[med-svn] [python-biopython] 05/06: Merge tag 'upstream/1.67+dfsg'
Andreas Tille
tille at debian.org
Wed Jun 8 20:01:32 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository python-biopython.
commit ce6d3986a4f6caf63bf3934d37d95f80d3148098
Merge: 08009fc f356f2a
Author: Andreas Tille <tille at debian.org>
Date: Wed Jun 8 21:26:08 2016 +0200
Merge tag 'upstream/1.67+dfsg'
Upstream version 1.67+dfsg
.gitattributes | 20 +
.gitignore | 89 +
.travis.yml | 76 +
Bio/Affy/CelFile.py | 2 -
Bio/Affy/__init__.py | 2 -
Bio/Align/AlignInfo.py | 67 +-
Bio/Align/Applications/_ClustalOmega.py | 12 +-
Bio/Align/Applications/_Clustalw.py | 12 +-
Bio/Align/Applications/_Dialign.py | 19 +-
Bio/Align/Applications/_MSAProbs.py | 12 +-
Bio/Align/Applications/_Mafft.py | 1 -
Bio/Align/Applications/_Muscle.py | 14 +-
Bio/Align/Applications/_Prank.py | 15 +-
Bio/Align/Applications/_Probcons.py | 11 +-
Bio/Align/Applications/_TCoffee.py | 12 +-
Bio/Align/Applications/__init__.py | 2 -
Bio/Align/Generic.py | 26 +-
Bio/Align/__init__.py | 11 +-
Bio/AlignIO/ClustalIO.py | 4 +-
Bio/AlignIO/EmbossIO.py | 2 -
Bio/AlignIO/FastaIO.py | 8 +-
Bio/AlignIO/Interfaces.py | 2 -
Bio/AlignIO/NexusIO.py | 1 -
Bio/AlignIO/PhylipIO.py | 1 -
Bio/AlignIO/StockholmIO.py | 14 +-
Bio/AlignIO/__init__.py | 13 +-
Bio/Alphabet/IUPAC.py | 2 -
Bio/Alphabet/Reduced.py | 1 -
Bio/Alphabet/__init__.py | 2 -
Bio/Application/__init__.py | 3 +-
Bio/Blast/Applications.py | 64 +-
Bio/Blast/NCBIStandalone.py | 33 +-
Bio/Blast/NCBIWWW.py | 23 +-
Bio/Blast/NCBIXML.py | 12 +-
Bio/Blast/Record.py | 10 +-
Bio/Blast/__init__.py | 2 -
Bio/CAPS/__init__.py | 2 -
Bio/Cluster/__init__.py | 8 +-
Bio/Compass/__init__.py | 2 -
Bio/Crystal/__init__.py | 2 -
Bio/Data/CodonTable.py | 25 +-
Bio/Data/IUPACData.py | 2 -
Bio/Data/SCOPData.py | 2 -
Bio/Data/__init__.py | 2 -
Bio/DocSQL.py | 1 -
Bio/Emboss/Applications.py | 13 +-
Bio/Emboss/Primer3.py | 3 +-
Bio/Emboss/PrimerSearch.py | 2 -
Bio/Emboss/__init__.py | 3 +-
Bio/Entrez/Parser.py | 20 +-
Bio/Entrez/XSDs/IPGReportSet.xsd | 94 +
Bio/Entrez/__init__.py | 68 +-
Bio/ExPASy/Enzyme.py | 2 -
Bio/ExPASy/Prodoc.py | 2 -
Bio/ExPASy/Prosite.py | 2 -
Bio/ExPASy/ScanProsite.py | 2 -
Bio/ExPASy/__init__.py | 2 -
Bio/FSSP/FSSPTools.py | 20 +-
Bio/FSSP/__init__.py | 2 +
Bio/FSSP/fssp_rec.py | 6 +-
Bio/File.py | 25 +-
Bio/GA/Crossover/GeneralPoint.py | 6 +-
Bio/GA/Crossover/Uniform.py | 2 -
Bio/GenBank/Record.py | 2 -
Bio/GenBank/Scanner.py | 92 +-
Bio/GenBank/__init__.py | 15 +-
Bio/GenBank/utils.py | 2 -
Bio/Geo/Record.py | 2 +-
Bio/Graphics/BasicChromosome.py | 19 +-
Bio/Graphics/ColorSpiral.py | 2 -
Bio/Graphics/Comparative.py | 10 +-
Bio/Graphics/DisplayRepresentation.py | 3 +-
Bio/Graphics/Distribution.py | 4 +-
Bio/Graphics/GenomeDiagram/_AbstractDrawer.py | 7 +-
Bio/Graphics/GenomeDiagram/_CircularDrawer.py | 5 +-
Bio/Graphics/GenomeDiagram/_CrossLink.py | 2 +-
Bio/Graphics/GenomeDiagram/_Diagram.py | 374 +-
Bio/Graphics/GenomeDiagram/_FeatureSet.py | 17 +-
Bio/Graphics/GenomeDiagram/_LinearDrawer.py | 4 +-
Bio/Graphics/GenomeDiagram/_Track.py | 6 +-
Bio/Graphics/GenomeDiagram/__init__.py | 8 +-
Bio/Graphics/KGML_vis.py | 3 -
Bio/Graphics/__init__.py | 1 -
Bio/HMM/DynamicProgramming.py | 2 +-
Bio/HMM/Trainer.py | 2 -
Bio/Index.py | 6 +-
Bio/KDTree/KDTree.py | 2 -
Bio/KDTree/__init__.py | 2 -
Bio/KEGG/Enzyme/__init__.py | 29 +
Bio/KEGG/KGML/KGML_parser.py | 2 -
Bio/KEGG/KGML/KGML_pathway.py | 2 -
Bio/KEGG/REST.py | 8 +-
Bio/KEGG/__init__.py | 5 +-
Bio/MarkovModel.py | 2 +-
Bio/Medline/__init__.py | 4 +-
Bio/Motif/Applications/__init__.py | 9 -
Bio/Motif/Parsers/AlignAce.py | 53 -
Bio/Motif/Parsers/MAST.py | 150 -
Bio/Motif/Parsers/MEME.py | 358 -
Bio/Motif/Parsers/__init__.py | 0
Bio/Motif/Thresholds.py | 94 -
Bio/Motif/_Motif.py | 800 -
Bio/Motif/__init__.py | 172 -
Bio/Motif/_pwm.c | 166 -
Bio/NMR/NOEtools.py | 2 -
Bio/NMR/xpktools.py | 1 -
Bio/NaiveBayes.py | 102 +-
Bio/NeuralNetwork/Gene/Motif.py | 6 +-
Bio/NeuralNetwork/Gene/Pattern.py | 6 +-
Bio/NeuralNetwork/Gene/Schema.py | 8 +-
Bio/NeuralNetwork/Gene/Signature.py | 4 +-
Bio/NeuralNetwork/Training.py | 8 +-
Bio/Nexus/.project | 17 +
Bio/Nexus/Nexus.py | 351 +-
Bio/Nexus/Nodes.py | 21 +-
Bio/Nexus/StandardData.py | 107 +
Bio/Nexus/Trees.py | 3 +-
Bio/PDB/Chain.py | 6 +-
Bio/PDB/DSSP.py | 8 +-
Bio/PDB/Entity.py | 5 +-
Bio/PDB/FragmentMapper.py | 6 +-
Bio/PDB/HSExposure.py | 2 -
Bio/PDB/MMCIFParser.py | 241 +-
Bio/PDB/NACCESS.py | 1 +
Bio/PDB/NeighborSearch.py | 2 +-
Bio/PDB/PDBIO.py | 7 +-
Bio/PDB/PDBList.py | 2 -
Bio/PDB/PDBParser.py | 6 +-
Bio/PDB/QCPSuperimposer/__init__.py | 1 +
Bio/PDB/Residue.py | 1 +
Bio/PDB/Selection.py | 2 +-
Bio/PDB/StructureAlignment.py | 4 +-
Bio/PDB/StructureBuilder.py | 4 +-
Bio/PDB/__init__.py | 8 +-
Bio/PDB/mmCIF/Makefile | 31 +
Bio/PDB/mmCIF/__init__.py | 1 +
Bio/PDB/mmCIF/mmcif.lex | 62 +
Bio/ParserSupport.py | 161 +-
Bio/Pathway/Rep/Graph.py | 6 +-
Bio/Pathway/Rep/MultiGraph.py | 6 +-
Bio/Pathway/__init__.py | 25 +-
Bio/Phylo/Applications/_Fasttree.py | 1 -
Bio/Phylo/Applications/_Phyml.py | 9 +-
Bio/Phylo/Applications/_Raxml.py | 7 +-
Bio/Phylo/Applications/__init__.py | 1 -
Bio/Phylo/BaseTree.py | 23 +-
Bio/Phylo/CDAO.py | 1 -
Bio/Phylo/CDAOIO.py | 5 +-
Bio/Phylo/Consensus.py | 6 -
Bio/Phylo/NeXML.py | 1 -
Bio/Phylo/NeXMLIO.py | 5 +-
Bio/Phylo/Newick.py | 2 -
Bio/Phylo/NewickIO.py | 23 +-
Bio/Phylo/NexusIO.py | 3 +-
Bio/Phylo/PAML/_paml.py | 17 +-
Bio/Phylo/PAML/_parse_baseml.py | 7 +-
Bio/Phylo/PAML/_parse_codeml.py | 44 +-
Bio/Phylo/PAML/_parse_yn00.py | 2 +-
Bio/Phylo/PAML/baseml.py | 53 +-
Bio/Phylo/PAML/chi2.py | 10 +-
Bio/Phylo/PAML/codeml.py | 68 +-
Bio/Phylo/PAML/yn00.py | 23 +-
Bio/Phylo/PhyloXML.py | 8 +-
Bio/Phylo/PhyloXMLIO.py | 5 +-
Bio/Phylo/TreeConstruction.py | 39 +-
Bio/Phylo/__init__.py | 1 -
Bio/Phylo/_cdao_owl.py | 1 +
Bio/Phylo/_io.py | 8 +-
Bio/Phylo/_utils.py | 36 +-
Bio/PopGen/Async/Local.py | 42 +-
Bio/PopGen/Async/__init__.py | 77 +-
Bio/PopGen/FDist/Async.py | 6 +-
Bio/PopGen/FDist/Controller.py | 4 +-
Bio/PopGen/FDist/Utils.py | 1 +
Bio/PopGen/FDist/__init__.py | 2 -
Bio/PopGen/GenePop/Controller.py | 6 +-
Bio/PopGen/GenePop/EasyController.py | 2 -
Bio/PopGen/GenePop/FileParser.py | 189 +-
Bio/PopGen/GenePop/__init__.py | 2 -
Bio/PopGen/SimCoal/Cache.py | 22 +-
Bio/PopGen/SimCoal/Controller.py | 6 +-
Bio/PopGen/SimCoal/Template.py | 45 +-
Bio/PopGen/SimCoal/__init__.py | 5 +-
Bio/PopGen/__init__.py | 4 +-
Bio/Restriction/PrintFormat.py | 31 +-
Bio/Restriction/RanaConfig.py | 95 +-
Bio/Restriction/Restriction.py | 436 +-
Bio/Restriction/Restriction_Dictionary.py | 3781 +-
Bio/Restriction/__init__.py | 3 +-
Bio/SCOP/Raf.py | 8 +-
Bio/SCOP/Residues.py | 2 +-
Bio/SCOP/__init__.py | 15 +-
Bio/SVDSuperimposer/__init__.py | 26 +-
Bio/SearchIO/BlastIO/__init__.py | 2 -
Bio/SearchIO/BlastIO/blast_tab.py | 8 +-
Bio/SearchIO/BlastIO/blast_text.py | 2 -
Bio/SearchIO/BlastIO/blast_xml.py | 26 +-
Bio/SearchIO/BlatIO.py | 4 +-
Bio/SearchIO/ExonerateIO/exonerate_vulgar.py | 2 +-
Bio/SearchIO/FastaIO.py | 9 +-
Bio/SearchIO/HmmerIO/__init__.py | 5 +-
Bio/SearchIO/HmmerIO/_base.py | 4 +-
Bio/SearchIO/HmmerIO/hmmer2_text.py | 1 -
Bio/SearchIO/HmmerIO/hmmer3_domtab.py | 3 -
Bio/SearchIO/HmmerIO/hmmer3_tab.py | 4 +-
Bio/SearchIO/HmmerIO/hmmer3_text.py | 6 +-
Bio/SearchIO/__init__.py | 2 -
Bio/SearchIO/_index.py | 3 -
Bio/SearchIO/_model/__init__.py | 2 -
Bio/SearchIO/_model/_base.py | 3 -
Bio/SearchIO/_model/hit.py | 7 +-
Bio/SearchIO/_model/hsp.py | 7 +-
Bio/SearchIO/_model/query.py | 7 +-
Bio/Seq.py | 83 +-
Bio/SeqFeature.py | 38 +-
Bio/SeqIO/AbiIO.py | 11 +-
Bio/SeqIO/AceIO.py | 8 +-
Bio/SeqIO/FastaIO.py | 76 +-
Bio/SeqIO/IgIO.py | 49 +-
Bio/SeqIO/InsdcIO.py | 259 +-
Bio/SeqIO/Interfaces.py | 2 -
Bio/SeqIO/PdbIO.py | 62 +-
Bio/SeqIO/PhdIO.py | 12 +-
Bio/SeqIO/PirIO.py | 37 +-
Bio/SeqIO/QualityIO.py | 14 +-
Bio/SeqIO/SeqXmlIO.py | 24 +-
Bio/SeqIO/SffIO.py | 88 +-
Bio/SeqIO/SwissIO.py | 26 +-
Bio/SeqIO/TabIO.py | 44 +-
Bio/SeqIO/UniprotIO.py | 12 +-
Bio/SeqIO/__init__.py | 87 +-
Bio/SeqIO/_convert.py | 74 +-
Bio/SeqIO/_index.py | 13 +-
Bio/SeqRecord.py | 33 +-
Bio/SeqUtils/CheckSum.py | 56 +-
Bio/SeqUtils/CodonUsage.py | 2 -
Bio/SeqUtils/CodonUsageIndices.py | 2 -
Bio/SeqUtils/IsoelectricPoint.py | 1 -
Bio/SeqUtils/MeltingTemp.py | 361 +-
Bio/SeqUtils/ProtParam.py | 2 -
Bio/SeqUtils/ProtParamData.py | 4 +-
Bio/SeqUtils/__init__.py | 85 +-
Bio/SeqUtils/lcc.py | 18 +-
Bio/Sequencing/Ace.py | 2 -
Bio/Sequencing/Applications/_Novoalign.py | 10 +-
Bio/Sequencing/Applications/__init__.py | 1 +
Bio/Sequencing/Applications/_bwa.py | 13 +-
Bio/Sequencing/Applications/_samtools.py | 12 +-
Bio/Sequencing/Phd.py | 1 -
Bio/Statistics/lowess.py | 1 +
Bio/SubsMat/FreqTable.py | 89 +-
Bio/SubsMat/MatrixInfo.py | 4981 ++-
Bio/SubsMat/__init__.py | 1 -
Bio/SwissProt/KeyWList.py | 2 -
Bio/SwissProt/__init__.py | 10 +-
Bio/TogoWS/__init__.py | 3 +-
Bio/UniGene/__init__.py | 4 +-
Bio/UniProt/GOA.py | 1 +
Bio/Wise/__init__.py | 16 +-
Bio/Wise/dnal.py | 17 +-
Bio/Wise/psw.py | 17 +-
Bio/__init__.py | 10 +-
Bio/_py3k/__init__.py | 124 +-
Bio/_py3k/_ordereddict.py | 1 +
Bio/_utils.py | 2 +-
Bio/bgzf.py | 8 +-
Bio/codonalign/__init__.py | 65 +-
Bio/codonalign/chisq.py | 255 +-
Bio/codonalign/codonalignment.py | 24 +-
Bio/codonalign/codonalphabet.py | 12 +-
Bio/codonalign/codonseq.py | 74 +-
Bio/kNN.py | 4 +-
Bio/motifs/__init__.py | 14 +-
Bio/motifs/applications/__init__.py | 2 -
Bio/motifs/applications/_alignace.py | 146 -
Bio/motifs/applications/_xxmotif.py | 11 +-
Bio/motifs/jaspar/__init__.py | 2 +-
Bio/motifs/jaspar/db.py | 5 +-
Bio/motifs/matrix.py | 100 +-
Bio/motifs/meme.py | 10 +-
Bio/motifs/thresholds.py | 4 +-
Bio/motifs/transfac.py | 23 +-
Bio/pairwise2.py | 3 +-
Bio/phenotype/__init__.py | 244 +
Bio/phenotype/phen_micro.py | 1131 +
Bio/phenotype/pm_fitting.py | 133 +
Bio/triefind.py | 1 +
BioSQL/BioSeq.py | 19 +-
BioSQL/BioSeqDatabase.py | 54 +-
BioSQL/DBUtils.py | 19 +-
BioSQL/Loader.py | 129 +-
CONTRIB | 26 +-
DEPRECATED | 36 +-
Doc/Tutorial.html | 10952 ------
Doc/Tutorial.pdf | 34830 -------------------
Doc/Tutorial.tex | 8 +-
Doc/Tutorial/chapter_align.tex | 5 +-
Doc/Tutorial/chapter_appendix.tex | 91 +-
Doc/Tutorial/chapter_blast.tex | 4 +
Doc/Tutorial/chapter_cluster.tex | 39 +-
Doc/Tutorial/chapter_cookbook.tex | 37 +-
Doc/Tutorial/chapter_entrez.tex | 38 +-
Doc/Tutorial/chapter_graphics.tex | 1 -
Doc/Tutorial/chapter_kegg.tex | 6 +-
Doc/Tutorial/chapter_learning.tex | 3 +-
Doc/Tutorial/chapter_motifs.tex | 61 +-
Doc/Tutorial/chapter_phenotype.tex | 271 +
Doc/Tutorial/chapter_quick_start.tex | 6 +-
Doc/Tutorial/chapter_searchio.tex | 7 +-
Doc/Tutorial/chapter_seq_annot.tex | 60 +-
Doc/Tutorial/chapter_seqio.tex | 101 +-
Doc/biopdb_faq.lyx | 2724 ++
Doc/biopdb_faq.pdf | Bin 174565 -> 0 bytes
Doc/cookbook/README | 13 +
Doc/cookbook/Restriction/Restriction.html | 1942 +-
Doc/cookbook/Restriction/Restriction.md | 1625 +
Doc/cookbook/motif/Makefile | 30 -
Doc/cookbook/motif/motif.tex | 590 -
Doc/doc.rst | 508 +
Doc/examples/ACT_example.py | 95 +-
Doc/examples/Plates.csv | 1202 +
Doc/examples/Proux_et_al_2002_Figure_6.py | 5 +-
Doc/examples/clustal_run.py | 1 -
Doc/examples/getgene.py | 63 +-
Doc/examples/nmr/simplepredict.py | 76 +-
Doc/examples/www_blast.py | 7 +-
Doc/images/BlastRecord.dia | Bin 0 -> 3498 bytes
Doc/images/BlastRecord.png | Bin 64168 -> 83852 bytes
Doc/images/PSIBlastRecord.dia | Bin 0 -> 2513 bytes
Doc/images/smcra.dia | Bin 0 -> 2251 bytes
Doc/images/smcra.eps | 2453 ++
Doc/install/Installation.html | 385 -
Doc/install/Installation.pdf | Bin 127585 -> 0 bytes
MANIFEST.in | 8 +-
NEWS | 109 +
PKG-INFO | 11 -
README | 21 +-
README.rst | 1 +
Scripts/GenBank/check_output.py | 4 +-
Scripts/GenBank/check_output_simple.py | 57 +-
Scripts/Performance/biosql_performance_load.py | 5 +-
Scripts/Performance/biosql_performance_read.py | 7 +-
Scripts/Restriction/ranacompiler.py | 255 +-
Scripts/Restriction/rebase_update.py | 40 +-
Scripts/SeqGui/SeqGui.py | 1 +
Scripts/Structure/hsexpo | 9 +-
Scripts/debug/debug_blast_parser.py | 3 +-
Scripts/xbbtools/nextorf.py | 22 +-
Scripts/xbbtools/xbb_blast.py | 10 +-
Scripts/xbbtools/xbb_blastbg.py | 49 +-
Scripts/xbbtools/xbb_help.py | 8 +-
Scripts/xbbtools/xbb_search.py | 13 +-
Scripts/xbbtools/xbb_translations.py | 38 +-
Scripts/xbbtools/xbb_utils.py | 14 +-
Scripts/xbbtools/xbb_widget.py | 26 +-
Scripts/xbbtools/xbbtools.py | 7 +-
Tests/.cvsignore | 2 +
Tests/BioSQL/biosqldb-pg.sql | 9 +
Tests/BioSQL/biosqldb-sqlite.sql | 116 +-
Tests/EMBL/DS830848.embl | 86 +
Tests/GenBank/.cvsignore | 1 +
Tests/GenBank/DS830848.gb | 73 +
Tests/GenBank/EU851978.gbk | 87 +
Tests/GenBank/HM138502.gbk | 79 +
Tests/GenBank/KF527485.gbk | 82 +
Tests/Graphics/.cvsignore | 6 +
Tests/NeuralNetwork/.cvsignore | 1 +
Tests/Nexus/vSysLab_Ganaspidium_multistate.nex | 48 +
.../vSysLab_Heptascelio_no-states_10+chars.nex | 105 +
.../vSysLab_Oreiscelio_discrete+continuous.nex | 162 +
Tests/PAML/Control_files/codeml/m2a_rel.ctl | 25 +
Tests/PAML/Results/codeml/m2a_rel/m2a_rel-4_6.out | 145 +
Tests/PAML/Results/codeml/m2a_rel/m2a_rel-4_7.out | 145 +
Tests/PAML/Results/codeml/m2a_rel/m2a_rel-4_8.out | 145 +
Tests/PAML/Results/codeml/m2a_rel/m2a_rel-4_9a.out | 144 +
Tests/PAML/gen_results.py | 10 +-
Tests/PDB/1LCD.pdb | 3884 +++
Tests/PDB/1MOT.pdb | 8220 -----
Tests/PDB/4zhl.cif | 3693 ++
Tests/PDB/a_structure.pdb | 1646 +-
Tests/biosql.ini.sample | 25 +
Tests/common_BioSQL.py | 281 +-
Tests/output/test_KEGG | 94 +
Tests/output/test_SeqIO | 16 +
Tests/phenotype/BadPlate.json | 1 +
Tests/phenotype/Plate.json | 1 +
Tests/phenotype/Plate_2.json | 1 +
Tests/phenotype/Plates.csv | 602 +
Tests/phenotype/SmallPlate.json | 1 +
Tests/phenotype/SmallPlate_2.json | 1 +
Tests/phenotype/SmallPlates.csv | 600 +
Tests/run_tests.py | 43 +-
Tests/search_tests_common.py | 12 +-
Tests/seq_tests_common.py | 7 +-
Tests/test_AlignIO.py | 12 +-
Tests/test_AlignInfo.py | 119 +
Tests/test_BioSQL_MySQLdb.py | 16 +-
Tests/test_BioSQL_mysql_connector.py | 16 +-
Tests/test_BioSQL_psycopg2.py | 15 +-
Tests/test_BioSQL_sqlite3.py | 9 +-
Tests/test_Chi2.py | 6 +-
Tests/test_Cluster.py | 4 +-
Tests/test_Crystal.py | 4 -
Tests/test_Emboss.py | 42 +-
Tests/test_Entrez.py | 323 +-
Tests/test_Entrez_online.py | 9 +
Tests/test_GAOrganism.py | 6 +-
Tests/test_GenBank_unittest.py | 60 +
Tests/test_GenomeDiagram.py | 211 +-
Tests/test_KEGG.py | 13 +-
Tests/test_KEGG_online.py | 60 +-
Tests/test_KGML_graphics.py | 8 +-
Tests/test_MMCIF.py | 137 +-
Tests/test_Mafft_tool.py | 10 +-
Tests/test_Motif.py | 1536 -
Tests/test_Muscle_tool.py | 4 +-
Tests/test_NCBI_BLAST_tools.py | 41 +-
Tests/test_NCBI_qblast.py | 17 +-
Tests/test_NNGene.py | 49 +-
Tests/test_NaiveBayes.py | 116 +
Tests/test_Nexus.py | 305 +-
Tests/test_PAML_baseml.py | 102 +-
Tests/test_PAML_codeml.py | 50 +-
Tests/test_PDB.py | 117 +-
Tests/test_PDB_KDTree.py | 2 +-
Tests/test_Pathway.py | 20 +-
Tests/test_Phylo.py | 28 +
Tests/test_PhyloXML.py | 12 +-
Tests/test_Phylo_NeXML.py | 6 +-
Tests/test_Phylo_depend.py | 30 +
Tests/test_PopGen_GenePop_nodepend.py | 30 +-
Tests/test_PopGen_SimCoal_nodepend.py | 11 +-
Tests/test_Prank_tool.py | 10 +-
Tests/test_QCPSuperimposer.py | 8 +-
Tests/test_RCSBFormats.py | 69 +
Tests/test_SCOP_Raf.py | 9 +
Tests/test_SCOP_Scop.py | 2 +-
Tests/test_SVDSuperimposer.py | 15 +-
Tests/test_SearchIO_model.py | 12 +-
Tests/test_SeqFeature.py | 28 +
Tests/test_SeqIO.py | 260 +-
Tests/test_SeqIO_FastaIO.py | 32 +-
Tests/test_SeqIO_PdbIO.py | 12 +-
Tests/test_SeqIO_QualityIO.py | 8 +-
Tests/test_SeqIO_convert.py | 9 +-
Tests/test_SeqIO_features.py | 40 +-
Tests/test_SeqIO_index.py | 235 +-
Tests/test_SeqIO_online.py | 4 +-
Tests/test_SeqIO_write.py | 8 +-
Tests/test_SeqRecord.py | 30 +
Tests/test_Seq_objs.py | 1 +
Tests/test_SffIO.py | 225 +-
Tests/test_SwissProt.py | 295 +-
Tests/test_TogoWS.py | 4 +-
Tests/test_Tutorial.py | 92 +-
Tests/test_XXmotif_tool.py | 2 +-
Tests/test_codonalign.py | 8 +-
Tests/test_motifs.py | 19 +-
Tests/test_motifs_online.py | 42 +-
Tests/test_phenotype.py | 304 +
Tests/test_phenotype_fit.py | 63 +
Tests/test_phyml_tool.py | 19 +-
Tests/test_prodoc.py | 192 +-
Tests/test_prosite1.py | 24 +-
Tests/test_prosite2.py | 21 +-
Tests/test_raxml_tool.py | 9 +-
Tests/test_samtools_tool.py | 15 +-
Tests/test_seq.py | 112 +-
setup.py | 11 +-
469 files changed, 35382 insertions(+), 69360 deletions(-)
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