[med-svn] [python-biopython] branch upstream updated (f356f2a -> 9511db1)
Andreas Tille
tille at debian.org
Mon Aug 29 12:16:55 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 f356f2a Imported Upstream version 1.67+dfsg
new 9511db1 Imported Upstream version 1.68+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:
.codecov.yml | 7 +
.gitattributes | 3 +
.travis-tox.ini | 110 +
.travis.yml | 76 +-
Bio/Align/Applications/_Muscle.py | 7 +-
Bio/Align/Applications/_TCoffee.py | 108 +-
Bio/Align/Generic.py | 12 +-
Bio/Align/__init__.py | 18 +-
Bio/AlignIO/ClustalIO.py | 42 +-
Bio/AlignIO/NexusIO.py | 4 +-
Bio/AlignIO/PhylipIO.py | 44 +-
Bio/Alphabet/Reduced.py | 3 +-
Bio/Blast/Applications.py | 14 +-
Bio/Blast/NCBIStandalone.py | 55 +-
Bio/Blast/NCBIWWW.py | 5 +-
Bio/Compass/__init__.py | 2 +-
Bio/Data/CodonTable.py | 248 +-
Bio/Emboss/Applications.py | 1801 +++----
Bio/Entrez/DTDs/{NCBI_RNA.dtd => NCBI_Systems.dtd} | 14 +-
Bio/Entrez/Parser.py | 14 +-
Bio/Entrez/__init__.py | 118 +-
Bio/File.py | 12 +-
Bio/GenBank/Scanner.py | 15 +-
Bio/GenBank/__init__.py | 70 +-
Bio/Graphics/BasicChromosome.py | 55 +-
Bio/Graphics/Comparative.py | 10 +-
Bio/Graphics/DisplayRepresentation.py | 2 +-
Bio/Graphics/__init__.py | 2 +-
Bio/HMM/DynamicProgramming.py | 6 +-
Bio/MarkovModel.py | 24 +-
Bio/Nexus/Nexus.py | 29 +-
Bio/Nexus/Trees.py | 4 +-
Bio/PDB/DSSP.py | 174 +-
Bio/PDB/HSExposure.py | 6 +-
Bio/PDB/QCPSuperimposer/__init__.py | 11 +-
Bio/PDB/mmtf/DefaultParser.py | 162 +
Bio/PDB/mmtf/__init__.py | 36 +
Bio/PDB/parse_pdb_header.py | 3 +-
Bio/Phylo/Applications/_Fasttree.py | 424 +-
Bio/Phylo/Applications/_Phyml.py | 316 +-
Bio/Phylo/Applications/_Raxml.py | 251 +-
Bio/Phylo/BaseTree.py | 66 +-
Bio/Phylo/NewickIO.py | 16 +-
Bio/Phylo/PAML/_parse_baseml.py | 32 +-
Bio/Phylo/PAML/_parse_codeml.py | 30 +-
Bio/Phylo/_cdao_owl.py | 448 +-
Bio/PopGen/Async/Local.py | 6 +-
Bio/PopGen/Async/__init__.py | 10 +-
Bio/PopGen/FDist/Async.py | 3 +-
Bio/PopGen/FDist/Controller.py | 2 +-
Bio/PopGen/FDist/Utils.py | 1 +
Bio/PopGen/FDist/__init__.py | 13 +-
Bio/PopGen/SimCoal/Async.py | 4 +-
Bio/PopGen/SimCoal/Cache.py | 2 +-
Bio/PopGen/SimCoal/Controller.py | 5 +-
Bio/PopGen/SimCoal/Template.py | 2 +
Bio/PopGen/SimCoal/__init__.py | 10 +-
Bio/Restriction/Restriction.py | 354 +-
Bio/Restriction/Restriction_Dictionary.py | 936 +++-
Bio/Seq.py | 10 +-
Bio/SeqFeature.py | 101 +-
Bio/SeqIO/InsdcIO.py | 125 +-
Bio/SeqIO/PdbIO.py | 6 +-
Bio/SeqIO/__init__.py | 9 +-
Bio/SeqRecord.py | 40 +-
Bio/SeqUtils/CodonUsage.py | 4 +-
Bio/SeqUtils/ProtParamData.py | 24 +-
Bio/SeqUtils/__init__.py | 2 +-
Bio/Sequencing/Applications/_Novoalign.py | 3 +-
Bio/Sequencing/Applications/_bwa.py | 429 +-
Bio/SubsMat/MatrixInfo.py | 5052 ++++++++++----------
Bio/UniProt/GOA.py | 31 +-
Bio/__init__.py | 2 +-
Bio/_utils.py | 7 +-
Bio/bgzf.py | 47 +-
Bio/codonalign/__init__.py | 2 +-
Bio/codonalign/codonalignment.py | 2 +-
Bio/codonalign/codonseq.py | 49 +-
Bio/cpairwise2module.c | 464 +-
Bio/motifs/__init__.py | 5 +-
Bio/motifs/_pwm.c | 4 +
Bio/motifs/jaspar/db.py | 29 +-
Bio/motifs/matrix.py | 5 +-
Bio/motifs/transfac.py | 2 +-
Bio/pairwise2.py | 937 ++--
BioSQL/BioSeq.py | 39 +-
BioSQL/BioSeqDatabase.py | 10 +-
BioSQL/Loader.py | 114 +-
CONTRIB | 145 +-
DEPRECATED | 17 +-
Doc/Tutorial.tex | 3 +-
Doc/Tutorial/chapter_align.tex | 155 +-
Doc/Tutorial/chapter_introduction.tex | 19 +-
Doc/Tutorial/chapter_pdb.tex | 32 +
Doc/Tutorial/chapter_popgen.tex | 475 --
Doc/Tutorial/chapter_seq_annot.tex | 2 +-
Doc/Tutorial/chapter_testing.tex | 84 +-
Doc/examples/ACT_example.py | 4 +-
Doc/examples/Proux_et_al_2002_Figure_6.py | 26 +-
Doc/examples/alpha.faa | 4 +
Doc/examples/beta.faa | 4 +
Doc/examples/getgene.py | 40 +-
Doc/examples/nmr/simplepredict.py | 6 +-
Doc/images/bottle.png | Bin 1589 -> 0 bytes
MANIFEST.in | 1 +
NEWS | 56 +
Scripts/GenBank/check_output.py | 4 +-
Scripts/Performance/biosql_performance_load.py | 2 +-
Scripts/Performance/biosql_performance_read.py | 2 +-
Scripts/Restriction/ranacompiler.py | 14 +-
Scripts/SeqGui/SeqGui.py | 412 +-
Scripts/scop_pdb.py | 4 +-
Scripts/update_ncbi_codon_table.py | 96 +
Scripts/xbbtools/nextorf.py | 25 +-
Scripts/xbbtools/test.fas | 2 +-
Scripts/xbbtools/testrp.fas | 2 +-
Scripts/xbbtools/xbb_blast.py | 273 +-
Scripts/xbbtools/xbb_blastbg.py | 148 +-
Scripts/xbbtools/xbb_help.py | 66 +-
Scripts/xbbtools/xbb_search.py | 92 +-
Scripts/xbbtools/xbb_translations.py | 111 +-
Scripts/xbbtools/xbb_utils.py | 50 +-
Scripts/xbbtools/xbb_widget.py | 352 +-
Scripts/xbbtools/xbbtools.py | 26 +-
Tests/EMBL/embl_with_0_line.embl | 48 +
Tests/PAML/gen_results.py | 6 +-
Tests/PDB/1A8O.mmtf | Bin 0 -> 12510 bytes
Tests/PDB/4CUP.cif | 3305 +++++++++++++
Tests/PDB/4CUP.mmtf | Bin 0 -> 19438 bytes
Tests/PDB/{4zhl.cif => 4ZHL.cif} | 0
Tests/PDB/4ZHL.mmtf | Bin 0 -> 27073 bytes
Tests/PDB/Miller_RASA.txt | 130 +
Tests/PDB/Sander_RASA.txt | 130 +
Tests/PDB/Wilke_RASA.txt | 130 +
Tests/PDB/dssp_xtra_Sander.txt | 130 +
Tests/common_BioSQL.py | 95 +-
Tests/common_BioSQL_online.py | 111 +
Tests/output/test_GenBank | 1267 +----
Tests/output/test_SeqIO | 24 +-
Tests/seq_tests_common.py | 62 +-
Tests/test_AlignIO_ClustalIO.py | 7 +-
Tests/test_AlignIO_EmbossIO.py | 6 +-
Tests/test_BioSQL_MySQLdb.py | 2 +-
...QL_MySQLdb.py => test_BioSQL_MySQLdb_online.py} | 13 +-
Tests/test_BioSQL_mysql_connector.py | 2 +-
...or.py => test_BioSQL_mysql_connector_online.py} | 13 +-
Tests/test_BioSQL_psycopg2.py | 2 +-
..._psycopg2.py => test_BioSQL_psycopg2_online.py} | 13 +-
Tests/test_BioSQL_sqlite3.py | 2 +-
...QL_MySQLdb.py => test_BioSQL_sqlite3_online.py} | 23 +-
Tests/test_CAPS.py | 49 +-
Tests/test_CelFile.py | 58 +-
Tests/test_Cluster.py | 2 +-
Tests/test_CodonTable.py | 8 +
Tests/test_Compass.py | 7 +-
Tests/test_EMBL_unittest.py | 11 +
Tests/test_EmbossPrimer.py | 36 +-
Tests/test_Entrez.py | 4306 +----------------
Tests/test_Entrez_online.py | 29 +-
Tests/{test_Entrez.py => test_Entrez_parser.py} | 185 +-
Tests/test_GAQueens.py | 6 +-
Tests/test_GenBank.py | 4 +-
Tests/test_GenBank_unittest.py | 109 +-
Tests/test_KGML_nographics.py | 30 +-
Tests/test_MMCIF.py | 2 +-
Tests/test_NCBITextParser.py | 8 +-
Tests/test_NCBIXML.py | 2 +-
Tests/test_NCBI_BLAST_tools.py | 3 +-
Tests/test_Nexus.py | 2 +-
Tests/test_PAML_codeml.py | 1 -
Tests/test_PAML_yn00.py | 8 +-
Tests/test_PDB.py | 143 +-
Tests/test_Phylo.py | 40 +-
Tests/test_PhyloXML.py | 103 +-
...st_Phylo_depend.py => test_Phylo_matplotlib.py} | 34 +-
Tests/test_Phylo_networkx.py | 40 +
Tests/test_PopGen_DFDist.py | 10 +-
Tests/test_PopGen_FDist.py | 11 +-
Tests/test_PopGen_FastSimCoal.py | 10 +-
Tests/test_PopGen_SimCoal.py | 10 +-
Tests/test_PopGen_SimCoal_nodepend.py | 8 +-
Tests/test_QCPSuperimposer.py | 6 +-
Tests/test_RCSBFormats.py | 13 +-
Tests/test_Restriction.py | 12 +-
Tests/test_SCOP_Residues.py | 24 +-
Tests/test_SearchIO_hmmer2_text_index.py | 10 +-
Tests/test_SearchIO_hmmer3_domtab.py | 4 +-
Tests/test_SearchIO_hmmer3_text_index.py | 6 +-
Tests/test_SeqIO_AbiIO.py | 2 +-
Tests/test_SeqIO_Insdc.py | 18 +
Tests/test_SeqIO_QualityIO.py | 2 +-
Tests/test_SeqIO_SeqXML.py | 7 +-
Tests/test_SeqIO_features.py | 70 +-
Tests/test_SeqIO_write.py | 9 +-
Tests/test_SeqRecord.py | 19 +-
Tests/test_SeqUtils.py | 2 +-
Tests/test_Seq_objs.py | 53 +-
Tests/test_TreeConstruction.py | 20 +-
Tests/test_Tutorial.py | 43 +-
Tests/test_Uniprot.py | 2 +-
Tests/test_mmtf.py | 100 +
Tests/test_pairwise2.py | 280 +-
Tests/test_prosite1.py | 2 +-
Tests/test_raxml_tool.py | 2 +-
setup.py | 29 +-
205 files changed, 14369 insertions(+), 13727 deletions(-)
create mode 100644 .codecov.yml
create mode 100644 .travis-tox.ini
copy Bio/Entrez/DTDs/{NCBI_RNA.dtd => NCBI_Systems.dtd} (91%)
create mode 100644 Bio/PDB/mmtf/DefaultParser.py
create mode 100644 Bio/PDB/mmtf/__init__.py
create mode 100644 Doc/examples/alpha.faa
create mode 100644 Doc/examples/beta.faa
delete mode 100644 Doc/images/bottle.png
create mode 100644 Scripts/update_ncbi_codon_table.py
create mode 100644 Tests/EMBL/embl_with_0_line.embl
create mode 100644 Tests/PDB/1A8O.mmtf
create mode 100644 Tests/PDB/4CUP.cif
create mode 100644 Tests/PDB/4CUP.mmtf
rename Tests/PDB/{4zhl.cif => 4ZHL.cif} (100%)
create mode 100644 Tests/PDB/4ZHL.mmtf
create mode 100644 Tests/PDB/Miller_RASA.txt
create mode 100644 Tests/PDB/Sander_RASA.txt
create mode 100644 Tests/PDB/Wilke_RASA.txt
create mode 100644 Tests/PDB/dssp_xtra_Sander.txt
create mode 100644 Tests/common_BioSQL_online.py
copy Tests/{test_BioSQL_MySQLdb.py => test_BioSQL_MySQLdb_online.py} (71%)
copy Tests/{test_BioSQL_mysql_connector.py => test_BioSQL_mysql_connector_online.py} (71%)
copy Tests/{test_BioSQL_psycopg2.py => test_BioSQL_psycopg2_online.py} (71%)
copy Tests/{test_BioSQL_MySQLdb.py => test_BioSQL_sqlite3_online.py} (58%)
copy Tests/{test_Entrez.py => test_Entrez_parser.py} (98%)
rename Tests/{test_Phylo_depend.py => test_Phylo_matplotlib.py} (83%)
create mode 100644 Tests/test_Phylo_networkx.py
create mode 100644 Tests/test_mmtf.py
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