[med-svn] [python-biopython] branch upstream updated (80d5869 -> f356f2a)
Andreas Tille
tille at debian.org
Wed Jun 8 20:01:34 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository python-biopython.
from 80d5869 Imported Upstream version 1.66+dfsg
new f356f2a Imported Upstream version 1.67+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:
.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 +
.../codeml/{all_NSsites.ctl => m2a_rel.ctl} | 2 +-
.../NSsite3-4_4c.out => m2a_rel/m2a_rel-4_6.out} | 31 +-
.../NSsite3-4_5.out => m2a_rel/m2a_rel-4_7.out} | 34 +-
.../NSsite3-4_5.out => m2a_rel/m2a_rel-4_8.out} | 72 +-
.../NSsite3-4_4c.out => m2a_rel/m2a_rel-4_9a.out} | 72 +-
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, 34886 insertions(+), 69463 deletions(-)
create mode 100644 .gitattributes
create mode 100644 .gitignore
create mode 100644 .travis.yml
create mode 100644 Bio/Entrez/XSDs/IPGReportSet.xsd
delete mode 100644 Bio/Motif/Applications/__init__.py
delete mode 100644 Bio/Motif/Parsers/AlignAce.py
delete mode 100644 Bio/Motif/Parsers/MAST.py
delete mode 100644 Bio/Motif/Parsers/MEME.py
delete mode 100644 Bio/Motif/Parsers/__init__.py
delete mode 100644 Bio/Motif/Thresholds.py
delete mode 100644 Bio/Motif/_Motif.py
delete mode 100644 Bio/Motif/__init__.py
delete mode 100644 Bio/Motif/_pwm.c
create mode 100644 Bio/Nexus/.project
create mode 100644 Bio/Nexus/StandardData.py
create mode 100644 Bio/PDB/mmCIF/Makefile
create mode 100644 Bio/PDB/mmCIF/__init__.py
create mode 100644 Bio/PDB/mmCIF/mmcif.lex
delete mode 100644 Bio/motifs/applications/_alignace.py
create mode 100644 Bio/phenotype/__init__.py
create mode 100644 Bio/phenotype/phen_micro.py
create mode 100644 Bio/phenotype/pm_fitting.py
delete mode 100644 Doc/Tutorial.html
delete mode 100644 Doc/Tutorial.pdf
create mode 100644 Doc/Tutorial/chapter_phenotype.tex
create mode 100644 Doc/biopdb_faq.lyx
delete mode 100644 Doc/biopdb_faq.pdf
create mode 100644 Doc/cookbook/README
create mode 100644 Doc/cookbook/Restriction/Restriction.md
delete mode 100644 Doc/cookbook/motif/Makefile
delete mode 100644 Doc/cookbook/motif/motif.tex
create mode 100644 Doc/doc.rst
create mode 100644 Doc/examples/Plates.csv
create mode 100644 Doc/images/BlastRecord.dia
create mode 100644 Doc/images/PSIBlastRecord.dia
create mode 100644 Doc/images/smcra.dia
create mode 100644 Doc/images/smcra.eps
delete mode 100644 Doc/install/Installation.html
delete mode 100644 Doc/install/Installation.pdf
delete mode 100644 PKG-INFO
create mode 120000 README.rst
create mode 100644 Tests/.cvsignore
create mode 100644 Tests/EMBL/DS830848.embl
create mode 100644 Tests/GenBank/.cvsignore
create mode 100644 Tests/GenBank/DS830848.gb
create mode 100644 Tests/GenBank/EU851978.gbk
create mode 100644 Tests/GenBank/HM138502.gbk
create mode 100644 Tests/GenBank/KF527485.gbk
create mode 100644 Tests/Graphics/.cvsignore
create mode 100644 Tests/NeuralNetwork/.cvsignore
create mode 100644 Tests/Nexus/vSysLab_Ganaspidium_multistate.nex
create mode 100644 Tests/Nexus/vSysLab_Heptascelio_no-states_10+chars.nex
create mode 100644 Tests/Nexus/vSysLab_Oreiscelio_discrete+continuous.nex
copy Tests/PAML/Control_files/codeml/{all_NSsites.ctl => m2a_rel.ctl} (93%)
copy Tests/PAML/Results/codeml/{NSsite3/NSsite3-4_4c.out => m2a_rel/m2a_rel-4_6.out} (90%)
copy Tests/PAML/Results/codeml/{NSsite3/NSsite3-4_5.out => m2a_rel/m2a_rel-4_7.out} (87%)
copy Tests/PAML/Results/codeml/{NSsite3/NSsite3-4_5.out => m2a_rel/m2a_rel-4_8.out} (64%)
copy Tests/PAML/Results/codeml/{NSsite3/NSsite3-4_4c.out => m2a_rel/m2a_rel-4_9a.out} (64%)
create mode 100644 Tests/PDB/1LCD.pdb
delete mode 100644 Tests/PDB/1MOT.pdb
create mode 100644 Tests/PDB/4zhl.cif
create mode 100644 Tests/biosql.ini.sample
create mode 100644 Tests/phenotype/BadPlate.json
create mode 100644 Tests/phenotype/Plate.json
create mode 100644 Tests/phenotype/Plate_2.json
create mode 100644 Tests/phenotype/Plates.csv
create mode 100644 Tests/phenotype/SmallPlate.json
create mode 100644 Tests/phenotype/SmallPlate_2.json
create mode 100644 Tests/phenotype/SmallPlates.csv
create mode 100644 Tests/test_AlignInfo.py
delete mode 100644 Tests/test_Motif.py
create mode 100644 Tests/test_NaiveBayes.py
create mode 100644 Tests/test_RCSBFormats.py
create mode 100644 Tests/test_SeqFeature.py
create mode 100644 Tests/test_phenotype.py
create mode 100644 Tests/test_phenotype_fit.py
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