[med-svn] [bioperl] branch master updated (54f6c21 -> 0ffe53a)
Andreas Tille
tille at debian.org
Sun Dec 3 18:00:40 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository bioperl.
from 54f6c21 Upload to unstable
new 51c2815 New upstream version
new 469af47 New upstream version 1.7.2
new a33ec2f Update upstream source from tag 'upstream/1.7.2'
new 4312cd2 cme fix dpkg-copyright
new 6735676 Standards-Version: 4.1.1
new 0ffe53a Upload to unstable
The 6 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 | 81 +-
Bio/AlignIO/phylip.pm | 529 +++---
Bio/AlignIO/xmfa.pm | 30 +-
Bio/AnalysisI.pm | 2 +-
Bio/Annotation/OntologyTerm.pm | 2 +-
Bio/AnnotationCollectionI.pm | 2 +-
Bio/Assembly/Contig.pm | 40 +-
Bio/Assembly/ScaffoldI.pm | 2 +-
Bio/Assembly/Singlet.pm | 2 +-
Bio/Assembly/Tools/ContigSpectrum.pm | 2 +-
Bio/Cluster/UniGene.pm | 4 +-
Bio/DB/EMBL.pm | 2 +-
Bio/DB/Fasta.pm | 2 +-
Bio/DB/Flat/BinarySearch.pm | 2 +-
Bio/DB/GFF.pm | 6 +-
Bio/DB/GFF/Adaptor/dbi.pm | 2 +-
Bio/DB/GFF/Adaptor/dbi/mysql.pm | 2 +-
Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm | 2 +-
Bio/DB/GFF/Adaptor/dbi/oracle.pm | 2 +-
Bio/DB/GFF/Adaptor/dbi/pg.pm | 2 +-
Bio/DB/GFF/Segment.pm | 6 +-
Bio/DB/GenBank.pm | 2 +-
Bio/DB/GenPept.pm | 2 +-
Bio/DB/GenericWebAgent.pm | 24 +-
Bio/DB/HIV/HIVQueryHelper.pm | 2 +-
Bio/DB/IndexedBase.pm | 78 +-
Bio/DB/LocationI.pm | 20 +-
Bio/DB/MeSH.pm | 4 +-
Bio/DB/Qual.pm | 2 +-
Bio/DB/Query/HIVQuery.pm | 2 +-
Bio/DB/RefSeq.pm | 4 +-
Bio/DB/ReferenceI.pm | 20 +-
Bio/DB/Registry.pm | 38 +-
Bio/DB/SeqFeature/Store.pm | 2 +-
Bio/DB/SeqFeature/Store/DBI/SQLite.pm | 2 +-
Bio/DB/SeqFeature/Store/GFF2Loader.pm | 2 +-
Bio/DB/SeqFeature/Store/GFF3Loader.pm | 6 +-
Bio/DB/SeqFeature/Store/Loader.pm | 2 +-
Bio/DB/TFBS/transfac_pro.pm | 8 +-
Bio/DB/Taxonomy/entrez.pm | 122 +-
Bio/DB/Taxonomy/flatfile.pm | 2 +-
Bio/DB/Taxonomy/sqlite.pm | 6 +-
Bio/DB/WebDBSeqI.pm | 4 +-
Bio/DescribableI.pm | 2 +-
Bio/Factory/ApplicationFactoryI.pm | 12 +-
Bio/Factory/ObjectFactoryI.pm | 2 +-
Bio/Index/Abstract.pm | 68 +-
Bio/Index/AbstractSeq.pm | 2 +-
Bio/Index/Blast.pm | 60 +-
Bio/Index/BlastTable.pm | 52 +-
Bio/Index/Hmmer.pm | 54 +-
Bio/Index/Stockholm.pm | 6 +-
Bio/LiveSeq/IO/Loader.pm | 2 +-
Bio/LiveSeq/IO/README | 2 +-
Bio/LiveSeq/Mutation.pm | 2 +-
Bio/LiveSeq/SeqI.pm | 4 +-
Bio/LocatableSeq.pm | 2 +-
Bio/Location/Atomic.pm | 10 +-
Bio/Location/Fuzzy.pm | 2 +-
Bio/Location/FuzzyLocationI.pm | 2 +-
Bio/Location/Simple.pm | 6 +-
Bio/Location/Split.pm | 2 +-
Bio/Location/SplitLocationI.pm | 2 +-
Bio/LocationI.pm | 2 +-
Bio/Map/CytoMarker.pm | 2 +-
Bio/Map/CytoPosition.pm | 6 +-
Bio/Map/GeneRelative.pm | 4 +-
Bio/Map/Microsatellite.pm | 2 +-
Bio/Map/OrderedPosition.pm | 2 +-
Bio/Map/Physical.pm | 2 +-
Bio/Map/Position.pm | 2 +-
Bio/Map/PositionI.pm | 2 +-
Bio/Map/Relative.pm | 2 +-
Bio/Map/TranscriptionFactor.pm | 2 +-
Bio/Matrix/Generic.pm | 6 +-
Bio/Matrix/PSM/IO.pm | 2 +-
Bio/Matrix/PSM/IO/masta.pm | 6 +-
Bio/Matrix/PSM/InstanceSite.pm | 2 +-
Bio/Matrix/PSM/ProtMatrix.pm | 6 +-
Bio/Matrix/PSM/ProtPsm.pm | 2 +-
Bio/Matrix/PSM/Psm.pm | 4 +-
Bio/Matrix/PSM/PsmI.pm | 4 +-
Bio/Matrix/PSM/SiteMatrix.pm | 12 +-
Bio/Matrix/PSM/SiteMatrixI.pm | 4 +-
Bio/Ontology/OntologyStore.pm | 2 +-
Bio/Ontology/SimpleOntologyEngine.pm | 2 +-
Bio/Ontology/Term.pm | 4 +-
Bio/Ontology/TermI.pm | 2 +-
Bio/OntologyIO/Handlers/BaseSAXHandler.pm | 26 +-
Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm | 4 +-
Bio/OntologyIO/obo.pm | 22 +-
Bio/ParameterBaseI.pm | 22 +-
Bio/Perl.pm | 2 +-
Bio/PopGen/HtSNP.pm | 6 +-
Bio/PopGen/Individual.pm | 2 +-
Bio/PopGen/Population.pm | 4 +-
Bio/PopGen/TagHaplotype.pm | 4 +-
Bio/PrimarySeq.pm | 10 +-
Bio/PrimarySeqI.pm | 8 +-
Bio/PullParserI.pm | 2 +-
Bio/Restriction/Analysis.pm | 2 +-
Bio/Restriction/Enzyme.pm | 2 +-
Bio/Restriction/EnzymeI.pm | 2 +-
Bio/Restriction/IO/base.pm | 6 +-
Bio/Restriction/IO/itype2.pm | 2 +-
Bio/Root/Exception.pm | 2 +-
Bio/Root/Root.pm | 2 +-
Bio/Root/Storable.pm | 4 +-
Bio/Root/Test.pm | 6 +-
Bio/Root/Utilities.pm | 10 +-
Bio/Root/Version.pm | 2 +-
Bio/Search/BlastUtils.pm | 2 +-
Bio/Search/HSP/BlastPullHSP.pm | 2 +-
Bio/Search/HSP/GenericHSP.pm | 2 +-
Bio/Search/HSP/HMMERHSP.pm | 2 +-
Bio/Search/HSP/HSPI.pm | 2 +-
Bio/Search/HSP/ModelHSP.pm | 2 +-
Bio/Search/HSP/PullHSPI.pm | 2 +-
Bio/Search/Hit/GenericHit.pm | 2 +-
Bio/Search/Hit/HMMERHit.pm | 2 +-
Bio/Search/Hit/ModelHit.pm | 2 +-
Bio/Search/Iteration/IterationI.pm | 2 +-
Bio/Search/SearchUtils.pm | 2 +-
Bio/Search/Tiling/TilingI.pm | 2 +-
Bio/SearchDist.pm | 2 +-
Bio/SearchIO.pm | 58 +-
Bio/SearchIO/Writer/HTMLResultWriter.pm | 2 +-
Bio/SearchIO/Writer/TextResultWriter.pm | 2 +-
Bio/SearchIO/exonerate.pm | 2 +-
Bio/SearchIO/fasta.pm | 48 +-
Bio/SearchIO/hmmer3.pm | 2 +-
Bio/Seq.pm | 6 +-
Bio/Seq/EncodedSeq.pm | 2 +-
Bio/Seq/Meta/Array.pm | 4 +-
Bio/Seq/MetaI.pm | 8 +-
Bio/Seq/PrimaryQual.pm | 4 +-
Bio/Seq/PrimedSeq.pm | 2 +-
Bio/Seq/QualI.pm | 8 +-
Bio/Seq/RichSeqI.pm | 2 +-
Bio/Seq/SeqBuilder.pm | 4 +-
Bio/Seq/SeqWithQuality.pm | 14 +-
Bio/Seq/SequenceTrace.pm | 6 +-
Bio/Seq/SimulatedRead.pm | 2 +-
Bio/SeqFeature/AnnotationAdaptor.pm | 46 +-
Bio/SeqFeature/Computation.pm | 6 +-
Bio/SeqFeature/Generic.pm | 4 +-
Bio/SeqFeature/Lite.pm | 2 +-
Bio/SeqFeature/PositionProxy.pm | 2 +-
Bio/SeqFeature/SubSeq.pm | 2 +-
Bio/SeqFeature/Tools/Unflattener.pm | 2 +-
Bio/SeqFeature/TypedSeqFeatureI.pm | 2 +-
Bio/SeqIO.pm | 24 +-
Bio/SeqIO/ace.pm | 2 +-
Bio/SeqIO/bsml.pm | 20 +-
Bio/SeqIO/chadoxml.pm | 4 +-
Bio/SeqIO/chaos.pm | 2 +-
Bio/SeqIO/embl.pm | 6 +-
Bio/SeqIO/fasta.pm | 2 +-
Bio/SeqIO/fastq.pm | 2 +-
Bio/SeqIO/game/gameHandler.pm | 2 +-
Bio/SeqIO/gcg.pm | 4 +-
Bio/SeqIO/genbank.pm | 12 +-
Bio/SeqIO/interpro.pm | 2 +-
Bio/SeqIO/lasergene.pm | 2 +-
Bio/SeqIO/mbsout.pm | 2 +-
Bio/SeqIO/msout.pm | 2 +-
Bio/SeqIO/pir.pm | 59 +-
Bio/SeqIO/seqxml.pm | 2 +-
Bio/SeqIO/swiss.pm | 4 +-
Bio/SeqIO/tigr.pm | 4 +-
Bio/SeqUtils.pm | 2 +-
Bio/Structure/Entry.pm | 4 +-
Bio/Structure/Residue.pm | 4 +-
Bio/Structure/SecStr/DSSP/Res.pm | 8 +-
Bio/Structure/SecStr/STRIDE/Res.pm | 2 +-
Bio/Taxonomy.pm | 4 +-
Bio/Tools/AlignFactory.pm | 26 +-
Bio/Tools/Analysis/DNA/ESEfinder.pm | 2 +-
Bio/Tools/Analysis/Protein/ELM.pm | 2 +-
Bio/Tools/Analysis/Protein/NetPhos.pm | 4 +-
Bio/Tools/ECnumber.pm | 2 +-
Bio/Tools/GFF.pm | 140 +-
Bio/Tools/Phylo/Gerp.pm | 2 +-
Bio/Tools/Phylo/PAML.pm | 1872 --------------------
Bio/Tools/Phylo/PAML/Codeml.pm | 255 ---
Bio/Tools/Phylo/PAML/ModelResult.pm | 564 ------
Bio/Tools/Phylo/PAML/Result.pm | 1238 -------------
Bio/Tools/PrositeScan.pm | 49 +-
Bio/Tools/SiRNA.pm | 2 +-
Bio/Tools/Sigcleave.pm | 2 +-
Bio/Tools/dpAlign.pm | 2 +-
Bio/Tools/pSW.pm | 4 +-
Bio/Tree/AlleleNode.pm | 2 +-
Bio/Tree/NodeI.pm | 2 +-
Bio/Tree/TreeFunctionsI.pm | 6 +-
Bio/TreeIO/nexus.pm | 2 +-
Bio/TreeIO/pag.pm | 2 +-
Bio/Variation/AAReverseMutate.pm | 2 +-
Bio/Variation/VariantI.pm | 6 +-
Changes | 21 +
DEPENDENCIES | 361 ++--
INSTALL.md | 81 +-
MANIFEST | 39 +-
META.json | 1619 +++++++++--------
META.yml | 1615 +++++++++--------
debian/changelog | 7 +
debian/control | 4 +-
debian/copyright | 29 +-
deobfuscator/Deobfuscator/bin/deob_index.pl | 30 +-
deobfuscator/Deobfuscator/cgi-bin/deob_detail.cgi | 2 +-
deobfuscator/Deobfuscator/cgi-bin/deob_help.html | 4 +-
.../Deobfuscator/cgi-bin/deob_interface.cgi | 4 +-
deobfuscator/Deobfuscator/lib/Deobfuscator.pm | 28 +-
examples/searchio/blast_example.pl | 4 +-
scripts/DB/bp_flanks.pl | 2 +-
scripts/index/bp_fetch.pl | 6 +-
scripts/index/bp_index.pl | 4 +-
scripts/seq/bp_seqcut.pl | 2 +-
scripts/seq/bp_unflatten_seq.pl | 2 +-
scripts/utilities/bp_netinstall.pl | 2 +-
scripts/utilities/bp_pairwise_kaks.pl | 211 ---
scripts/utilities/bp_search2gff.pl | 2 +-
t/LocalDB/Flat.t | 11 +-
t/RemoteDB/SeqVersion.t | 2 +-
t/RemoteDB/Taxonomy.t | 49 +-
t/SeqIO/pir.t | 48 +-
t/Tools/Phylo/PAML.t | 545 ------
t/Tools/PrositeScan.t | 44 +
t/data/M0.mlc | 159 --
t/data/aaml.mlc | 54 -
t/data/aaml_pairwise.mlc | 49 -
t/data/baseml.pairwise | 31 -
t/data/baseml.usertree | 42 -
t/data/branchSite.mlc | 115 --
t/data/bug3331.mlc | 128 --
t/data/codeml.mlc | 190 --
t/data/codeml315.mlc | 132 --
t/data/codeml4.mlc | 230 ---
t/data/codeml43.mlc | 231 ---
t/data/codeml43_nssites.mlc | 251 ---
t/data/codeml45.mlc | 460 -----
t/data/codeml_lysozyme/2NG.dN | 8 -
t/data/codeml_lysozyme/2NG.dS | 8 -
t/data/codeml_lysozyme/2NG.tt | 8 -
t/data/codeml_lysozyme/4fold.nuc | 26 -
t/data/codeml_lysozyme/lnf | 170 --
t/data/codeml_lysozyme/lysozymeSmall.ctl | 37 -
t/data/codeml_lysozyme/lysozymeSmall.trees | 36 -
t/data/codeml_lysozyme/lysozymeSmall.txt | 64 -
t/data/codeml_lysozyme/mlc | 273 ---
t/data/codeml_lysozyme/rst | 1165 ------------
t/data/codeml_lysozyme/rst1 | 1 -
t/data/codeml_lysozyme/rub | 48 -
t/data/codeml_nan.mlc | 177 --
t/data/codeml_nssites.mlc | 329 ----
t/data/ps_scan/out.PrositeScan | 10 +
t/data/seqfile-no-desc.pir | 9 +
t/data/singleNSsite.mlc | 152 --
t/data/testaln.xmfa | 14 +-
t/data/yn00.mlc | 106 --
t/data/yn00_45.mlc | 595 -------
travis_scripts/trigger-dockerhub.sh | 5 +
262 files changed, 3329 insertions(+), 13011 deletions(-)
delete mode 100644 Bio/Tools/Phylo/PAML.pm
delete mode 100644 Bio/Tools/Phylo/PAML/Codeml.pm
delete mode 100644 Bio/Tools/Phylo/PAML/ModelResult.pm
delete mode 100644 Bio/Tools/Phylo/PAML/Result.pm
delete mode 100644 scripts/utilities/bp_pairwise_kaks.pl
delete mode 100644 t/Tools/Phylo/PAML.t
create mode 100644 t/Tools/PrositeScan.t
delete mode 100644 t/data/M0.mlc
delete mode 100644 t/data/aaml.mlc
delete mode 100644 t/data/aaml_pairwise.mlc
delete mode 100644 t/data/baseml.pairwise
delete mode 100644 t/data/baseml.usertree
delete mode 100644 t/data/branchSite.mlc
delete mode 100644 t/data/bug3331.mlc
delete mode 100644 t/data/codeml.mlc
delete mode 100644 t/data/codeml315.mlc
delete mode 100644 t/data/codeml4.mlc
delete mode 100644 t/data/codeml43.mlc
delete mode 100644 t/data/codeml43_nssites.mlc
delete mode 100644 t/data/codeml45.mlc
delete mode 100644 t/data/codeml_lysozyme/2NG.dN
delete mode 100644 t/data/codeml_lysozyme/2NG.dS
delete mode 100644 t/data/codeml_lysozyme/2NG.tt
delete mode 100644 t/data/codeml_lysozyme/4fold.nuc
delete mode 100644 t/data/codeml_lysozyme/lnf
delete mode 100644 t/data/codeml_lysozyme/lysozymeSmall.ctl
delete mode 100644 t/data/codeml_lysozyme/lysozymeSmall.trees
delete mode 100644 t/data/codeml_lysozyme/lysozymeSmall.txt
delete mode 100644 t/data/codeml_lysozyme/mlc
delete mode 100644 t/data/codeml_lysozyme/rst
delete mode 100644 t/data/codeml_lysozyme/rst1
delete mode 100644 t/data/codeml_lysozyme/rub
delete mode 100644 t/data/codeml_nan.mlc
delete mode 100644 t/data/codeml_nssites.mlc
create mode 100644 t/data/ps_scan/out.PrositeScan
create mode 100644 t/data/seqfile-no-desc.pir
delete mode 100644 t/data/singleNSsite.mlc
delete mode 100644 t/data/yn00.mlc
delete mode 100644 t/data/yn00_45.mlc
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