raw ... ok
test_fastq_Quality_wrapping_original_sanger_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/wrapping_original_sanger.fastq with key function ... ok
test_fastq_Quality_wrapping_original_sanger_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/wrapping_original_sanger.fastq defaults ... ok
test_fastq_Quality_zero_length_fastq_get_raw (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/zero_length.fastq get_raw ... ok
test_fastq_Quality_zero_length_fastq_keyf (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/zero_length.fastq with key function ... ok
test_fastq_Quality_zero_length_fastq_simple (test_SeqIO_index.IndexDictTests)
Index fastq file Quality/zero_length.fastq defaults ... ok
test_gb_GenBank_NC_005816_gb_get_raw (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/NC_005816.gb get_raw ... ok
test_gb_GenBank_NC_005816_gb_keyf (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/NC_005816.gb with key function ... ok
test_gb_GenBank_NC_005816_gb_simple (test_SeqIO_index.IndexDictTests)
Index gb file GenBank/NC_005816.gb defaults ... ok
test_genbank_GenBank_cor6_6_gb_get_raw (test_SeqIO_index.IndexDictTests)
Index genbank file GenBank/cor6_6.gb get_raw ... ok
test_genbank_GenBank_cor6_6_gb_keyf (test_SeqIO_index.IndexDictTests)
Index genbank file GenBank/cor6_6.gb with key function ... ok
test_genbank_GenBank_cor6_6_gb_simple (test_SeqIO_index.IndexDictTests)
Index genbank file GenBank/cor6_6.gb defaults ... ok
test_ig_IntelliGenetics_TAT_mase_nuc_txt_get_raw (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/TAT_mase_nuc.txt get_raw ... ok
test_ig_IntelliGenetics_TAT_mase_nuc_txt_keyf (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/TAT_mase_nuc.txt with key function ... ok
test_ig_IntelliGenetics_TAT_mase_nuc_txt_simple (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/TAT_mase_nuc.txt defaults ... ok
test_ig_IntelliGenetics_VIF_mase-pro_txt_get_raw (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/VIF_mase-pro.txt get_raw ... ok
test_ig_IntelliGenetics_VIF_mase-pro_txt_keyf (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/VIF_mase-pro.txt with key function ... ok
test_ig_IntelliGenetics_VIF_mase-pro_txt_simple (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/VIF_mase-pro.txt defaults ... ok
test_ig_IntelliGenetics_vpu_nucaligned_txt_get_raw (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/vpu_nucaligned.txt get_raw ... ok
test_ig_IntelliGenetics_vpu_nucaligned_txt_keyf (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/vpu_nucaligned.txt with key function ... ok
test_ig_IntelliGenetics_vpu_nucaligned_txt_simple (test_SeqIO_index.IndexDictTests)
Index ig file IntelliGenetics/vpu_nucaligned.txt defaults ... ok
test_imgt_EMBL_A04195_imgt_get_raw (test_SeqIO_index.IndexDictTests)
Index imgt file EMBL/A04195.imgt get_raw ... ok
test_imgt_EMBL_A04195_imgt_keyf (test_SeqIO_index.IndexDictTests)
Index imgt file EMBL/A04195.imgt with key function ... ok
test_imgt_EMBL_A04195_imgt_simple (test_SeqIO_index.IndexDictTests)
Index imgt file EMBL/A04195.imgt defaults ... ok
test_phd_Phd_phd1_get_raw (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd1 get_raw ... ok
test_phd_Phd_phd1_keyf (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd1 with key function ... ok
test_phd_Phd_phd1_simple (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd1 defaults ... ok
test_phd_Phd_phd2_get_raw (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd2 get_raw ... ok
test_phd_Phd_phd2_keyf (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd2 with key function ... ok
test_phd_Phd_phd2_simple (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd2 defaults ... ok
test_phd_Phd_phd_454_get_raw (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd_454 get_raw ... ok
test_phd_Phd_phd_454_keyf (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd_454 with key function ... ok
test_phd_Phd_phd_454_simple (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd_454 defaults ... ok
test_phd_Phd_phd_solexa_get_raw (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd_solexa get_raw ... ok
test_phd_Phd_phd_solexa_keyf (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd_solexa with key function ... ok
test_phd_Phd_phd_solexa_simple (test_SeqIO_index.IndexDictTests)
Index phd file Phd/phd_solexa defaults ... ok
test_pir_NBRF_B_nuc_pir_get_raw (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/B_nuc.pir get_raw ... ok
test_pir_NBRF_B_nuc_pir_keyf (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/B_nuc.pir with key function ... ok
test_pir_NBRF_B_nuc_pir_simple (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/B_nuc.pir defaults ... ok
test_pir_NBRF_Cw_prot_pir_get_raw (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/Cw_prot.pir get_raw ... ok
test_pir_NBRF_Cw_prot_pir_keyf (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/Cw_prot.pir with key function ... ok
test_pir_NBRF_Cw_prot_pir_simple (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/Cw_prot.pir defaults ... ok
test_pir_NBRF_clustalw_pir_get_raw (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/clustalw.pir get_raw ... ok
test_pir_NBRF_clustalw_pir_keyf (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/clustalw.pir with key function ... ok
test_pir_NBRF_clustalw_pir_simple (test_SeqIO_index.IndexDictTests)
Index pir file NBRF/clustalw.pir defaults ... ok
test_sff-trim_Roche_E3MFGYR02_random_10_reads_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/E3MFGYR02_random_10_reads.sff get_raw ... ok
test_sff-trim_Roche_E3MFGYR02_random_10_reads_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/E3MFGYR02_random_10_reads.sff with key function ... ok
test_sff-trim_Roche_E3MFGYR02_random_10_reads_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/E3MFGYR02_random_10_reads.sff defaults ... ok
test_sff-trim_Roche_greek_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/greek.sff get_raw ... ok
test_sff-trim_Roche_greek_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/greek.sff with key function ... ok
test_sff-trim_Roche_greek_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/greek.sff defaults ... ok
test_sff-trim_Roche_paired_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/paired.sff get_raw ... ok
test_sff-trim_Roche_paired_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/paired.sff with key function ... ok
test_sff-trim_Roche_paired_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff-trim file Roche/paired.sff defaults ... ok
test_sff_Roche_E3MFGYR02_alt_index_at_end_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_at_end.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_alt_index_at_end_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_at_end.sff with key function ... ok
test_sff_Roche_E3MFGYR02_alt_index_at_end_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_at_end.sff defaults ... ok
test_sff_Roche_E3MFGYR02_alt_index_at_start_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_at_start.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_alt_index_at_start_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_at_start.sff with key function ... ok
test_sff_Roche_E3MFGYR02_alt_index_at_start_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_at_start.sff defaults ... ok
test_sff_Roche_E3MFGYR02_alt_index_in_middle_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_in_middle.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_alt_index_in_middle_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_in_middle.sff with key function ... ok
test_sff_Roche_E3MFGYR02_alt_index_in_middle_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_alt_index_in_middle.sff defaults ... ok
test_sff_Roche_E3MFGYR02_index_at_start_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_index_at_start.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_index_at_start_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_index_at_start.sff with key function ... ok
test_sff_Roche_E3MFGYR02_index_at_start_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_index_at_start.sff defaults ... ok
test_sff_Roche_E3MFGYR02_index_in_middle_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_index_in_middle.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_index_in_middle_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_index_in_middle.sff with key function ... ok
test_sff_Roche_E3MFGYR02_index_in_middle_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_index_in_middle.sff defaults ... ok
test_sff_Roche_E3MFGYR02_no_manifest_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_no_manifest.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_no_manifest_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_no_manifest.sff with key function ... ok
test_sff_Roche_E3MFGYR02_no_manifest_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_no_manifest.sff defaults ... ok
test_sff_Roche_E3MFGYR02_random_10_reads_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_random_10_reads.sff get_raw ... ok
test_sff_Roche_E3MFGYR02_random_10_reads_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_random_10_reads.sff with key function ... ok
test_sff_Roche_E3MFGYR02_random_10_reads_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/E3MFGYR02_random_10_reads.sff defaults ... ok
test_sff_Roche_greek_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/greek.sff get_raw ... ok
test_sff_Roche_greek_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/greek.sff with key function ... ok
test_sff_Roche_greek_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/greek.sff defaults ... ok
test_sff_Roche_paired_sff_get_raw (test_SeqIO_index.IndexDictTests)
Index sff file Roche/paired.sff get_raw ... ok
test_sff_Roche_paired_sff_keyf (test_SeqIO_index.IndexDictTests)
Index sff file Roche/paired.sff with key function ... ok
test_sff_Roche_paired_sff_simple (test_SeqIO_index.IndexDictTests)
Index sff file Roche/paired.sff defaults ... ok
test_swiss_SwissProt_multi_ex_txt_get_raw (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/multi_ex.txt get_raw ... ok
test_swiss_SwissProt_multi_ex_txt_keyf (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/multi_ex.txt with key function ... ok
test_swiss_SwissProt_multi_ex_txt_simple (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/multi_ex.txt defaults ... ok
test_swiss_SwissProt_sp001_get_raw (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp001 get_raw ... ok
test_swiss_SwissProt_sp001_keyf (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp001 with key function ... ok
test_swiss_SwissProt_sp001_simple (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp001 defaults ... ok
test_swiss_SwissProt_sp010_get_raw (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp010 get_raw ... ok
test_swiss_SwissProt_sp010_keyf (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp010 with key function ... ok
test_swiss_SwissProt_sp010_simple (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp010 defaults ... ok
test_swiss_SwissProt_sp016_get_raw (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp016 get_raw ... ok
test_swiss_SwissProt_sp016_keyf (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp016 with key function ... ok
test_swiss_SwissProt_sp016_simple (test_SeqIO_index.IndexDictTests)
Index swiss file SwissProt/sp016 defaults ... ok
test_tab_GenBank_NC_005816_tsv_get_raw (test_SeqIO_index.IndexDictTests)
Index tab file GenBank/NC_005816.tsv get_raw ... ok
test_tab_GenBank_NC_005816_tsv_keyf (test_SeqIO_index.IndexDictTests)
Index tab file GenBank/NC_005816.tsv with key function ... ok
test_tab_GenBank_NC_005816_tsv_simple (test_SeqIO_index.IndexDictTests)
Index tab file GenBank/NC_005816.tsv defaults ... ok
test_uniprot-xml_SwissProt_multi_ex_xml_get_raw (test_SeqIO_index.IndexDictTests)
Index uniprot-xml file SwissProt/multi_ex.xml get_raw ... ok
test_uniprot-xml_SwissProt_multi_ex_xml_keyf (test_SeqIO_index.IndexDictTests)
Index uniprot-xml file SwissProt/multi_ex.xml with key function ... ok
test_uniprot-xml_SwissProt_multi_ex_xml_simple (test_SeqIO_index.IndexDictTests)
Index uniprot-xml file SwissProt/multi_ex.xml defaults ... ok
test_child_folder_rel (test_SeqIO_index.NewIndexTest)
Check relative links to child folder. ... ok
test_same_folder (test_SeqIO_index.NewIndexTest)
Check relative links in same folder. ... ok
test_some_abs (test_SeqIO_index.NewIndexTest)
Check absolute filenames in index. ... ok
test_old (test_SeqIO_index.OldIndexTest)
Load existing index with no options (from parent directory). ... ok
test_old_contents (test_SeqIO_index.OldIndexTest)
Check actual filenames in existing indexes. ... ok
test_old_files (test_SeqIO_index.OldIndexTest)
Load existing index with correct files (from parent directory). ... ok
test_old_files_same_dir (test_SeqIO_index.OldIndexTest)
Load existing index with correct files (from same directory). ... ok
test_old_files_wrong (test_SeqIO_index.OldIndexTest)
Load existing index with wrong files. ... ok
test_old_files_wrong2 (test_SeqIO_index.OldIndexTest)
Load existing index with wrong number of files. ... ok
test_old_format (test_SeqIO_index.OldIndexTest)
Load existing index with correct format. ... ok
test_old_format_wrong (test_SeqIO_index.OldIndexTest)
Load existing index with wrong format. ... ok
test_old_rel (test_SeqIO_index.OldIndexTest)
Load existing index (with relative paths) with no options (from parent directory). ... ok
test_old_same_dir (test_SeqIO_index.OldIndexTest)
Load existing index with no options (from same directory). ... ok
test_old_same_dir_rel (test_SeqIO_index.OldIndexTest)
Load existing index (with relative paths) with no options (from same directory). ... ok
----------------------------------------------------------------------
Ran 1 test in 15.958 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqIO_online.py
test_SeqIO_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.004 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqIO_write.py
test_SeqIO_write ... ok
test_bad_handle (test_SeqIO_write.WriterTests) ... ok
test_clustal_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
clustal for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_clustal_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
clustal for alignment with repeated record ... ok
test_clustal_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
clustal for three DNA sequence alignment ... ok
test_clustal_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
clustal for three peptides of different lengths ... ok
test_clustal_three_proteins_alignment (test_SeqIO_write.WriterTests)
clustal for three proteins alignment ... ok
test_clustal_zero_records (test_SeqIO_write.WriterTests)
clustal for zero records ... ok
test_embl_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
embl for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_embl_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
embl for alignment with repeated record ... ok
test_embl_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
embl for three DNA sequence alignment ... ok
test_embl_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
embl for three peptides of different lengths ... ok
test_embl_three_proteins_alignment (test_SeqIO_write.WriterTests)
embl for three proteins alignment ... ok
test_embl_zero_records (test_SeqIO_write.WriterTests)
embl for zero records ... ok
test_fasta_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
fasta for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_fasta_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
fasta for alignment with repeated record ... ok
test_fasta_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
fasta for three DNA sequence alignment ... ok
test_fasta_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
fasta for three peptides of different lengths ... ok
test_fasta_three_proteins_alignment (test_SeqIO_write.WriterTests)
fasta for three proteins alignment ... ok
test_fasta_zero_records (test_SeqIO_write.WriterTests)
fasta for zero records ... ok
test_fastq-illumina_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
fastq-illumina for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_fastq-illumina_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
fastq-illumina for alignment with repeated record ... ok
test_fastq-illumina_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
fastq-illumina for three DNA sequence alignment ... ok
test_fastq-illumina_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
fastq-illumina for three peptides of different lengths ... ok
test_fastq-illumina_three_proteins_alignment (test_SeqIO_write.WriterTests)
fastq-illumina for three proteins alignment ... ok
test_fastq-illumina_zero_records (test_SeqIO_write.WriterTests)
fastq-illumina for zero records ... ok
test_fastq-solexa_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
fastq-solexa for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_fastq-solexa_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
fastq-solexa for alignment with repeated record ... ok
test_fastq-solexa_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
fastq-solexa for three DNA sequence alignment ... ok
test_fastq-solexa_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
fastq-solexa for three peptides of different lengths ... ok
test_fastq-solexa_three_proteins_alignment (test_SeqIO_write.WriterTests)
fastq-solexa for three proteins alignment ... ok
test_fastq-solexa_zero_records (test_SeqIO_write.WriterTests)
fastq-solexa for zero records ... ok
test_fastq_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
fastq for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_fastq_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
fastq for alignment with repeated record ... ok
test_fastq_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
fastq for three DNA sequence alignment ... ok
test_fastq_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
fastq for three peptides of different lengths ... ok
test_fastq_three_proteins_alignment (test_SeqIO_write.WriterTests)
fastq for three proteins alignment ... ok
test_fastq_zero_records (test_SeqIO_write.WriterTests)
fastq for zero records ... ok
test_genbank_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
genbank for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_genbank_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
genbank for alignment with repeated record ... ok
test_genbank_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
genbank for three DNA sequence alignment ... ok
test_genbank_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
genbank for three peptides of different lengths ... ok
test_genbank_three_proteins_alignment (test_SeqIO_write.WriterTests)
genbank for three proteins alignment ... ok
test_genbank_zero_records (test_SeqIO_write.WriterTests)
genbank for zero records ... ok
test_imgt_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
imgt for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_imgt_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
imgt for alignment with repeated record ... ok
test_imgt_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
imgt for three DNA sequence alignment ... ok
test_imgt_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
imgt for three peptides of different lengths ... ok
test_imgt_three_proteins_alignment (test_SeqIO_write.WriterTests)
imgt for three proteins alignment ... ok
test_imgt_zero_records (test_SeqIO_write.WriterTests)
imgt for zero records ... ok
test_nexus_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
nexus for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_nexus_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
nexus for alignment with repeated record ... ok
test_nexus_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
nexus for three DNA sequence alignment ... ok
test_nexus_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
nexus for three peptides of different lengths ... ok
test_nexus_three_proteins_alignment (test_SeqIO_write.WriterTests)
nexus for three proteins alignment ... ok
test_nexus_zero_records (test_SeqIO_write.WriterTests)
nexus for zero records ... ok
test_phd_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
phd for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_phd_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
phd for alignment with repeated record ... ok
test_phd_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
phd for three DNA sequence alignment ... ok
test_phd_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
phd for three peptides of different lengths ... ok
test_phd_three_proteins_alignment (test_SeqIO_write.WriterTests)
phd for three proteins alignment ... ok
test_phd_zero_records (test_SeqIO_write.WriterTests)
phd for zero records ... ok
test_phylip-relaxed_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
phylip-relaxed for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_phylip-relaxed_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
phylip-relaxed for alignment with repeated record ... ok
test_phylip-relaxed_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
phylip-relaxed for three DNA sequence alignment ... ok
test_phylip-relaxed_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
phylip-relaxed for three peptides of different lengths ... ok
test_phylip-relaxed_three_proteins_alignment (test_SeqIO_write.WriterTests)
phylip-relaxed for three proteins alignment ... ok
test_phylip-relaxed_zero_records (test_SeqIO_write.WriterTests)
phylip-relaxed for zero records ... ok
test_phylip-sequential_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
phylip-sequential for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_phylip-sequential_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
phylip-sequential for alignment with repeated record ... ok
test_phylip-sequential_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
phylip-sequential for three DNA sequence alignment ... ok
test_phylip-sequential_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
phylip-sequential for three peptides of different lengths ... ok
test_phylip-sequential_three_proteins_alignment (test_SeqIO_write.WriterTests)
phylip-sequential for three proteins alignment ... ok
test_phylip-sequential_zero_records (test_SeqIO_write.WriterTests)
phylip-sequential for zero records ... ok
test_phylip_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
phylip for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_phylip_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
phylip for alignment with repeated record ... ok
test_phylip_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
phylip for three DNA sequence alignment ... ok
test_phylip_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
phylip for three peptides of different lengths ... ok
test_phylip_three_proteins_alignment (test_SeqIO_write.WriterTests)
phylip for three proteins alignment ... ok
test_phylip_zero_records (test_SeqIO_write.WriterTests)
phylip for zero records ... ok
test_qual_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
qual for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_qual_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
qual for alignment with repeated record ... ok
test_qual_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
qual for three DNA sequence alignment ... ok
test_qual_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
qual for three peptides of different lengths ... ok
test_qual_three_proteins_alignment (test_SeqIO_write.WriterTests)
qual for three proteins alignment ... ok
test_qual_zero_records (test_SeqIO_write.WriterTests)
qual for zero records ... ok
test_seqxml_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
seqxml for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_seqxml_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
seqxml for alignment with repeated record ... ok
test_seqxml_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
seqxml for three DNA sequence alignment ... ok
test_seqxml_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
seqxml for three peptides of different lengths ... ok
test_seqxml_three_proteins_alignment (test_SeqIO_write.WriterTests)
seqxml for three proteins alignment ... ok
test_seqxml_zero_records (test_SeqIO_write.WriterTests)
seqxml for zero records ... ok
test_sff_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
sff for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_sff_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
sff for alignment with repeated record ... ok
test_sff_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
sff for three DNA sequence alignment ... ok
test_sff_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
sff for three peptides of different lengths ... ok
test_sff_three_proteins_alignment (test_SeqIO_write.WriterTests)
sff for three proteins alignment ... ok
test_sff_zero_records (test_SeqIO_write.WriterTests)
sff for zero records ... ok
test_stockholm_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
stockholm for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_stockholm_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
stockholm for alignment with repeated record ... ok
test_stockholm_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
stockholm for three DNA sequence alignment ... ok
test_stockholm_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
stockholm for three peptides of different lengths ... ok
test_stockholm_three_proteins_alignment (test_SeqIO_write.WriterTests)
stockholm for three proteins alignment ... ok
test_stockholm_zero_records (test_SeqIO_write.WriterTests)
stockholm for zero records ... ok
test_tab_3_DNA_seq_alignment_with_CR/LF_in_name/descr (test_SeqIO_write.WriterTests)
tab for 3 DNA seq alignment with CR/LF in name/descr ... ok
test_tab_alignment_with_repeated_record (test_SeqIO_write.WriterTests)
tab for alignment with repeated record ... ok
test_tab_three_DNA_sequence_alignment (test_SeqIO_write.WriterTests)
tab for three DNA sequence alignment ... ok
test_tab_three_peptides_of_different_lengths (test_SeqIO_write.WriterTests)
tab for three peptides of different lengths ... ok
test_tab_three_proteins_alignment (test_SeqIO_write.WriterTests)
tab for three proteins alignment ... ok
test_tab_zero_records (test_SeqIO_write.WriterTests)
tab for zero records ... ok
----------------------------------------------------------------------
Ran 1 test in 0.161 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqRecord.py
test_SeqRecord ... ok
test_annotations (test_SeqRecord.SeqRecordCreation)
Pass in annotations to SeqRecords ... ok
test_letter_annotations (test_SeqRecord.SeqRecordCreation)
Pass in letter annotations to SeqRecords ... ok
test_valid_annotations (test_SeqRecord.SeqRecordCreation) ... ok
test_valid_dbxrefs (test_SeqRecord.SeqRecordCreation) ... ok
test_valid_description (test_SeqRecord.SeqRecordCreation) ... ok
test_valid_features (test_SeqRecord.SeqRecordCreation) ... ok
test_valid_id (test_SeqRecord.SeqRecordCreation) ... ok
test_valid_name (test_SeqRecord.SeqRecordCreation) ... ok
test_add_seq (test_SeqRecord.SeqRecordMethods)
Simple addition of Seq or string ... ok
test_add_seq_left (test_SeqRecord.SeqRecordMethods)
Simple left addition of Seq or string ... ok
test_add_seqrecord (test_SeqRecord.SeqRecordMethods)
Simple left addition of SeqRecord from genbank file. ... ok
test_add_simple (test_SeqRecord.SeqRecordMethods)
Simple addition ... ok
test_contains (test_SeqRecord.SeqRecordMethods) ... ok
test_format (test_SeqRecord.SeqRecordMethods) ... ok
test_iter (test_SeqRecord.SeqRecordMethods) ... ok
test_lower (test_SeqRecord.SeqRecordMethods) ... ok
test_repr (test_SeqRecord.SeqRecordMethods) ... ok
test_reverse_complement_mutable_seq (test_SeqRecord.SeqRecordMethods) ... ok
test_reverse_complement_seq (test_SeqRecord.SeqRecordMethods) ... ok
test_slice_add_shift (test_SeqRecord.SeqRecordMethods)
Simple slice and add to shift ... ok
test_slice_add_simple (test_SeqRecord.SeqRecordMethods)
Simple slice and add ... ok
test_slice_simple (test_SeqRecord.SeqRecordMethods)
Simple slice ... ok
test_slice_variants (test_SeqRecord.SeqRecordMethods)
Simple slices using different start/end values ... ok
test_slice_zero (test_SeqRecord.SeqRecordMethods)
Zero slice ... ok
test_slicing (test_SeqRecord.SeqRecordMethods) ... ok
test_str (test_SeqRecord.SeqRecordMethods) ... ok
test_upper (test_SeqRecord.SeqRecordMethods) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.317 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SeqUtils.py
test_SeqUtils ... ok
test_GC (test_SeqUtils.SeqUtilsTests) ... ok
test_checksum1 (test_SeqUtils.SeqUtilsTests) ... ok
test_checksum2 (test_SeqUtils.SeqUtilsTests) ... ok
test_checksum3 (test_SeqUtils.SeqUtilsTests) ... ok
test_codon_usage_custom (test_SeqUtils.SeqUtilsTests)
Test Codon Adaptation Index (CAI) using FASTA file for background. ... ok
test_codon_usage_ecoli (test_SeqUtils.SeqUtilsTests)
Test Codon Adaptation Index (CAI) using default E. coli data. ... ok
test_crc_checksum_collision (test_SeqUtils.SeqUtilsTests) ... ok
test_seq1_seq3 (test_SeqUtils.SeqUtilsTests) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.134 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Seq_objs.py
test_Seq_objs ... ok
test_init_typeerror (test_Seq_objs.StringMethodTests)
Check Seq __init__ gives TypeError exceptions. ... ok
test_str_comparison (test_Seq_objs.StringMethodTests) ... ok
test_str_count (test_Seq_objs.StringMethodTests)
Check matches the python string count method. ... ok
test_str_endswith (test_Seq_objs.StringMethodTests)
Check matches the python string endswith method. ... ok
test_str_find (test_Seq_objs.StringMethodTests)
Check matches the python string find method. ... ok
test_str_getitem (test_Seq_objs.StringMethodTests)
Check slicing and indexing works like a string. ... ok
test_str_hash (test_Seq_objs.StringMethodTests) ... ok
test_str_length (test_Seq_objs.StringMethodTests)
Check matches the python string __len__ method. ... ok
test_str_lower (test_Seq_objs.StringMethodTests)
Check matches the python string lower method. ... ok
test_str_lsplit (test_Seq_objs.StringMethodTests)
Check matches the python string rstrip method. ... ok
test_str_rfind (test_Seq_objs.StringMethodTests)
Check matches the python string rfind method. ... ok
test_str_rsplit (test_Seq_objs.StringMethodTests)
Check matches the python string rstrip method. ... ok
test_str_rstrip (test_Seq_objs.StringMethodTests)
Check matches the python string rstrip method. ... ok
test_str_split (test_Seq_objs.StringMethodTests)
Check matches the python string rstrip method. ... ok
test_str_startswith (test_Seq_objs.StringMethodTests)
Check matches the python string startswith method. ... ok
test_str_strip (test_Seq_objs.StringMethodTests)
Check matches the python string strip method. ... ok
test_str_upper (test_Seq_objs.StringMethodTests)
Check matches the python string upper method. ... ok
test_the_back_transcription (test_Seq_objs.StringMethodTests)
Check obj.back_transcribe() method. ... ok
test_the_complement (test_Seq_objs.StringMethodTests)
Check obj.complement() method. ... ok
test_the_reverse_complement (test_Seq_objs.StringMethodTests)
Check obj.reverse_complement() method. ... ok
test_the_transcription (test_Seq_objs.StringMethodTests)
Check obj.transcribe() method. ... ok
test_the_translate (test_Seq_objs.StringMethodTests)
Check obj.translate() method. ... ok
test_the_translation_of_ambig_codons (test_Seq_objs.StringMethodTests)
Check obj.translate() method with ambiguous codons. ... ok
test_the_translation_of_invalid_codons (test_Seq_objs.StringMethodTests)
Check obj.translate() method with invalid codons. ... ok
test_the_translation_of_stops (test_Seq_objs.StringMethodTests)
Check obj.translate() method with stop codons. ... ok
test_tomutable (test_Seq_objs.StringMethodTests)
Check obj.tomutable() method. ... ok
test_toseq (test_Seq_objs.StringMethodTests)
Check obj.toseq() method. ... ok
----------------------------------------------------------------------
Ran 1 test in 4.160 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SffIO.py
test_SffIO ... ok
test_index1 (test_SffIO.TestConcatenated) ... ok
test_index2 (test_SffIO.TestConcatenated) ... ok
test_parse1 (test_SffIO.TestConcatenated) ... ok
test_parse2 (test_SffIO.TestConcatenated) ... ok
test_parses_gzipped_stream (test_SffIO.TestConcatenated) ... ok
test_coords (test_SffIO.TestUAN) ... ok
test_region (test_SffIO.TestUAN) ... ok
test_time (test_SffIO.TestUAN) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.126 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SubsMat.py
test_SubsMat ... ok
runTest (__main__.ComparisonTestCase)
test_SubsMat ... ok
----------------------------------------------------------------------
Ran 1 test in 0.064 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_SwissProt.py
test_SwissProt ... ok
test_sp001 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp001 ... ok
test_sp002 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp002 ... ok
test_sp003 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp003 ... ok
test_sp004 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp004 ... ok
test_sp005 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp005 ... ok
test_sp006 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp006 ... ok
test_sp007 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp007 ... ok
test_sp008 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp008 ... ok
test_sp009 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp009 ... ok
test_sp010 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp010 ... ok
test_sp011 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp011 ... ok
test_sp012 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp012 ... ok
test_sp013 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp013 ... ok
test_sp014 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp014 ... ok
test_sp015 (test_SwissProt.TestSwissProt)
Parsing SwissProt file sp015 ... ok
----------------------------------------------------------------------
Ran 1 test in 0.181 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_TCoffee_tool.py
test_TCoffee_tool ... skipping. Install TCOFFEE if you want to use the Bio.Align.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.124 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_TogoWS.py
test_TogoWS ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.024 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_TreeConstruction.py
test_TreeConstruction ... ok
test_known_matrices (test_TreeConstruction.DistanceCalculatorTest) ... ok
test_nonmatching_seqs (test_TreeConstruction.DistanceCalculatorTest) ... ok
test_bad_construction (test_TreeConstruction.DistanceMatrixTest) ... ok
test_bad_manipulation (test_TreeConstruction.DistanceMatrixTest) ... ok
test_good_construction (test_TreeConstruction.DistanceMatrixTest) ... ok
test_good_manipulation (test_TreeConstruction.DistanceMatrixTest) ... ok
test_built_tree (test_TreeConstruction.DistanceTreeConstructorTest) ... ok
test_nj (test_TreeConstruction.DistanceTreeConstructorTest) ... ok
test_upgma (test_TreeConstruction.DistanceTreeConstructorTest) ... ok
test_get_neighbors (test_TreeConstruction.NNITreeSearcherTest) ... ok
test_get_score (test_TreeConstruction.ParsimonyScorerTest) ... ok
test_build_tree (test_TreeConstruction.ParsimonyTreeConstructorTest) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.677 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_UniGene.py
test_UniGene ... ok
test_parse (test_UniGene.TestUniGene) ... ok
test_read (test_UniGene.TestUniGene) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.029 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Uniprot.py
test_Uniprot ... ok
test_F2CXE6 (test_Uniprot.TestUniprot)
Compare SwissProt text and uniprot XML versions of F2CXE6. ... ok
test_H2CNN8 (test_Uniprot.TestUniprot)
Compare SwissProt text and uniprot XML versions of H2CNN8. ... ok
test_Q13639 (test_Uniprot.TestUniprot)
Compare SwissProt text and uniprot XML versions of Q13639. ... ok
test_multi_ex (test_Uniprot.TestUniprot)
Compare SwissProt text and uniprot XML versions of several examples. ... ok
test_multi_ex_index (test_Uniprot.TestUniprot)
Index SwissProt text and uniprot XML versions of several examples. ... ok
test_uni001 (test_Uniprot.TestUniprot)
Parsing Uniprot file uni001 ... ok
test_uni003 (test_Uniprot.TestUniprot)
Parsing Uniprot file uni003 ... ok
----------------------------------------------------------------------
Ran 1 test in 0.312 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_Wise.py
test_Wise ... ok
test_align (test_Wise.TestWise)
Call dnal with optional arguments, and do a trivial check on the output. ... ok
test_dnal (test_Wise.TestWiseDryRun)
Call dnal, and do a trivial check on its output. ... ok
test_psw (test_Wise.TestWiseDryRun)
Call psw, and do a trivial check on its output. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.126 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_XXmotif_tool.py
test_XXmotif_tool ... /builddir/build/BUILD/python-biopython-1.66/python2/build/lib.linux-i686-2.7/Bio/Motif/__init__.py:26: BiopythonDeprecationWarning: The module Bio.Motif has been deprecated and will be removed in a future release of Biopython. Instead please use the new module Bio.motifs instead. Please be aware that though the functionality of Bio.Motif is retained (and extended) in Bio.motifs, usage may be different.
  BiopythonDeprecationWarning)
skipping. Install XXmotif if you want to use XXmotif from Biopython.
----------------------------------------------------------------------
Ran 1 test in 0.134 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_align.py
test_align ... ok
runTest (__main__.ComparisonTestCase)
test_align ... ok
----------------------------------------------------------------------
Ran 1 test in 0.289 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_bgzf.py
test_bgzf ... ok
test_bam_ex1 (test_bgzf.BgzfTests)
Reproduce BGZF compression for BAM file ... ok
test_example_cor6 (test_bgzf.BgzfTests)
Reproduce BGZF compression for cor6_6.gb GenBank file ... ok
test_example_fastq (test_bgzf.BgzfTests)
Reproduce BGZF compression for a FASTQ file ... ok
test_example_gb (test_bgzf.BgzfTests)
Reproduce BGZF compression for NC_000932 GenBank file ... ok
test_example_wnts_xml (test_bgzf.BgzfTests)
Reproduce BGZF compression for wnts.xml BLAST file ... ok
test_iter_bam_ex1 (test_bgzf.BgzfTests)
Check iteration over SamBam/ex1.bam ... ok
test_iter_example_cor6 (test_bgzf.BgzfTests)
Check iteration over GenBank/cor6_6.gb.bgz ... ok
test_iter_example_fastq (test_bgzf.BgzfTests)
Check iteration over Quality/example.fastq.bgz ... ok
test_iter_example_gb (test_bgzf.BgzfTests)
Check iteration over GenBank/NC_000932.gb.bgz ... ok
test_iter_wnts_xml (test_bgzf.BgzfTests)
Check iteration over Blast/wnts.xml.bgz ... ok
test_random_bam_ex1 (test_bgzf.BgzfTests)
Check random access to SamBam/ex1.bam ... ok
test_random_bam_ex1_header (test_bgzf.BgzfTests)
Check random access to SamBam/ex1_header.bam ... ok
test_random_bam_ex1_refresh (test_bgzf.BgzfTests)
Check random access to SamBam/ex1_refresh.bam ... ok
test_random_example_cor6 (test_bgzf.BgzfTests)
Check random access to GenBank/cor6_6.gb.bgz ... ok
test_random_example_dos_fastq (test_bgzf.BgzfTests)
Check random access to Quality/example_dos.fastq.bgz (DOS newlines) ... ok
test_random_example_fastq (test_bgzf.BgzfTests)
Check random access to Quality/example.fastq.bgz (Unix newlines) ... ok
test_random_wnts_xml (test_bgzf.BgzfTests)
Check random access to Blast/wnts.xml.bgz ... ok
test_text_example_fastq (test_bgzf.BgzfTests)
Check text mode access to Quality/example.fastq.bgz ... ok
test_text_wnts_xml (test_bgzf.BgzfTests)
Check text mode access to Blast/wnts.xml.bgz ... ok
test_write_tell (test_bgzf.BgzfTests)
Check offset works during BGZF writing ... ok
----------------------------------------------------------------------
Ran 1 test in 7.822 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_codonalign.py
test_codonalign ... ok
test_IO (test_codonalign.TestBuildAndIO) ... ok
test_align (test_codonalign.TestCodonAlignment) ... ok
test_seq (test_codonalign.TestCodonSeq) ... ok
test_mk (test_codonalign.Test_MK) ... ok
test_build (test_codonalign.Test_build) ... ok
test_dn_ds (test_codonalign.Test_dn_ds) ... ok
----------------------------------------------------------------------
Ran 1 test in 9.980 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_geo.py
test_geo ... ok
runTest (__main__.ComparisonTestCase)
test_geo ... ok
----------------------------------------------------------------------
Ran 1 test in 0.028 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_kNN.py
test_kNN ... ok
test_calculate_model (test_kNN.TestKNN) ... ok
test_calculate_probability (test_kNN.TestKNN) ... ok
test_classify (test_kNN.TestKNN) ... ok
test_leave_one_out (test_kNN.TestKNN) ... ok
test_model_accuracy (test_kNN.TestKNN) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.015 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_lowess.py
test_lowess ... ok
test_Precomputed (test_lowess.test_lowess) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.024 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_motifs.py
test_motifs ... ok
test_simple (test_motifs.MotifTestPWM)
Test if Bio.motifs PWM scoring works. ... ok
test_with_alt_alphabet (test_motifs.MotifTestPWM)
Test motif search using alternative instance of alphabet. ... ok
test_with_bad_char (test_motifs.MotifTestPWM)
Test if Bio.motifs PWM scoring works with unexpected letters like N. ... ok
test_with_mixed_case (test_motifs.MotifTestPWM)
Test if Bio.motifs PWM scoring works with mixed case. ... ok
test_TFoutput (test_motifs.MotifTestsBasic)
Ensure that we can write proper TransFac output files. ... ok
test_alignace_parsing (test_motifs.MotifTestsBasic)
Test if Bio.motifs can parse AlignAce output files. ... ok
test_format (test_motifs.MotifTestsBasic) ... ok
test_pfm_parsing (test_motifs.MotifTestsBasic)
Test if Bio.motifs can parse JASPAR-style pfm files. ... ok
test_sites_parsing (test_motifs.MotifTestsBasic)
Test if Bio.motifs can parse JASPAR-style sites files. ... ok
test_mast_parser_1 (test_motifs.TestMAST)
Test if Bio.motifs can parse MAST output files (first test) ... ok
test_mast_parser_2 (test_motifs.TestMAST)
Test if Bio.motifs can parse MAST output files (second test) ... ok
test_mast_parser_3 (test_motifs.TestMAST)
Test if Bio.motifs can parse MAST output files (third test) ... ok
test_meme_parser_1 (test_motifs.TestMEME)
Test if Bio.motifs can parse MEME output files (first test) ... ok
test_meme_parser_2 (test_motifs.TestMEME)
Test if Bio.motifs can parse MEME output files (second test) ... ok
test_meme_parser_3 (test_motifs.TestMEME)
Test if Bio.motifs can parse MEME output files (third test) ... ok
test_meme_parser_4 (test_motifs.TestMEME)
Test if Bio.motifs can parse MEME output files (fourth test) ... ok
test_transfac_parser (test_motifs.TestTransfac)
Test if Bio.motifs can parse TRANSFAC files ... ok
----------------------------------------------------------------------
Ran 1 test in 0.146 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_motifs_online.py
test_motifs_online ... skipping. internet not available
----------------------------------------------------------------------
Ran 1 test in 0.003 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_pairwise2.py
test_pairwise2 ... ok
test_extend_penalty1 (test_pairwise2.TestPairwiseExtendPenalty) ... ok
test_extend_penalty2 (test_pairwise2.TestPairwiseExtendPenalty) ... ok
test_globalxx_simple (test_pairwise2.TestPairwiseGlobal) ... ok
test_localxs (test_pairwise2.TestPairwiseLocal) ... ok
test_match_dictionary1 (test_pairwise2.TestPairwiseMatchDictionary) ... ok
test_match_dictionary2 (test_pairwise2.TestPairwiseMatchDictionary) ... ok
test_match_dictionary3 (test_pairwise2.TestPairwiseMatchDictionary) ... ok
test_align_one_char1 (test_pairwise2.TestPairwiseOneCharacter) ... ok
test_align_one_char2 (test_pairwise2.TestPairwiseOneCharacter) ... ok
test_align_one_char3 (test_pairwise2.TestPairwiseOneCharacter) ... ok
test_match_score_open_penalty1 (test_pairwise2.TestPairwiseOpenPenalty) ... ok
test_match_score_open_penalty2 (test_pairwise2.TestPairwiseOpenPenalty) ... ok
test_match_score_open_penalty3 (test_pairwise2.TestPairwiseOpenPenalty) ... ok
test_match_score_open_penalty4 (test_pairwise2.TestPairwiseOpenPenalty) ... ok
test_penalize_end_gaps (test_pairwise2.TestPairwisePenalizeEndgaps) ... ok
test_penalize_extend_when_opening (test_pairwise2.TestPairwisePenalizeExtendWhenOpening) ... ok
test_separate_gap_penalties1 (test_pairwise2.TestPairwiseSeparateGapPenalties) ... ok
test_separate_gap_penalties2 (test_pairwise2.TestPairwiseSeparateGapPenalties) ... ok
test_separate_gap_penalties_with_extension (test_pairwise2.TestPairwiseSeparateGapPenaltiesWithExtension) ... ok
test_gap_here_only_1 (test_pairwise2.TestPersiteGapPenalties) ... ok
test_gap_here_only_2 (test_pairwise2.TestPersiteGapPenalties)
Force a bad alignment. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.059 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_phyml_tool.py
test_phyml_tool ... skipping. Install PhyML 3.0 if you want to use the Bio.Phylo.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.142 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_prodoc.py
test_prodoc ... ok
test_parse_pdoc (test_prodoc.TestProdocParse)
Parsing an excerpt of prosite.doc ... ok
test_read_pdoc00100 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00100 ... ok
test_read_pdoc00113 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00113 ... ok
test_read_pdoc00144 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00144 ... ok
test_read_pdoc00149 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00149 ... ok
test_read_pdoc00340 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00340 ... ok
test_read_pdoc00424 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00424 ... ok
test_read_pdoc00472 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00472 ... ok
test_read_pdoc00640 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00640 ... ok
test_read_pdoc00787 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00787 ... ok
test_read_pdoc0933 (test_prodoc.TestProdocRead)
Reading Prodoc record PDOC00933 ... ok
----------------------------------------------------------------------
Ran 1 test in 0.032 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_prosite1.py
test_prosite1 ... ok
test_read1 (test_prosite1.TestPrositeRead)
Parsing Prosite record ps00107.txt ... ok
test_read2 (test_prosite1.TestPrositeRead)
Parsing Prosite record ps00159.txt ... ok
test_read3 (test_prosite1.TestPrositeRead)
Parsing Prosite record ps00165.txt ... ok
----------------------------------------------------------------------
Ran 1 test in 0.095 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_prosite2.py
test_prosite2 ... ok
test_read4 (test_prosite2.TestPrositeRead)
Parsing Prosite record ps00432.txt ... ok
test_read5 (test_prosite2.TestPrositeRead)
Parsing Prosite record ps00488.txt ... ok
test_read6 (test_prosite2.TestPrositeRead)
Parsing Prosite record ps00546.txt ... ok
----------------------------------------------------------------------
Ran 1 test in 0.041 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_psw.py
test_psw ... ok
test_AlignmentColumn_assertions (test_psw.TestPSW) ... ok
test_AlignmentColumn_full (test_psw.TestPSW) ... ok
test_AlignmentColumn_kinds (test_psw.TestPSW) ... ok
test_AlignmentColumn_repr (test_psw.TestPSW) ... ok
test_Alignment_assertions (test_psw.TestPSW) ... ok
test_Alignment_normal (test_psw.TestPSW) ... ok
test_ColumnUnit (test_psw.TestPSW) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.117 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_py3k.py
test_py3k ... ok
test_od (test_py3k.ODTest)
Quick test OrderedDict works. ... ok
----------------------------------------------------------------------
Ran 1 test in 0.021 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_raxml_tool.py
test_raxml_tool ... skipping. Install RAxML (binary raxmlHPC) if you want to test the Bio.Phylo.Applications wrapper.
----------------------------------------------------------------------
Ran 1 test in 0.141 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_samtools_tool.py
test_samtools_tool ... skipping. Install samtools and correctly set the file path to the program
        if you want to use it from Biopython
----------------------------------------------------------------------
Ran 1 test in 0.033 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_seq.py
test_seq ... ok
test_ambiguous_values (test_seq.TestAmbiguousComplements)
Test that other tests do not introduce characters to our values ... ok
test_complement_ambiguous_dna_values (test_seq.TestComplement) ... ok
test_complement_ambiguous_rna_values (test_seq.TestComplement) ... ok
test_complement_incompatible_alphabets (test_seq.TestComplement) ... ok
test_reverse_complements (test_seq.TestDoubleReverseComplement)
Test double reverse complement preserves the sequence ... ok
test_add_method (test_seq.TestMutableSeq)
Test adding wrong type to MutableSeq ... ok
test_appending (test_seq.TestMutableSeq) ... ok
test_as_string (test_seq.TestMutableSeq) ... ok
test_complement (test_seq.TestMutableSeq) ... ok
test_complement_dna_string (test_seq.TestMutableSeq) ... ok
test_complement_mixed_aphabets (test_seq.TestMutableSeq) ... ok
test_complement_rna (test_seq.TestMutableSeq) ... ok
test_complement_rna_string (test_seq.TestMutableSeq) ... ok
test_converting_to_immutable (test_seq.TestMutableSeq) ... ok
test_count (test_seq.TestMutableSeq) ... ok
test_delete_stride_slice (test_seq.TestMutableSeq) ... ok
test_deleting_item (test_seq.TestMutableSeq) ... ok
test_deleting_slice (test_seq.TestMutableSeq) ... ok
test_equal_comparison (test_seq.TestMutableSeq)
Test __eq__ comparison method ... ok
test_equal_comparison_of_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
test_extend_method (test_seq.TestMutableSeq) ... ok
test_extend_with_mutable_seq (test_seq.TestMutableSeq) ... ok
test_extract_third_nucleotide (test_seq.TestMutableSeq)
Test extracting every third nucleotide (slicing with stride 3) ... ok
test_first_nucleotide (test_seq.TestMutableSeq) ... ok
test_index (test_seq.TestMutableSeq) ... ok
test_inserting (test_seq.TestMutableSeq) ... ok
test_length (test_seq.TestMutableSeq) ... ok
test_less_than_comparison (test_seq.TestMutableSeq)
Test __lt__ comparison method ... ok
test_less_than_comparison_of_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
test_less_than_comparison_without_alphabet (test_seq.TestMutableSeq) ... ok
test_less_than_or_equal_comparison (test_seq.TestMutableSeq)
Test __le__ comparison method ... ok
test_less_than_or_equal_comparison_of_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
test_less_than_or_equal_comparison_without_alphabet (test_seq.TestMutableSeq) ... ok
test_mutableseq_creation (test_seq.TestMutableSeq)
Test creating MutableSeqs in multiple ways ... ok
test_not_equal_comparison (test_seq.TestMutableSeq)
Test __ne__ comparison method ... ok
test_popping_last_item (test_seq.TestMutableSeq) ... ok
test_radd_method (test_seq.TestMutableSeq) ... ok
test_radd_method_incompatible_alphabets (test_seq.TestMutableSeq) ... ok
test_radd_method_using_seq_object (test_seq.TestMutableSeq) ... ok
test_radd_method_wrong_type (test_seq.TestMutableSeq) ... ok
test_remove_items (test_seq.TestMutableSeq) ... ok
test_repr (test_seq.TestMutableSeq) ... ok
test_reverse (test_seq.TestMutableSeq)
Test using reverse method ... ok
test_reverse_complement (test_seq.TestMutableSeq) ... ok
test_reverse_complement_of_protein (test_seq.TestMutableSeq) ... ok
test_reverse_with_stride (test_seq.TestMutableSeq)
Test reverse using -1 stride ... ok
test_set_wobble_codon_to_n (test_seq.TestMutableSeq)
Test setting wobble codon to N (set slice with stride 3) ... ok
test_setting_item (test_seq.TestMutableSeq) ... ok
test_setting_slices (test_seq.TestMutableSeq) ... ok
test_to_string_method (test_seq.TestMutableSeq)
This method is currently deprecated, probably will need to remove this test soon ... ok
test_truncated_repr (test_seq.TestMutableSeq) ... ok
test_complement_on_proteins (test_seq.TestReverseComplement)
Test complement shouldn't work on a protein! ... ok
test_reverse_complement (test_seq.TestReverseComplement) ... ok
test_reverse_complement_of_dna (test_seq.TestReverseComplement) ... ok
test_reverse_complement_of_mixed_dna_rna (test_seq.TestReverseComplement) ... ok
test_reverse_complement_of_rna (test_seq.TestReverseComplement) ... ok
test_reverse_complement_on_proteins (test_seq.TestReverseComplement)
Test reverse complement shouldn't work on a protein! ... ok
test_alphabet (test_seq.TestSeq)
Test alphabet of derived Seq object ... ok
test_alphabet_letters (test_seq.TestSeq)
Test nucleotides in DNA Seq ... ok
test_as_string (test_seq.TestSeq)
Test converting Seq to string ... ok
test_concatenation_error (test_seq.TestSeq)
Test DNA Seq objects cannot be concatenated with Protein Seq ... ok
test_concatenation_of_ambiguous_and_unambiguous_dna (test_seq.TestSeq)
Test concatenated Seq object with ambiguous and unambiguous DNA ... ok
test_concatenation_of_seq (test_seq.TestSeq) ... ok
test_construction_using_a_seq_object (test_seq.TestSeq)
Test using a Seq object to initialize another Seq object ... ok
test_extract_third_nucleotide (test_seq.TestSeq)
Test extracting every third nucleotide (slicing with stride 3) ... ok
test_first_nucleotide (test_seq.TestSeq)
Test getting first nucleotide of Seq ... ok
test_last_nucleotide (test_seq.TestSeq)
Test getting last nucleotide of Seq ... ok
test_length (test_seq.TestSeq)
Test len method on Seq object ... ok
test_length_concatenated_unambiguous_seq (test_seq.TestSeq)
Test length of concatenated Seq object with unambiguous DNA ... ok
test_repr (test_seq.TestSeq)
Test representation of Seq object ... ok
test_reverse (test_seq.TestSeq)
Test reverse using -1 stride ... ok
test_slicing (test_seq.TestSeq)
Test slicing of Seq ... ok
test_truncated_repr (test_seq.TestSeq) ... ok
test_ungap (test_seq.TestSeq) ... ok
test_adding_generic_nucleotide_with_other_nucleotides (test_seq.TestSeqAddition) ... ok
test_addition_dna_rna_with_generic_nucleotides (test_seq.TestSeqAddition) ... ok
test_addition_dna_with_dna (test_seq.TestSeqAddition) ... ok
test_addition_dna_with_rna (test_seq.TestSeqAddition) ... ok
test_addition_proteins (test_seq.TestSeqAddition) ... ok
test_addition_rna_with_rna (test_seq.TestSeqAddition) ... ok
test_exception_when_added_protein_has_more_than_one_gap_type (test_seq.TestSeqAddition)
Test resulting protein has gap types '-' and '.' ... ok
test_exception_when_added_protein_has_more_than_one_stop_codon_type (test_seq.TestSeqAddition)
Test resulting protein has stop codon types '*' and '@' ... ok
test_exception_when_added_rna_has_more_than_one_gap_type (test_seq.TestSeqAddition)
Test resulting sequence has gap types '-' and '.' ... ok
test_exception_when_adding_protein_with_nucletides (test_seq.TestSeqAddition) ... ok
test_add_method_using_wrong_object (test_seq.TestSeqStringMethods) ... ok
test_append_nucleotides (test_seq.TestSeqStringMethods) ... ok
test_append_proteins (test_seq.TestSeqStringMethods) ... ok
test_contains_method (test_seq.TestSeqStringMethods) ... ok
test_counting_characters (test_seq.TestSeqStringMethods) ... ok
test_endswith (test_seq.TestSeqStringMethods) ... ok
test_equal_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
Test __eq__ comparison method ... ok
test_exception_when_clashing_alphabets (test_seq.TestSeqStringMethods)
Test by setting up clashing alphabet sequences ... ok
test_finding_characters (test_seq.TestSeqStringMethods) ... ok
test_hash (test_seq.TestSeqStringMethods) ... ok
test_less_than_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
Test __lt__ comparison method ... ok
test_less_than_or_equal_comparison_of_incompatible_alphabets (test_seq.TestSeqStringMethods)
Test __lt__ comparison method ... ok
test_not_equal_comparsion (test_seq.TestSeqStringMethods)
Test __ne__ comparison method ... ok
test_radd_method (test_seq.TestSeqStringMethods) ... ok
test_radd_method_using_incompatible_alphabets (test_seq.TestSeqStringMethods) ... ok
test_radd_method_using_wrong_object (test_seq.TestSeqStringMethods) ... ok
test_splits (test_seq.TestSeqStringMethods) ... ok
test_startswith (test_seq.TestSeqStringMethods) ... ok
test_string_methods (test_seq.TestSeqStringMethods) ... ok
test_stripping_characters (test_seq.TestSeqStringMethods) ... ok
test_to_string_deprecated_method (test_seq.TestSeqStringMethods) ... ok
test_sequence_alphabets (test_seq.TestSequenceAlphabets)
Sanity test on the test sequence alphabets (see also enhancement ... ok
test_stops (test_seq.TestStopCodons) ... ok
test_translation_of_stops (test_seq.TestStopCodons) ... ok
test_back_transcribe_rna_into_dna (test_seq.TestTranscription) ... ok
test_back_transcribe_rna_string_into_dna (test_seq.TestTranscription) ... ok
test_back_transcription_of_dna (test_seq.TestTranscription)
Test back-transcription shouldn't work on DNA! ... ok
test_back_transcription_of_proteins (test_seq.TestTranscription)
Test back-transcription shouldn't work on a protein! ... ok
test_seq_object_back_transcription_method (test_seq.TestTranscription) ... ok
test_seq_object_transcription_method (test_seq.TestTranscription) ... ok
test_transcription_dna_into_rna (test_seq.TestTranscription) ... ok
test_transcription_dna_string_into_rna (test_seq.TestTranscription) ... ok
test_transcription_of_proteins (test_seq.TestTranscription)
Test transcription shouldn't work on a protein! ... ok
test_transcription_of_rna (test_seq.TestTranscription)
Test transcription shouldn't work on RNA! ... ok
test_translation (test_seq.TestTranslating) ... ok
test_translation_extra_stop_codon (test_seq.TestTranslating) ... ok
test_translation_incomplete_codon (test_seq.TestTranslating) ... ok
test_translation_of_asparagine (test_seq.TestTranslating) ... ok
test_translation_of_glutamine (test_seq.TestTranslating) ... ok
test_translation_of_invalid_codon (test_seq.TestTranslating) ... ok
test_translation_of_leucine (test_seq.TestTranslating) ... ok
test_translation_of_string (test_seq.TestTranslating) ... ok
test_translation_on_proteins (test_seq.TestTranslating)
Test translation shouldn't work on a protein! ... ok
test_translation_to_stop (test_seq.TestTranslating) ... ok
test_translation_using_cds (test_seq.TestTranslating) ... ok
test_translation_with_bad_table_argument (test_seq.TestTranslating) ... ok
test_translation_with_codon_table_as_table_argument (test_seq.TestTranslating) ... ok
test_translation_wrong_type (test_seq.TestTranslating)
Test translation table cannot be CodonTable ... ok
test_add_method (test_seq.TestUnknownSeq) ... ok
test_back_transcribe (test_seq.TestUnknownSeq) ... ok
test_complement (test_seq.TestUnknownSeq) ... ok
test_complement_of_protein (test_seq.TestUnknownSeq)
Test reverse complement shouldn't work on a protein! ... ok
test_construction (test_seq.TestUnknownSeq) ... ok
test_count (test_seq.TestUnknownSeq) ... ok
test_getitem_method (test_seq.TestUnknownSeq) ... ok
test_length (test_seq.TestUnknownSeq) ... ok
test_lower (test_seq.TestUnknownSeq) ... ok
test_repr (test_seq.TestUnknownSeq) ... ok
test_reverse_complement (test_seq.TestUnknownSeq) ... ok
test_reverse_complement_of_protein (test_seq.TestUnknownSeq) ... ok
test_transcribe (test_seq.TestUnknownSeq) ... ok
test_translation (test_seq.TestUnknownSeq) ... ok
test_translation_of_proteins (test_seq.TestUnknownSeq) ... ok
test_ungap (test_seq.TestUnknownSeq) ... ok
test_upper (test_seq.TestUnknownSeq) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.137 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_translate.py
test_translate ... ok
runTest (__main__.ComparisonTestCase)
test_translate ... ok
----------------------------------------------------------------------
Ran 1 test in 0.078 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ for test in '`ls test_*.py | grep -v Tutorial`'
+ /usr/bin/python2 run_tests.py --offline -v test_trie.py
test_trie ... ok
test_get_approximate (test_trie.TestTrie) ... ok
test_get_set (test_trie.TestTrie) ... ok
test_prefix (test_trie.TestTrie) ... ok
test_save (test_trie.TestTrie) ... ok
test_with_prefix (test_trie.TestTrie) ... ok
test_find (test_trie.TestTrieFind) ... ok
----------------------------------------------------------------------
Ran 1 test in 0.008 seconds
Skipping any tests requiring internet access
Python version: 2.7.5 (default, Nov 20 2015, 01:24:18) 
[GCC 4.8.5 20150623 (Red Hat 4.8.5-4)]
Operating system: posix linux2
+ popd
~/build/BUILD/python-biopython-1.66
+ exit 0
Processing files: python-biopython-1.66-3.el7.i686
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.pop00L
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.66
+ DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/share/doc/python-biopython-1.66
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/share/doc/python-biopython-1.66
+ cp -pr python2/Scripts /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/share/doc/python-biopython-1.66
+ cp -pr python2/CONTRIB /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/share/doc/python-biopython-1.66
+ cp -pr python2/DEPRECATED /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/share/doc/python-biopython-1.66
+ cp -pr python2/NEWS /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/share/doc/python-biopython-1.66
+ cp -pr python2/README /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/share/doc/python-biopython-1.66
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.o1Wc4w
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.66
+ LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/share/licenses/python-biopython-1.66
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/share/licenses/python-biopython-1.66
+ cp -pr python2/LICENSE /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/share/licenses/python-biopython-1.66
+ exit 0
Provides: python-biopython = 1.66-3.el7 python-biopython(x86-32) = 1.66-3.el7
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.4) libpthread.so.0 libpython2.7.so.1.0 python(abi) = 2.7 rtld(GNU_HASH)
Processing files: python-biopython-doc-1.66-3.el7.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.zAH4FG
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.66
+ DOCDIR=/builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/share/doc/python-biopython-doc-1.66
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/share/doc/python-biopython-doc-1.66
+ cp -pr python2/Doc /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/share/doc/python-biopython-doc-1.66
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.qOqYlQ
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.66
+ LICENSEDIR=/builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/share/licenses/python-biopython-doc-1.66
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/share/licenses/python-biopython-doc-1.66
+ cp -pr python2/LICENSE /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/share/licenses/python-biopython-doc-1.66
+ exit 0
warning: Recognition of file "/builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386/usr/share/doc/python-biopython-doc-1.66/Doc/examples/ls_orchid.gbk.bgz" failed: mode 100644 zlib: invalid distance too far backempty (gzip compressed data, extra field)
Provides: python-biopython-doc = 1.66-3.el7
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: python-biopython-debuginfo-1.66-3.el7.i686
Provides: python-biopython-debuginfo = 1.66-3.el7 python-biopython-debuginfo(x86-32) = 1.66-3.el7
Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386
warning: Could not canonicalize hostname: worker1.bsys.centos.org
Wrote: /builddir/build/RPMS/python-biopython-1.66-3.el7.i686.rpm
Wrote: /builddir/build/RPMS/python-biopython-doc-1.66-3.el7.noarch.rpm
Wrote: /builddir/build/RPMS/python-biopython-debuginfo-1.66-3.el7.i686.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.sqyMUS
+ umask 022
+ cd /builddir/build/BUILD
+ cd python-biopython-1.66
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/python-biopython-1.66-3.el7.i386
+ exit 0
Child return code was: 0
LEAVE do -->