[med-svn] [python-biopython] branch upstream updated (9511db1 -> d029800)
Andreas Tille
tille at debian.org
Tue Dec 19 11:02:18 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository python-biopython.
from 9511db1 Imported Upstream version 1.68+dfsg
new d029800 New upstream version 1.70+dfsg
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.appveyor.yml | 48 +
.codecov.yml | 2 +-
.gitignore | 7 +
.travis-tox.ini | 75 +-
.travis.yml | 88 +-
Bio/.flake8 | 58 +
Bio/Affy/CelFile.py | 257 +-
Bio/Affy/__init__.py | 3 +-
Bio/Align/AlignInfo.py | 251 +-
Bio/Align/Applications/_ClustalOmega.py | 6 +-
Bio/Align/Applications/_Clustalw.py | 4 +-
Bio/Align/Applications/_Dialign.py | 4 +-
Bio/Align/Applications/_MSAProbs.py | 3 +-
Bio/Align/Applications/_Mafft.py | 9 +-
Bio/Align/Applications/_Muscle.py | 486 +-
Bio/Align/Applications/_Prank.py | 9 +-
Bio/Align/Applications/_Probcons.py | 4 +-
Bio/Align/Applications/_TCoffee.py | 1 +
Bio/Align/Applications/__init__.py | 4 +-
Bio/Align/Generic.py | 452 -
Bio/Align/__init__.py | 308 +-
Bio/AlignIO/ClustalIO.py | 8 +-
Bio/AlignIO/EmbossIO.py | 22 +-
Bio/AlignIO/FastaIO.py | 21 +-
Bio/AlignIO/Interfaces.py | 49 +-
Bio/AlignIO/MafIO.py | 718 +
Bio/AlignIO/MauveIO.py | 321 +
Bio/AlignIO/NexusIO.py | 94 +-
Bio/AlignIO/PhylipIO.py | 22 +-
Bio/AlignIO/StockholmIO.py | 107 +-
Bio/AlignIO/__init__.py | 90 +-
Bio/Alphabet/IUPAC.py | 41 +-
Bio/Alphabet/Reduced.py | 12 +
Bio/Alphabet/__init__.py | 26 +-
Bio/Application/__init__.py | 95 +-
Bio/Blast/Applications.py | 31 +
Bio/Blast/NCBIStandalone.py | 24 +-
Bio/Blast/NCBIXML.py | 156 +-
Bio/Blast/ParseBlastTable.py | 1 +
Bio/Blast/Record.py | 10 +
Bio/CAPS/__init__.py | 6 +-
Bio/Cluster/__init__.py | 523 +-
Bio/Compass/__init__.py | 1 +
Bio/Crystal/__init__.py | 8 +-
Bio/Data/CodonTable.py | 4 +-
Bio/Data/IUPACData.py | 3 +
Bio/DocSQL.py | 15 +-
Bio/Emboss/Applications.py | 23 +-
Bio/Emboss/Primer3.py | 5 +-
Bio/Emboss/PrimerSearch.py | 15 +-
Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd | 280 +
Bio/Entrez/Parser.py | 20 +-
Bio/Entrez/__init__.py | 53 +-
Bio/ExPASy/Enzyme.py | 32 +-
Bio/ExPASy/Prodoc.py | 24 +-
Bio/ExPASy/Prosite.py | 141 +-
Bio/ExPASy/ScanProsite.py | 2 +-
Bio/ExPASy/__init__.py | 111 +-
Bio/ExPASy/cellosaurus.py | 164 +
Bio/FSSP/FSSPTools.py | 6 +-
Bio/FSSP/__init__.py | 15 +-
Bio/FSSP/fssp_rec.py | 1 +
Bio/File.py | 119 +-
Bio/GA/Crossover/General.py | 15 +-
Bio/GA/Crossover/GeneralPoint.py | 77 +-
Bio/GA/Crossover/Point.py | 4 +-
Bio/GA/Crossover/TwoPoint.py | 15 +-
Bio/GA/Crossover/Uniform.py | 8 +-
Bio/GA/Evolver.py | 24 +-
Bio/GA/Mutation/General.py | 20 +-
Bio/GA/Mutation/Simple.py | 30 +-
Bio/GA/Organism.py | 95 +-
Bio/GA/Repair/Stabilizing.py | 19 +-
Bio/GA/Selection/Abstract.py | 22 +-
Bio/GA/Selection/Diversity.py | 15 +-
Bio/GA/Selection/RouletteWheel.py | 34 +-
Bio/GA/Selection/Tournament.py | 18 +-
Bio/GA/__init__.py | 16 +-
Bio/GenBank/Record.py | 245 +-
Bio/GenBank/Scanner.py | 330 +-
Bio/GenBank/__init__.py | 269 +-
Bio/GenBank/utils.py | 10 +-
Bio/Geo/Record.py | 1 +
Bio/Graphics/BasicChromosome.py | 126 +-
Bio/Graphics/ColorSpiral.py | 17 +-
Bio/Graphics/Comparative.py | 8 +-
Bio/Graphics/DisplayRepresentation.py | 31 +-
Bio/Graphics/Distribution.py | 13 +-
Bio/Graphics/GenomeDiagram/_AbstractDrawer.py | 191 +-
Bio/Graphics/GenomeDiagram/_CircularDrawer.py | 318 +-
Bio/Graphics/GenomeDiagram/_Colors.py | 155 +-
Bio/Graphics/GenomeDiagram/_CrossLink.py | 19 +-
Bio/Graphics/GenomeDiagram/_Diagram.py | 130 +-
Bio/Graphics/GenomeDiagram/_Feature.py | 197 +-
Bio/Graphics/GenomeDiagram/_FeatureSet.py | 16 +-
Bio/Graphics/GenomeDiagram/_Graph.py | 180 +-
Bio/Graphics/GenomeDiagram/_GraphSet.py | 157 +-
Bio/Graphics/GenomeDiagram/_LinearDrawer.py | 428 +-
Bio/Graphics/GenomeDiagram/_Track.py | 331 +-
Bio/Graphics/KGML_vis.py | 26 +-
Bio/Graphics/__init__.py | 2 +-
Bio/HMM/DynamicProgramming.py | 78 +-
Bio/HMM/MarkovModel.py | 100 +-
Bio/HMM/Trainer.py | 139 +-
Bio/HMM/Utilities.py | 10 +-
Bio/Index.py | 7 +-
Bio/KDTree/KDTree.py | 4 +
Bio/KEGG/Compound/__init__.py | 1 +
Bio/KEGG/Enzyme/__init__.py | 4 +-
Bio/KEGG/KGML/KGML_parser.py | 87 +-
Bio/KEGG/KGML/KGML_pathway.py | 116 +-
Bio/KEGG/KGML/__init__.py | 5 +-
Bio/KEGG/Map/__init__.py | 12 +-
Bio/KEGG/REST.py | 2 +-
Bio/KEGG/__init__.py | 18 +-
Bio/LogisticRegression.py | 1 +
Bio/MarkovModel.py | 66 +-
Bio/MaxEntropy.py | 158 +-
Bio/Medline/__init__.py | 2 +
Bio/NMR/NOEtools.py | 2 +-
Bio/NMR/xpktools.py | 11 +-
Bio/NaiveBayes.py | 70 +-
Bio/NeuralNetwork/BackPropagation/Layer.py | 89 +-
Bio/NeuralNetwork/BackPropagation/Network.py | 43 +-
Bio/NeuralNetwork/Gene/Motif.py | 41 +-
Bio/NeuralNetwork/Gene/Pattern.py | 56 +-
Bio/NeuralNetwork/Gene/Schema.py | 200 +-
Bio/NeuralNetwork/Gene/Signature.py | 46 +-
Bio/NeuralNetwork/StopTraining.py | 18 +-
Bio/NeuralNetwork/Training.py | 48 +-
Bio/NeuralNetwork/__init__.py | 15 +-
Bio/Nexus/Nexus.py | 125 +-
Bio/Nexus/StandardData.py | 18 +-
Bio/Nexus/Trees.py | 45 +-
Bio/PDB/AbstractPropertyMap.py | 17 +-
Bio/PDB/Atom.py | 10 +-
Bio/PDB/Chain.py | 30 +-
Bio/PDB/DSSP.py | 151 +-
Bio/PDB/Dice.py | 22 +-
Bio/PDB/Entity.py | 126 +-
Bio/PDB/FragmentMapper.py | 95 +-
Bio/PDB/HSExposure.py | 87 +-
Bio/PDB/MMCIF2Dict.py | 38 +-
Bio/PDB/MMCIFParser.py | 47 +-
Bio/PDB/Model.py | 14 +-
Bio/PDB/NeighborSearch.py | 8 +-
Bio/PDB/PDBIO.py | 33 +-
Bio/PDB/PDBList.py | 321 +-
Bio/PDB/PDBParser.py | 27 +-
Bio/PDB/PSEA.py | 4 +-
Bio/PDB/Polypeptide.py | 40 +-
Bio/PDB/QCPSuperimposer/__init__.py | 80 +-
Bio/PDB/Residue.py | 39 +-
Bio/PDB/ResidueDepth.py | 479 +-
Bio/PDB/Selection.py | 15 +-
Bio/PDB/Structure.py | 8 +-
Bio/PDB/StructureAlignment.py | 68 +-
Bio/PDB/StructureBuilder.py | 70 +-
Bio/PDB/Superimposer.py | 39 +-
Bio/PDB/Vector.py | 169 +-
Bio/PDB/mmtf/DefaultParser.py | 38 +-
Bio/PDB/mmtf/__init__.py | 7 +-
Bio/PDB/parse_pdb_header.py | 23 +-
Bio/ParserSupport.py | 55 +-
Bio/Pathway/__init__.py | 47 +-
Bio/Phylo/Applications/__init__.py | 4 +-
Bio/Phylo/BaseTree.py | 41 +-
Bio/Phylo/CDAO.py | 2 +
Bio/Phylo/CDAOIO.py | 29 +-
Bio/Phylo/Consensus.py | 26 +-
Bio/Phylo/NeXML.py | 2 +
Bio/Phylo/NeXMLIO.py | 11 +-
Bio/Phylo/Newick.py | 2 +
Bio/Phylo/NewickIO.py | 12 +-
Bio/Phylo/NexusIO.py | 2 +-
Bio/Phylo/PAML/_paml.py | 61 +-
Bio/Phylo/PAML/_parse_baseml.py | 18 +-
Bio/Phylo/PAML/_parse_codeml.py | 53 +-
Bio/Phylo/PAML/_parse_yn00.py | 29 +-
Bio/Phylo/PAML/baseml.py | 16 +-
Bio/Phylo/PAML/codeml.py | 19 +-
Bio/Phylo/PAML/yn00.py | 12 +-
Bio/Phylo/PhyloXML.py | 79 +-
Bio/Phylo/PhyloXMLIO.py | 20 +-
Bio/Phylo/TreeConstruction.py | 116 +-
Bio/Phylo/__init__.py | 3 +-
Bio/Phylo/_cdao_owl.py | 3 +-
Bio/Phylo/_io.py | 2 +-
Bio/Phylo/_utils.py | 17 +-
Bio/PopGen/Async/Local.py | 65 -
Bio/PopGen/Async/__init__.py | 122 -
Bio/PopGen/FDist/Async.py | 180 -
Bio/PopGen/FDist/Controller.py | 297 -
Bio/PopGen/FDist/Utils.py | 214 -
Bio/PopGen/FDist/__init__.py | 93 -
Bio/PopGen/GenePop/Controller.py | 104 +-
Bio/PopGen/GenePop/EasyController.py | 45 +-
Bio/PopGen/GenePop/FileParser.py | 81 +-
Bio/PopGen/GenePop/LargeFileParser.py | 12 +-
Bio/PopGen/GenePop/__init__.py | 37 +-
Bio/PopGen/SimCoal/Async.py | 31 -
Bio/PopGen/SimCoal/Cache.py | 86 -
Bio/PopGen/SimCoal/Controller.py | 222 -
Bio/PopGen/SimCoal/Template.py | 228 -
Bio/PopGen/SimCoal/__init__.py | 26 -
Bio/PopGen/SimCoal/data/bottle.par | 14 -
Bio/PopGen/SimCoal/data/decline_lambda.par | 14 -
Bio/PopGen/SimCoal/data/decline_split.par | 23 -
Bio/PopGen/SimCoal/data/island.par | 14 -
Bio/PopGen/SimCoal/data/simple.par | 12 -
Bio/PopGen/SimCoal/data/split_island.par | 17 -
Bio/PopGen/SimCoal/data/split_ssm_1d.par | 17 -
Bio/PopGen/SimCoal/data/split_ssm_2d.par | 17 -
Bio/PopGen/SimCoal/data/ssm_1d.par | 14 -
Bio/PopGen/SimCoal/data/ssm_2d.par | 14 -
Bio/Restriction/PrintFormat.py | 38 +-
Bio/Restriction/Restriction.py | 1132 +-
Bio/Restriction/Restriction_Dictionary.py | 20115 ++++----
Bio/Restriction/__init__.py | 4 +-
Bio/SCOP/Cla.py | 10 +-
Bio/SCOP/Des.py | 6 +-
Bio/SCOP/Dom.py | 7 +-
Bio/SCOP/Hie.py | 5 +-
Bio/SCOP/Raf.py | 57 +-
Bio/SCOP/__init__.py | 160 +-
Bio/SVDSuperimposer/__init__.py | 110 +-
Bio/SearchIO/BlastIO/__init__.py | 16 +-
Bio/SearchIO/BlastIO/blast_tab.py | 14 +-
Bio/SearchIO/BlastIO/blast_text.py | 3 +-
Bio/SearchIO/BlastIO/blast_xml.py | 142 +-
Bio/SearchIO/BlatIO.py | 27 +-
Bio/SearchIO/ExonerateIO/_base.py | 128 +-
Bio/SearchIO/ExonerateIO/exonerate_cigar.py | 8 +-
Bio/SearchIO/ExonerateIO/exonerate_text.py | 21 +-
Bio/SearchIO/ExonerateIO/exonerate_vulgar.py | 4 +-
Bio/SearchIO/FastaIO.py | 17 +-
Bio/SearchIO/HmmerIO/_base.py | 6 +-
Bio/SearchIO/HmmerIO/hmmer2_text.py | 5 +-
Bio/SearchIO/HmmerIO/hmmer3_domtab.py | 29 +-
Bio/SearchIO/HmmerIO/hmmer3_tab.py | 8 +-
Bio/SearchIO/HmmerIO/hmmer3_text.py | 15 +-
Bio/SearchIO/__init__.py | 2 +-
Bio/SearchIO/_index.py | 10 +-
Bio/SearchIO/_model/__init__.py | 2 +-
Bio/SearchIO/_model/_base.py | 2 -
Bio/SearchIO/_model/hit.py | 1 -
Bio/SearchIO/_model/hsp.py | 3 +-
Bio/SearchIO/_model/query.py | 17 +-
Bio/SearchIO/_utils.py | 6 +-
Bio/Seq.py | 677 +-
Bio/SeqFeature.py | 372 +-
Bio/SeqIO/AbiIO.py | 63 +-
Bio/SeqIO/FastaIO.py | 7 +-
Bio/SeqIO/IgIO.py | 1 +
Bio/SeqIO/InsdcIO.py | 183 +-
Bio/SeqIO/Interfaces.py | 63 +-
Bio/SeqIO/PirIO.py | 21 +-
Bio/SeqIO/QualityIO.py | 40 +-
Bio/SeqIO/SeqXmlIO.py | 29 +-
Bio/SeqIO/SffIO.py | 273 +-
Bio/SeqIO/SwissIO.py | 5 +
Bio/SeqIO/TabIO.py | 3 +-
Bio/SeqIO/UniprotIO.py | 76 +-
Bio/SeqIO/__init__.py | 122 +-
Bio/SeqIO/_index.py | 172 +-
Bio/SeqRecord.py | 74 +-
Bio/SeqUtils/CheckSum.py | 1 +
Bio/SeqUtils/CodonUsage.py | 1 -
Bio/SeqUtils/MeltingTemp.py | 14 +-
Bio/SeqUtils/ProtParam.py | 3 +-
Bio/SeqUtils/ProtParamData.py | 2 +-
Bio/SeqUtils/__init__.py | 50 +-
Bio/SeqUtils/lcc.py | 3 +-
Bio/Sequencing/Ace.py | 22 +-
Bio/Sequencing/Applications/_Novoalign.py | 1 +
Bio/Sequencing/Applications/__init__.py | 12 +-
Bio/Sequencing/Applications/_bwa.py | 9 +-
Bio/Sequencing/Applications/_samtools.py | 87 +-
Bio/Sequencing/Phd.py | 5 +-
Bio/Statistics/lowess.py | 14 +-
Bio/SubsMat/FreqTable.py | 4 +-
Bio/SubsMat/MatrixInfo.py | 80 +
Bio/SubsMat/__init__.py | 116 +-
Bio/SwissProt/KeyWList.py | 18 +-
Bio/SwissProt/__init__.py | 142 +-
Bio/TogoWS/__init__.py | 72 +-
Bio/UniGene/__init__.py | 38 +-
Bio/UniProt/GOA.py | 232 +-
Bio/Wise/__init__.py | 11 +-
Bio/Wise/dnal.py | 13 +-
Bio/Wise/psw.py | 12 +-
Bio/__init__.py | 16 +-
Bio/_py3k/__init__.py | 97 +-
Bio/_py3k/_ordereddict.py | 129 -
Bio/_utils.py | 4 +-
Bio/bgzf.py | 27 +-
Bio/codonalign/__init__.py | 99 +-
Bio/codonalign/chisq.py | 256 +-
Bio/codonalign/codonalignment.py | 90 +-
Bio/codonalign/codonalphabet.py | 24 +-
Bio/codonalign/codonseq.py | 83 +-
Bio/kNN.py | 34 +-
Bio/motifs/__init__.py | 40 +-
Bio/motifs/alignace.py | 5 +-
Bio/motifs/applications/_xxmotif.py | 2 +-
Bio/motifs/jaspar/__init__.py | 5 +-
Bio/motifs/jaspar/db.py | 71 +-
Bio/motifs/mast.py | 1 +
Bio/motifs/matrix.py | 73 +-
Bio/motifs/meme.py | 20 +-
Bio/motifs/thresholds.py | 18 +-
Bio/motifs/transfac.py | 186 +-
Bio/pairwise2.py | 199 +-
Bio/phenotype/__init__.py | 1 -
Bio/phenotype/phen_micro.py | 29 +-
Bio/phenotype/pm_fitting.py | 6 +-
Bio/trie.c | 18 +-
Bio/triefind.py | 5 +-
Bio/triemodule.c | 6 +
BioSQL/.flake8 | 15 +
BioSQL/BioSeq.py | 48 +-
BioSQL/BioSeqDatabase.py | 184 +-
BioSQL/DBUtils.py | 27 +-
BioSQL/Loader.py | 154 +-
BioSQL/__init__.py | 10 +-
CONTRIB | 162 +-
CONTRIB.rst | 214 +
CONTRIBUTING.rst | 113 +
DEPRECATED | 692 +-
DEPRECATED => DEPRECATED.rst | 143 +-
Doc/Tutorial.tex | 8 +-
Doc/Tutorial/chapter_align.tex | 2 +-
Doc/Tutorial/chapter_appendix.tex | 5 +-
Doc/Tutorial/chapter_blast.tex | 6 +-
Doc/Tutorial/chapter_cluster.tex | 34 +-
Doc/Tutorial/chapter_cookbook.tex | 184 +-
Doc/Tutorial/chapter_entrez.tex | 253 +-
Doc/Tutorial/chapter_graphics.tex | 6 +-
Doc/Tutorial/chapter_introduction.tex | 38 +-
Doc/Tutorial/chapter_kegg.tex | 15 +
Doc/Tutorial/chapter_motifs.tex | 18 +-
Doc/Tutorial/chapter_pdb.tex | 17 +-
Doc/Tutorial/chapter_phenotype.tex | 2 +-
Doc/Tutorial/chapter_phylo.tex | 2 +-
Doc/Tutorial/chapter_popgen.tex | 5 +-
Doc/Tutorial/chapter_searchio.tex | 12 +-
Doc/Tutorial/chapter_seq_annot.tex | 12 +-
Doc/Tutorial/chapter_seqio.tex | 154 +-
Doc/Tutorial/chapter_uniprot.tex | 25 +-
Doc/biopdb_faq.tex | 4 +-
Doc/examples/.flake8 | 14 +
Doc/examples/Proux_et_al_2002_Figure_6.py | 3 +-
Doc/examples/clustal_run.py | 5 +-
Doc/examples/ec_5.4.2.2.txt | 3636 ++
Doc/examples/fasta_iterator.py | 1 +
Doc/examples/getgene.py | 7 +-
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Doc/examples/make_subsmat.py | 3 +-
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LICENSE | 20 +-
LICENSE.rst | 68 +
MANIFEST.in | 17 +-
NEWS | 1915 +-
NEWS => NEWS.rst | 1383 +-
README | 261 +-
README.rst | 295 +-
Scripts/.flake8 | 27 +
Scripts/GenBank/check_output.py | 1 +
Scripts/Performance/biosql_performance_load.py | 4 +-
Scripts/Performance/biosql_performance_read.py | 4 +-
Scripts/Restriction/ranacompiler.py | 86 +-
Scripts/Restriction/rebase_update.py | 12 +-
Scripts/SeqGui/SeqGui.py | 1 +
Scripts/debug/debug_blast_parser.py | 14 +-
Scripts/query_pubmed.py | 1 +
Scripts/scop_pdb.py | 1 +
Scripts/xbbtools/nextorf.py | 17 +-
Scripts/xbbtools/xbb_blast.py | 2 +-
Scripts/xbbtools/xbb_blastbg.py | 3 +-
Scripts/xbbtools/xbb_translations.py | 3 +-
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Tests/Cluster/cyano.txt | 91 +
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Tests/run_tests.py | 111 +-
Tests/search_tests_common.py | 10 +-
Tests/seq_tests_common.py | 11 +-
Tests/test_Affy.py | 192 +
Tests/test_AlignIO.py | 71 +-
Tests/test_AlignIO_ClustalIO.py | 7 +-
Tests/test_AlignIO_EmbossIO.py | 6 +-
Tests/test_AlignIO_MauveIO.py | 111 +
Tests/test_AlignIO_convert.py | 1 +
Tests/test_AlignInfo.py | 36 +-
Tests/test_BWA_tool.py | 4 +-
Tests/test_BioSQL_MySQLdb.py | 6 +-
Tests/test_BioSQL_MySQLdb_online.py | 6 +-
Tests/test_BioSQL_mysql_connector.py | 6 +-
Tests/test_BioSQL_mysql_connector_online.py | 6 +-
Tests/test_BioSQL_psycopg2.py | 6 +-
Tests/test_BioSQL_psycopg2_online.py | 6 +-
Tests/test_BioSQL_sqlite3.py | 9 +-
Tests/test_BioSQL_sqlite3_online.py | 5 +-
Tests/test_CelFile.py | 6 +-
Tests/test_Chi2.py | 1 +
Tests/test_ClustalOmega_tool.py | 4 +-
Tests/test_Clustalw_tool.py | 2 +-
Tests/test_Cluster.py | 15 +-
Tests/test_ColorSpiral.py | 4 +-
Tests/test_Compass.py | 1 +
Tests/test_Consensus.py | 9 +-
Tests/test_Crystal.py | 12 +-
Tests/test_DSSP_tool.py | 39 +-
Tests/test_DocSQL.py | 6 +-
Tests/test_Emboss.py | 4 +-
Tests/test_EmbossPhylipNew.py | 1 +
Tests/test_EmbossPrimer.py | 10 +-
Tests/test_Entrez.py | 30 +-
Tests/test_Entrez_online.py | 83 +-
Tests/test_Entrez_parser.py | 19 +-
Tests/test_Enzyme.py | 29 +
Tests/test_ExPASy.py | 58 +
Tests/test_GACrossover.py | 19 +-
Tests/test_GAMutation.py | 13 +-
Tests/test_GAOrganism.py | 11 +-
Tests/test_GAQueens.py | 79 +-
Tests/test_GARepair.py | 11 +-
Tests/test_GASelection.py | 12 +-
Tests/test_GenBank.py | 82 +-
Tests/test_GenBank_unittest.py | 156 +-
Tests/test_GenomeDiagram.py | 20 +-
Tests/test_GraphicsBitmaps.py | 9 +-
Tests/test_GraphicsChromosome.py | 4 +-
Tests/test_GraphicsDistribution.py | 5 +-
Tests/test_GraphicsGeneral.py | 60 +-
Tests/test_HMMCasino.py | 6 +-
Tests/test_HMMGeneral.py | 6 +-
Tests/test_KDTree.py | 2 +
Tests/test_KEGG.py | 170 +-
Tests/test_KEGG_online.py | 11 +-
Tests/test_KGML_graphics.py | 2 -
Tests/test_KGML_graphics_online.py | 2 -
Tests/test_KGML_nographics.py | 18 +-
Tests/test_KeyWList.py | 1 +
Tests/test_LogisticRegression.py | 1 +
Tests/test_MafIO_index.py | 426 +
Tests/test_Mafft_tool.py | 35 +-
Tests/test_MarkovModel.py | 265 +-
Tests/test_Muscle_tool.py | 9 +-
Tests/test_NCBITextParser.py | 2 +-
Tests/test_NCBI_BLAST_tools.py | 6 +-
Tests/test_NCBI_qblast.py | 14 +-
Tests/test_NNExclusiveOr.py | 13 +-
Tests/test_NNGene.py | 23 +-
Tests/test_NNGeneral.py | 11 +-
Tests/test_NaiveBayes.py | 10 +
Tests/test_Nexus.py | 161 +-
Tests/test_PAML_baseml.py | 43 +-
Tests/test_PAML_codeml.py | 149 +-
Tests/test_PAML_tools.py | 16 +-
Tests/test_PAML_yn00.py | 29 +-
Tests/test_PDB.py | 315 +-
Tests/test_PDBList.py | 117 +
Tests/test_PDB_FragmentMapper.py | 40 +
Tests/test_PDB_MMCIF2Dict.py | 38 +
Tests/{test_MMCIF.py => test_PDB_MMCIFParser.py} | 82 +
Tests/test_PDB_Polypetide.py | 69 +
Tests/test_PDB_StructureAlignment.py | 49 +
Tests/test_PDB_Superimposer.py | 113 +
Tests/test_ParserSupport.py | 4 +
Tests/test_Phd.py | 1 +
Tests/test_Phylo.py | 2 +
Tests/test_PhyloXML.py | 1 +
Tests/test_Phylo_CDAO.py | 4 +-
Tests/test_Phylo_NeXML.py | 2 +
Tests/test_Phylo_matplotlib.py | 14 +-
Tests/test_PopGen_DFDist.py | 133 -
Tests/test_PopGen_FDist.py | 128 -
Tests/test_PopGen_FDist_nodepend.py | 108 -
Tests/test_PopGen_FastSimCoal.py | 63 -
Tests/test_PopGen_GenePop.py | 1 +
Tests/test_PopGen_GenePop_EasyController.py | 7 +
Tests/test_PopGen_GenePop_nodepend.py | 82 +-
Tests/test_PopGen_SimCoal.py | 65 -
Tests/test_PopGen_SimCoal_nodepend.py | 52 -
Tests/test_Prank_tool.py | 26 +-
Tests/test_QCPSuperimposer.py | 227 +-
Tests/test_RCSBFormats.py | 1 +
Tests/test_Restriction.py | 486 +-
Tests/test_SCOP_Astral.py | 6 +-
Tests/test_SCOP_Cla.py | 2 +-
Tests/test_SCOP_Residues.py | 2 +-
Tests/test_SCOP_online.py | 1 +
Tests/test_SVDSuperimposer.py | 142 +-
Tests/test_SearchIO_blast_text.py | 2 +-
Tests/test_SearchIO_blast_xml.py | 40 +-
Tests/test_SearchIO_blast_xml_index.py | 1 -
Tests/test_SearchIO_blat_psl.py | 107 +
Tests/test_SearchIO_exonerate.py | 70 +
Tests/test_SearchIO_hmmer2_text_index.py | 12 +-
Tests/test_SearchIO_hmmer3_domtab.py | 1 +
Tests/test_SearchIO_hmmer3_text.py | 31 +
Tests/test_SearchIO_hmmer3_text_index.py | 6 +-
Tests/test_SearchIO_model.py | 60 +-
Tests/test_SearchIO_write.py | 12 +
Tests/test_SeqFeature.py | 84 +-
Tests/test_SeqIO.py | 6 +-
Tests/test_SeqIO_AbiIO.py | 43 +-
Tests/test_SeqIO_FastaIO.py | 3 +-
Tests/test_SeqIO_Insdc.py | 12 +-
Tests/test_SeqIO_PdbIO.py | 5 +-
Tests/test_SeqIO_QualityIO.py | 14 +-
Tests/test_SeqIO_SeqXML.py | 4 +-
Tests/test_SeqIO_convert.py | 6 +-
Tests/test_SeqIO_features.py | 56 +-
Tests/test_SeqIO_index.py | 52 +-
Tests/test_SeqIO_online.py | 14 +-
Tests/test_SeqIO_write.py | 25 +-
Tests/test_SeqRecord.py | 15 +-
Tests/test_SeqUtils.py | 6 +-
Tests/test_Seq_objs.py | 164 +-
Tests/test_SffIO.py | 194 +-
Tests/test_SubsMat.py | 12 +-
Tests/test_SwissProt.py | 77 +-
Tests/test_TCoffee_tool.py | 12 +-
Tests/test_TogoWS.py | 85 +-
Tests/test_TreeConstruction.py | 72 +-
Tests/test_Tutorial.py | 62 +-
Tests/test_Uniprot.py | 57 +-
Tests/test_XXmotif_tool.py | 10 +-
Tests/test_align.py | 13 +-
Tests/test_bgzf.py | 16 +-
Tests/test_cellosaurus.py | 135 +
Tests/test_codonalign.py | 35 +-
Tests/test_kNN.py | 2 +
Tests/test_lowess.py | 1 +
Tests/test_mmtf.py | 11 +-
Tests/test_mmtf_online.py | 32 +
Tests/test_motifs.py | 152 +-
Tests/test_pairwise2.py | 62 +-
Tests/test_phenotype.py | 1 +
Tests/test_phenotype_fit.py | 5 +-
Tests/test_phyml_tool.py | 16 +-
Tests/test_psw.py | 1 +
Tests/test_py3k.py | 24 -
Tests/test_raxml_tool.py | 3 +-
Tests/test_samtools_tool.py | 31 +-
Tests/test_seq.py | 463 +-
Tests/test_trie.py | 40 +-
setup.py | 304 +-
647 files changed, 120244 insertions(+), 86711 deletions(-)
create mode 100644 .appveyor.yml
create mode 100644 Bio/.flake8
delete mode 100644 Bio/Align/Generic.py
create mode 100644 Bio/AlignIO/MafIO.py
create mode 100644 Bio/AlignIO/MauveIO.py
create mode 100644 Bio/Entrez/DTDs/nlmcatalogrecordset_170601.dtd
create mode 100644 Bio/ExPASy/cellosaurus.py
delete mode 100644 Bio/PopGen/Async/Local.py
delete mode 100644 Bio/PopGen/Async/__init__.py
delete mode 100644 Bio/PopGen/FDist/Async.py
delete mode 100644 Bio/PopGen/FDist/Controller.py
delete mode 100644 Bio/PopGen/FDist/Utils.py
delete mode 100644 Bio/PopGen/FDist/__init__.py
delete mode 100644 Bio/PopGen/SimCoal/Async.py
delete mode 100644 Bio/PopGen/SimCoal/Cache.py
delete mode 100644 Bio/PopGen/SimCoal/Controller.py
delete mode 100644 Bio/PopGen/SimCoal/Template.py
delete mode 100644 Bio/PopGen/SimCoal/__init__.py
delete mode 100644 Bio/PopGen/SimCoal/data/bottle.par
delete mode 100644 Bio/PopGen/SimCoal/data/decline_lambda.par
delete mode 100644 Bio/PopGen/SimCoal/data/decline_split.par
delete mode 100644 Bio/PopGen/SimCoal/data/island.par
delete mode 100644 Bio/PopGen/SimCoal/data/simple.par
delete mode 100644 Bio/PopGen/SimCoal/data/split_island.par
delete mode 100644 Bio/PopGen/SimCoal/data/split_ssm_1d.par
delete mode 100644 Bio/PopGen/SimCoal/data/split_ssm_2d.par
delete mode 100644 Bio/PopGen/SimCoal/data/ssm_1d.par
delete mode 100644 Bio/PopGen/SimCoal/data/ssm_2d.par
delete mode 100644 Bio/_py3k/_ordereddict.py
create mode 100644 BioSQL/.flake8
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copy DEPRECATED => DEPRECATED.rst (87%)
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create mode 100644 Doc/images/biopython_logo.pdf
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rename Doc/images/{biopython.jpg => biopython_logo_old.jpg} (100%)
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copy NEWS => NEWS.rst (67%)
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create mode 100644 Tests/Affy/affy_v4_example.CEL
create mode 100644 Tests/Blat/psl_35_001.psl
create mode 100644 Tests/Blat/psl_35_002.psl
create mode 100644 Tests/Blat/pslx_35_002.pslx
create mode 100644 Tests/Cellosaurus/cell_lines_1.txt
create mode 100644 Tests/Cellosaurus/cell_lines_2.txt
create mode 100644 Tests/Cellosaurus/cell_lines_3.txt
create mode 100644 Tests/Cluster/README
create mode 100644 Tests/Cluster/cyano.txt
create mode 100644 Tests/EMBL/hla_3260_sample.imgt
create mode 100644 Tests/EMBL/kipo_prt_sample.embl
create mode 100644 Tests/GenBank/EU851978_output.gbk
create mode 100644 Tests/GenBank/HM138502_output.gbk
create mode 100644 Tests/GenBank/KF527485_output.gbk
create mode 100644 Tests/Hmmer/text_31b2_hmmsearch_001.out
create mode 100644 Tests/Hmmer/text_31b2_hmmsearch_002.out
create mode 100644 Tests/KEGG/enzyme.4letter
create mode 100644 Tests/KEGG/ko00010.xml
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create mode 100644 Tests/MAF/bug2453.maf
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create mode 100644 Tests/MAF/ucsc_mm9_chr10.maf
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create mode 100644 Tests/MAF/unfinished.idx
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create mode 100644 Tests/Mauve/simple.xmfa
create mode 100644 Tests/Mauve/simple.xmfa.backbone
create mode 100644 Tests/Mauve/simple.xmfa.bbcols
create mode 100644 Tests/PAML/Alignments/longnames.fasta
copy Tests/PAML/Control_files/yn00/{yn00.ctl => yn00_long.ctl} (80%)
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create mode 100644 Tests/PAML/Results/yn00/yn00-4_8.out
create mode 100644 Tests/PAML/Results/yn00/yn00_long-4_8.out
create mode 100644 Tests/PDB/1A8O.xyzr
create mode 100644 Tests/PDB/1AS5.cif
create mode 100644 Tests/PDB/2BEG.cif
create mode 100644 Tests/PDB/3JQH.cif
create mode 100644 Tests/PDB/alignment_file.fa
create mode 100644 Tests/PDB/lib_10_z_5.txt
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create mode 100644 Tests/SwissProt/P84001.xml
create mode 100644 Tests/SwissProt/P97881.xml
create mode 100644 Tests/SwissProt/R5HY77.xml
create mode 100644 Tests/UniProt/goa_yeast.gaf
create mode 100644 Tests/biosql.ini.appveyor
create mode 100644 Tests/motifs/meme_v_4_11_4.txt
create mode 100644 Tests/output/test_AlignIO_MauveIO
delete mode 100644 Tests/output/test_KEGG
delete mode 100644 Tests/output/test_QCPSuperimposer
delete mode 100644 Tests/output/test_SVDSuperimposer
create mode 100644 Tests/test_Affy.py
create mode 100644 Tests/test_AlignIO_MauveIO.py
create mode 100644 Tests/test_ExPASy.py
create mode 100644 Tests/test_MafIO_index.py
create mode 100644 Tests/test_PDBList.py
create mode 100644 Tests/test_PDB_FragmentMapper.py
create mode 100644 Tests/test_PDB_MMCIF2Dict.py
rename Tests/{test_MMCIF.py => test_PDB_MMCIFParser.py} (73%)
create mode 100644 Tests/test_PDB_Polypetide.py
create mode 100644 Tests/test_PDB_StructureAlignment.py
create mode 100644 Tests/test_PDB_Superimposer.py
delete mode 100644 Tests/test_PopGen_DFDist.py
delete mode 100644 Tests/test_PopGen_FDist.py
delete mode 100644 Tests/test_PopGen_FDist_nodepend.py
delete mode 100644 Tests/test_PopGen_FastSimCoal.py
delete mode 100644 Tests/test_PopGen_SimCoal.py
delete mode 100644 Tests/test_PopGen_SimCoal_nodepend.py
create mode 100644 Tests/test_cellosaurus.py
create mode 100644 Tests/test_mmtf_online.py
delete mode 100644 Tests/test_py3k.py
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