[med-svn] [bioperl] branch master updated (e989e3c -> 344ba34)
Charles Plessy
plessy at moszumanska.debian.org
Mon Jul 11 13:09:17 UTC 2016
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository bioperl.
from e989e3c Upload to unstable
new fe0bb3a Use pristine-tar by default.
new 1ceb9ac Imported Upstream version 1.7~rc3
new 63205c0 Merge tag 'upstream/1.7_rc3'
new baf0367 Imported Upstream version 1.7~rc4
new 40a7b58 Merge tag 'upstream/1.7_rc4'
new 3333a58 New upstream pre-release. No new license statement.
new 95b6743 Delete previously applied patches.
new 01a3e5f Correct name of README file.
new 4cfcb99 Use secure VCS browser URL.
new 344ba34 Current changelog.
The 10 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 +-
debian/changelog | 9 +
debian/control | 2 +-
debian/docs | 2 +-
debian/gbp.conf | 5 +
debian/patches/BioPerl-1.006924-RT106756.patch | 21 -
debian/patches/fix_examples_perl_location | 60 -
debian/patches/series | 3 -
{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 +-
236 files changed, 7810 insertions(+), 24292 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
create mode 100644 debian/gbp.conf
delete mode 100644 debian/patches/BioPerl-1.006924-RT106756.patch
delete mode 100644 debian/patches/fix_examples_perl_location
delete mode 100644 debian/patches/series
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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