[med-svn] [bioperl] branch upstream updated (c325d45 -> baf0367)
Charles Plessy
plessy at moszumanska.debian.org
Mon Jul 11 13:09:20 UTC 2016
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch upstream
in repository bioperl.
from c325d45 Imported Upstream version 1.6.924
new 1ceb9ac Imported Upstream version 1.7~rc3
new baf0367 Imported Upstream version 1.7~rc4
The 2 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:
.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 | 328 ---
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 | 528 ++--
Changes | 40 +
DEPENDENCIES | 2 -
INSTALL | 446 ----
INSTALL-WIN.md | 163 ++
INSTALL.WIN | 672 ------
INSTALL.md | 176 ++
MANIFEST | 109 +-
META.json | 2521 +++++++-------------
META.yml | 896 +------
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/db/getGenBank.pl | 2 +-
examples/db/get_seqs.pl | 2 +-
examples/generate_random_seq.pl | 2 +-
examples/root/lib/TestInterface.pm | 37 -
examples/searchio/psiblast_features.pl | 2 +-
examples/structure/structure-io.pl | 2 +-
examples/tk/hitdisplay.pl | 2 +-
examples/tools/gb_to_gff.pl | 2 +-
maintenance/big_split/file_classification.csv | 6 -
.../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/Assembly/ContigSpectrum.t | 9 +-
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 | 217 ++
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 | 55 +-
t/Restriction/IO.t | 56 +-
t/Root/Exception.t | 10 +-
t/Root/HTTPget.t | 1 -
t/Root/IO.t | 25 +-
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 | 22 +-
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 | 35 -
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 +-
229 files changed, 7794 insertions(+), 24206 deletions(-)
delete mode 100644 Bio/Coordinate/Chain.pm
delete mode 100644 Bio/Coordinate/Collection.pm
delete mode 100644 Bio/Coordinate/ExtrapolatingPair.pm
delete mode 100644 Bio/Coordinate/GeneMapper.pm
delete mode 100644 Bio/Coordinate/Graph.pm
delete mode 100644 Bio/Coordinate/MapperI.pm
delete mode 100644 Bio/Coordinate/Pair.pm
delete mode 100644 Bio/Coordinate/Result.pm
delete mode 100644 Bio/Coordinate/Result/Gap.pm
delete mode 100644 Bio/Coordinate/Result/Match.pm
delete mode 100644 Bio/Coordinate/ResultI.pm
delete mode 100644 Bio/Coordinate/Utils.pm
delete mode 100644 Bio/DB/SeqHound.pm
create mode 100644 Bio/DB/Taxonomy/sqlite.pm
rename {examples/root/lib => Bio/Root}/TestObject.pm (96%)
create mode 100644 Bio/Search/Result/INFERNALResult.pm
delete mode 100644 Bio/SearchIO/Writer/BSMLResultWriter.pm
delete mode 100644 Bio/SearchIO/XML/BlastHandler.pm
delete mode 100644 Bio/SearchIO/XML/PsiBlastHandler.pm
delete mode 100644 Bio/SearchIO/blastxml.pm
delete mode 100644 Bio/Tools/Analysis/Protein/Mitoprot.pm
delete mode 100644 Bio/Tools/Run/StandAloneBlast.pm
delete mode 100644 Bio/Tools/Run/StandAloneNCBIBlast.pm
delete mode 100644 Bio/Tools/Run/StandAloneWUBlast.pm
delete mode 100644 Bio/Tools/Run/WrapperBase.pm
delete mode 100644 Bio/Tools/Run/WrapperBase/CommandExts.pm
delete mode 100644 Bio/Tools/Run/hmmer3.pm
delete mode 100644 INSTALL
create mode 100644 INSTALL-WIN.md
delete mode 100644 INSTALL.WIN
create mode 100644 INSTALL.md
delete mode 100644 README
rename {doc => deobfuscator}/Deobfuscator/Build.PL (100%)
rename {doc => deobfuscator}/Deobfuscator/Changes (100%)
rename {doc => deobfuscator}/Deobfuscator/LICENSE (100%)
rename {doc => deobfuscator}/Deobfuscator/MANIFEST (100%)
rename {doc => deobfuscator}/Deobfuscator/META.yml (100%)
rename {doc => deobfuscator}/Deobfuscator/Makefile.PL (100%)
rename {doc => deobfuscator}/Deobfuscator/README (100%)
rename {doc => deobfuscator}/Deobfuscator/bin/deob_index.pl (100%)
rename {doc => deobfuscator}/Deobfuscator/bin/run-deobfuscator-update.pl (100%)
rename {doc => deobfuscator}/Deobfuscator/cgi-bin/deob_detail.cgi (100%)
rename {doc => deobfuscator}/Deobfuscator/cgi-bin/deob_flowchart.png (100%)
rename {doc => deobfuscator}/Deobfuscator/cgi-bin/deob_help.html (100%)
rename {doc => deobfuscator}/Deobfuscator/cgi-bin/deob_interface.cgi (100%)
rename {doc => deobfuscator}/Deobfuscator/excluded_modules.txt (100%)
rename {doc => deobfuscator}/Deobfuscator/lib/Deobfuscator.pm (100%)
rename {doc => deobfuscator}/Deobfuscator/t/00.load.t (100%)
rename {doc => deobfuscator}/Deobfuscator/t/pod.t (100%)
rename {doc => deobfuscator}/makedoc.PL (100%)
delete mode 100644 doc/README
delete mode 100644 examples/root/lib/TestInterface.pm
mode change 100644 => 100755 scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
create mode 100644 scripts/utilities/bp_find-blast-matches.pl
delete mode 100644 scripts/utilities/bp_search2BSML.pl
delete mode 100644 t/Coordinate/CoordinateBoundaryTest.t
delete mode 100644 t/Coordinate/CoordinateGraph.t
delete mode 100644 t/Coordinate/CoordinateMapper.t
delete mode 100644 t/Coordinate/GeneCoordinateMapper.t
create mode 100644 t/LocalDB/Taxonomy/sqlite.t
delete mode 100644 t/RemoteDB/SeqHound.t
create mode 100644 t/Root/RootIO.t
delete mode 100644 t/SearchIO/blastxml.t
delete mode 100644 t/Tools/Analysis/Protein/Mitoprot.t
delete mode 100755 t/Tools/Run/Dummy.pm
delete mode 100755 t/Tools/Run/Dummy/Config.pm
delete mode 100644 t/Tools/Run/StandAloneBlast.t
delete mode 100755 t/Tools/Run/WBCommandExts.t
delete mode 100755 t/Tools/Run/WrapperBase.t
create mode 100644 t/data/AF222649-rc.gbk
create mode 100644 t/data/HM138502.gbk
create mode 100644 t/data/KF527485.gbk
create mode 100644 t/data/ORTHOMCL2345.cluster.aa.fa.aln.aa.phy.txt
create mode 100644 t/data/cmsearch.multi.out
create mode 100644 t/data/cmsearch.nohit.out
create mode 100644 t/data/cmsearch_output.txt
delete mode 100644 t/data/ecoli_domains.rps.xml
create mode 100644 t/data/hmmscan_qry_stop.txt
create mode 100644 t/data/ids-with-spaces.phy
delete mode 100644 t/data/mus.bls.xml
delete mode 100644 t/data/newblast.xml
create mode 100644 t/data/phmmer.out
delete mode 100644 t/data/plague_yeast.bls.xml
delete mode 100644 t/data/psiblast.xml
create mode 100644 t/data/test-1.tab
create mode 100644 t/data/test-1.tab.gb
create mode 100644 t/data/test_space.embl
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