[med-svn] [bioperl] 03/10: Merge tag 'upstream/1.7_rc3'
Charles Plessy
plessy at moszumanska.debian.org
Mon Jul 11 13:09:18 UTC 2016
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch master
in repository bioperl.
commit 63205c0eac4a0d8f0deb741023917b9347a2d008
Merge: fe0bb3a 1ceb9ac
Author: Charles Plessy <plessy at debian.org>
Date: Mon Jul 11 21:42:57 2016 +0900
Merge tag 'upstream/1.7_rc3'
Upstream version 1.7~rc3
# gpg: Signature faite le lun. 11 juil. 2016 21:42:57 JST
# gpg: avec la clef RSA 0xC5BD6C8F2295D502
# gpg: Bonne signature de « Charles Plessy <plessy at debian.org> »
# Empreinte de clef principale : 7347 1499 CC60 ED9E EE80 5946 C5BD 6C8F 2295 D502
.travis.yml | 25 +-
AUTHORS | 2 +
Bio/Align/Utilities.pm | 11 +-
Bio/AlignIO/nexml.pm | 43 +-
Bio/AlignIO/phylip.pm | 2 +-
Bio/AlignIO/stockholm.pm | 2 +-
Bio/Coordinate/Chain.pm | 151 --
Bio/Coordinate/Collection.pm | 363 ---
Bio/Coordinate/ExtrapolatingPair.pm | 185 --
Bio/Coordinate/GeneMapper.pm | 1286 ----------
Bio/Coordinate/Graph.pm | 336 ---
Bio/Coordinate/MapperI.pm | 133 --
Bio/Coordinate/Pair.pm | 381 ---
Bio/Coordinate/Result.pm | 230 --
Bio/Coordinate/Result/Gap.pm | 23 -
Bio/Coordinate/Result/Match.pm | 26 -
Bio/Coordinate/ResultI.pm | 23 -
Bio/Coordinate/Utils.pm | 188 --
Bio/DB/BioFetch.pm | 6 +-
Bio/DB/EMBL.pm | 2 +-
Bio/DB/Fasta.pm | 17 +-
Bio/DB/Flat.pm | 4 +-
Bio/DB/IndexedBase.pm | 58 +-
Bio/DB/NCBIHelper.pm | 4 +-
Bio/DB/Qual.pm | 9 +-
Bio/DB/Query/GenBank.pm | 2 +-
Bio/DB/Registry.pm | 4 +-
Bio/DB/SeqFeature/Store/DBI/SQLite.pm | 97 +-
Bio/DB/SeqFeature/Store/LoadHelper.pm | 2 +-
Bio/DB/SeqFeature/Store/Loader.pm | 8 +-
Bio/DB/SeqFeature/Store/memory.pm | 7 +-
Bio/DB/SeqHound.pm | 758 ------
Bio/DB/Taxonomy/entrez.pm | 2 +-
Bio/DB/Taxonomy/flatfile.pm | 27 +-
Bio/DB/Taxonomy/sqlite.pm | 696 ++++++
Bio/Factory/FTLocationFactory.pm | 47 +-
Bio/Index/Fasta.pm | 3 +-
Bio/Index/Qual.pm | 3 +-
Bio/Location/Split.pm | 207 +-
Bio/MolEvol/CodonModel.pm | 8 +-
Bio/NexmlIO.pm | 51 +-
Bio/Ontology/OBOEngine.pm | 14 +-
Bio/OntologyIO/obo.pm | 388 ++-
Bio/PrimarySeqI.pm | 15 +-
Bio/Restriction/Enzyme.pm | 29 +-
Bio/Restriction/IO/prototype.pm | 9 +-
Bio/Root/Build.pm | 802 +------
Bio/Root/Exception.pm | 7 +-
Bio/Root/IO.pm | 9 +-
Bio/Root/Root.pm | 14 +-
Bio/Root/RootI.pm | 23 +-
Bio/Root/Storable.pm | 8 +-
Bio/Root/Test.pm | 241 +-
{examples/root/lib => Bio/Root}/TestObject.pm | 8 +-
Bio/Root/Utilities.pm | 7 +-
Bio/Root/Version.pm | 13 +-
Bio/Search/HSP/HMMERHSP.pm | 1 +
Bio/Search/HSP/ModelHSP.pm | 19 +
Bio/Search/Result/INFERNALResult.pm | 121 +
Bio/Search/Tiling/MapTileUtils.pm | 1 +
Bio/SearchIO/Writer/BSMLResultWriter.pm | 354 ---
Bio/SearchIO/Writer/GbrowseGFF.pm | 2 +-
Bio/SearchIO/XML/BlastHandler.pm | 315 ---
Bio/SearchIO/XML/PsiBlastHandler.pm | 312 ---
Bio/SearchIO/blastxml.pm | 475 ----
Bio/SearchIO/fasta.pm | 2 +-
Bio/SearchIO/hmmer2.pm | 199 +-
Bio/SearchIO/hmmer3.pm | 261 +-
Bio/SearchIO/infernal.pm | 412 +++-
Bio/Seq.pm | 43 +-
Bio/SeqFeature/Generic.pm | 63 +-
Bio/SeqFeatureI.pm | 19 +-
Bio/SeqIO/embl.pm | 23 +-
Bio/SeqIO/embldriver.pm | 2 +-
Bio/SeqIO/entrezgene.pm | 2 +-
Bio/SeqIO/gbdriver.pm | 2 +-
Bio/SeqIO/genbank.pm | 30 +-
Bio/SeqIO/largefasta.pm | 2 +-
Bio/SeqIO/nexml.pm | 58 +-
Bio/SeqIO/phd.pm | 2 +-
Bio/SeqIO/swissdriver.pm | 2 +-
Bio/SeqIO/table.pm | 23 +-
Bio/Taxon.pm | 32 +-
Bio/Tools/Alignment/Consed.pm | 2 +-
Bio/Tools/Analysis/Protein/GOR4.pm | 8 +-
Bio/Tools/Analysis/Protein/HNN.pm | 7 +-
Bio/Tools/Analysis/Protein/Mitoprot.pm | 5 +-
Bio/Tools/Analysis/Protein/Sopma.pm | 7 +-
Bio/Tools/CodonTable.pm | 194 +-
Bio/Tools/Run/RemoteBlast.pm | 14 +-
Bio/Tools/Run/StandAloneBlast.pm | 634 -----
Bio/Tools/Run/StandAloneNCBIBlast.pm | 538 -----
Bio/Tools/Run/StandAloneWUBlast.pm | 299 ---
Bio/Tools/Run/WrapperBase.pm | 511 ----
Bio/Tools/Run/WrapperBase/CommandExts.pm | 1385 -----------
Bio/Tools/Run/hmmer3.pm | 0
Bio/Tools/SiRNA/Ruleset/tuschl.pm | 5 +-
Bio/Tree/Statistics.pm | 6 +-
Bio/TreeIO/nexml.pm | 30 +-
BioPerl.pm | 91 +-
Build.PL | 531 +++--
Changes | 40 +
INSTALL | 446 ----
INSTALL-WIN.md | 163 ++
INSTALL.WIN | 672 ------
INSTALL.md | 176 ++
MANIFEST | 107 +-
META.json | 2519 +++++++-------------
META.yml | 893 +------
README | 258 --
README.md | 81 +-
{doc => deobfuscator}/Deobfuscator/Build.PL | 0
{doc => deobfuscator}/Deobfuscator/Changes | 0
{doc => deobfuscator}/Deobfuscator/LICENSE | 0
{doc => deobfuscator}/Deobfuscator/MANIFEST | 0
{doc => deobfuscator}/Deobfuscator/META.yml | 0
{doc => deobfuscator}/Deobfuscator/Makefile.PL | 0
{doc => deobfuscator}/Deobfuscator/README | 0
.../Deobfuscator/bin/deob_index.pl | 0
.../Deobfuscator/bin/run-deobfuscator-update.pl | 0
.../Deobfuscator/cgi-bin/deob_detail.cgi | 0
.../Deobfuscator/cgi-bin/deob_flowchart.png | Bin
.../Deobfuscator/cgi-bin/deob_help.html | 0
.../Deobfuscator/cgi-bin/deob_interface.cgi | 0
.../Deobfuscator/excluded_modules.txt | 0
.../Deobfuscator/lib/Deobfuscator.pm | 0
{doc => deobfuscator}/Deobfuscator/t/00.load.t | 0
{doc => deobfuscator}/Deobfuscator/t/pod.t | 0
{doc => deobfuscator}/makedoc.PL | 0
doc/README | 2 -
examples/db/dbfetch | 4 +-
examples/root/lib/TestInterface.pm | 37 -
maintenance/big_split/file_classification.csv | 2 -
.../Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl | 14 +
scripts/DB/bp_biofetch_genbank_proxy.pl | 2 +-
scripts/seq/bp_seqcut.pl | 234 +-
scripts/seq/bp_translate_seq.pl | 19 +-
scripts/taxa/bp_taxid4species.pl | 53 +-
scripts/utilities/bp_find-blast-matches.pl | 487 ++++
scripts/utilities/bp_pairwise_kaks.pl | 82 +-
scripts/utilities/bp_search2BSML.pl | 70 -
t/Align/Utilities.t | 10 +-
t/AlignIO/nexml.t | 3 +-
t/AlignIO/phylip.t | 31 +-
t/Coordinate/CoordinateBoundaryTest.t | 527 ----
t/Coordinate/CoordinateGraph.t | 42 -
t/Coordinate/CoordinateMapper.t | 686 ------
t/Coordinate/GeneCoordinateMapper.t | 602 -----
t/LocalDB/Flat.t | 82 +-
t/LocalDB/Index/Index.t | 37 +-
t/LocalDB/Taxonomy/sqlite.t | 251 ++
t/Perl.t | 5 +-
t/RemoteDB/BioFetch.t | 9 +-
t/RemoteDB/EMBL.t | 16 +-
t/RemoteDB/HIV/HIV.t | 6 +-
t/RemoteDB/HIV/HIVQuery.t | 4 +-
t/RemoteDB/MeSH.t | 20 +-
t/RemoteDB/SeqHound.t | 59 -
t/RemoteDB/SeqRead_fail.t | 16 +-
t/RemoteDB/SeqVersion.t | 4 +-
t/RemoteDB/SwissProt.t | 3 +-
t/RemoteDB/Taxonomy.t | 56 +-
t/Restriction/IO.t | 56 +-
t/Root/Exception.t | 10 +-
t/Root/HTTPget.t | 1 -
t/Root/IO.t | 1 +
t/Root/RootI.t | 12 +-
t/Root/RootIO.t | 21 +
t/SearchIO/blastxml.t | 531 -----
t/SearchIO/hmmer.t | 192 +-
t/SearchIO/infernal.t | 172 +-
t/Seq/PrimarySeq.t | 15 +-
t/Seq/Seq.t | 11 +-
t/SeqFeature/Generic.t | 11 +-
t/SeqFeature/Location.t | 24 +-
t/SeqFeature/LocationFactory.t | 347 ++-
t/SeqIO/Splicedseq.t | 28 +-
t/SeqIO/embl.t | 20 +-
t/SeqIO/genbank.t | 63 +-
t/SeqIO/table.t | 40 +-
t/SeqTools/CodonTable.t | 67 +-
t/Species.t | 68 +-
t/Tools/Analysis/Protein/ELM.t | 4 +-
t/Tools/Analysis/Protein/GOR4.t | 38 +-
t/Tools/Analysis/Protein/HNN.t | 61 +-
t/Tools/Analysis/Protein/Mitoprot.t | 30 +-
t/Tools/Analysis/Protein/NetPhos.t | 1 -
t/Tools/Analysis/Protein/Sopma.t | 63 +-
t/Tools/Run/Dummy.pm | 21 -
t/Tools/Run/Dummy/Config.pm | 75 -
t/Tools/Run/RemoteBlast.t | 1 -
t/Tools/Run/RemoteBlast_rpsblast.t | 4 +-
t/Tools/Run/StandAloneBlast.t | 185 --
t/Tools/Run/WBCommandExts.t | 66 -
t/Tools/Run/WrapperBase.t | 129 -
t/Tools/SiRNA.t | 6 +-
t/Tree/TreeIO/nexml.t | 115 +-
t/Tree/TreeIO/nhx.t | 6 +-
t/data/AF222649-rc.gbk | 91 +
t/data/HM138502.gbk | 79 +
t/data/KF527485.gbk | 82 +
t/data/ORTHOMCL2345.cluster.aa.fa.aln.aa.phy.txt | 19 +
t/data/U58726.gb | 507 ++--
t/data/cmsearch.multi.out | 243 ++
t/data/cmsearch.nohit.out | 44 +
t/data/cmsearch_output.txt | 102 +
t/data/dmel_2Lchunk.gb | 36 +-
t/data/ecoli_domains.rps.xml | 610 -----
t/data/hmmscan_qry_stop.txt | 63 +
t/data/hmmscan_sec_struct.out | 47 +
t/data/ids-with-spaces.phy | 19 +
t/data/mus.bls.xml | 660 -----
t/data/newblast.xml | 1219 ----------
t/data/phmmer.out | 183 ++
t/data/plague_yeast.bls.xml | 383 ---
t/data/psiblast.xml | 1826 --------------
t/data/test-1.tab | 3 +
t/data/test-1.tab.gb | 16 +
t/data/test_space.embl | 19 +
travis_scripts/dependency_installs | 4 +-
220 files changed, 7811 insertions(+), 23832 deletions(-)
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