[med-svn] [bioperl] branch upstream updated (5a744a0 -> 469af47)
Andreas Tille
tille at debian.org
Sun Dec 3 18:00:42 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository bioperl.
from 5a744a0 New upstream version 1.7.1
new 469af47 New upstream version 1.7.2
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:
.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 +++++++++--------
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 +
259 files changed, 3305 insertions(+), 12995 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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