[med-svn] [bioperl] 01/05: Merge tag 'upstream/1.7'

[Andreas Tille]

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tille pushed a commit to tag debian/1.7.1-1
in repository bioperl.

commit 80d25649a32b911774e58f06eaa246c7ed2b57b0
Merge: 344ba34 532cf8a
Author: Andreas Tille <tille at debian.org>
Date:   Fri Oct 21 11:22:47 2016 +0200

    Merge tag 'upstream/1.7'
    
    Upstream version 1.7

 .travis.yml                             |  13 +-
 Bio/Align/AlignI.pm                     | 102 +++----
 Bio/AlignIO/fasta.pm                    |   2 +-
 Bio/AlignIO/maf.pm                      |   4 +-
 Bio/AnalysisI.pm                        |  14 +-
 Bio/DB/Expression/geo.pm                |   8 +-
 Bio/DB/GFF/Typename.pm                  |   2 +-
 Bio/DB/GenBank.pm                       |   2 +-
 Bio/DB/MeSH.pm                          |  98 ++++---
 Bio/DB/SeqVersion/gi.pm                 |   6 +-
 Bio/DB/Taxonomy/entrez.pm               |  59 ++--
 Bio/Index/Stockholm.pm                  |  60 ++--
 Bio/Restriction/IO/prototype.pm         |   2 +-
 Bio/Root/IO.pm                          |  29 +-
 Bio/Root/Version.pm                     |   2 +-
 Bio/Search/Hit/GenericHit.pm            |   5 +-
 Bio/Search/Hit/ModelHit.pm              |   3 +
 Bio/Search/Result/GenericResult.pm      |   4 +-
 Bio/Search/Result/ResultI.pm            |   4 +-
 Bio/SearchIO/Writer/HTMLResultWriter.pm |   4 +-
 Bio/SeqFeature/Tools/Unflattener.pm     |   2 +-
 Bio/SeqIO.pm                            |  18 +-
 Bio/SeqIO/bsml.pm                       |  49 ++--
 Bio/SeqIO/embl.pm                       |  29 +-
 Bio/SeqIO/tinyseq.pm                    |   4 +-
 Bio/SeqIO/tinyseq/tinyseqHandler.pm     |   6 +-
 Bio/Tools/CodonTable.pm                 |  28 +-
 Bio/Tools/ERPIN.pm                      | 350 -----------------------
 Bio/Tools/Infernal.pm                   | 492 --------------------------------
 Bio/Tools/RNAMotif.pm                   | 427 ---------------------------
 Bio/Tools/Run/RemoteBlast.pm            |   4 +-
 Build.PL                                |  10 +-
 Changes                                 |  52 +++-
 INSTALL-WIN.md                          |  87 +++---
 INSTALL.md                              | 160 ++++++++---
 MANIFEST                                |   6 +-
 META.json                               |  17 +-
 META.yml                                |  12 +-
 maintenance/authors.pl                  |   2 +-
 scripts/DB-HIV/bp_hivq.pl               |  24 +-
 scripts/DB/bp_biofetch_genbank_proxy.pl |   4 +-
 scripts/DB/bp_biogetseq.pl              |   2 +-
 scripts/seq/bp_extract_feature_seq.pl   |   6 +-
 scripts/seq/bp_seqcut.pl                |  17 +-
 scripts/taxa/bp_taxid4species.pl        |   2 +-
 scripts/utilities/bp_netinstall.pl      |  24 +-
 scripts/utilities/bp_search2gff.pl      |   4 +-
 t/AlignIO/fasta.t                       |   8 +-
 t/LocalDB/Fasta.t                       |  20 +-
 t/LocalDB/Taxonomy/sqlite.t             |   3 +-
 t/RemoteDB/MeSH.t                       |  21 +-
 t/RemoteDB/Taxonomy.t                   |  30 +-
 t/SeqIO/fastq.t                         |  16 +-
 t/SeqTools/CodonTable.t                 |  27 +-
 t/Tools/Analysis/Protein/ELM.t          |  40 +--
 t/Tools/rnamotif.t                      | 230 ---------------
 t/data/EG352462.gbxml                   |   2 +-
 t/data/dbfa/mixed_alphabet.fasta        |  12 +
 t/data/fastq/RT98876.fastq              |   4 +
 t/data/so.obo                           |  20 +-
 t/data/test.locuslink                   |  12 +-
 t/data/test.tseq                        |   2 +-
 travis_scripts/trigger-dockerhub.sh     |  49 ++++
 63 files changed, 797 insertions(+), 1960 deletions(-)

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