./biology/bioperl, Perl tools for computational molecular biology

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Branch: CURRENT, Version: 1.7.7, Package name: bioperl-1.7.7, Maintainer: pkgsrc-users

The Bioperl Project is an international association of developers of open
source Perl tools for bioinformatics, genomics and life science research.

Bioperl is a collection of object-oriented Perl modules created by the
Bioperl Project. It forms the basis of a large number of bioinformatics
and genomics applications.


Required to run:
[textproc/p5-XML-Simple] [textproc/p5-libxml] [textproc/p5-YAML] [textproc/p5-XML-DOM] [textproc/p5-XML-Parser] [textproc/p5-XML-SAX] [textproc/p5-XML-SAX-Writer] [textproc/p5-XML-Twig] [textproc/p5-XML-Writer] [www/p5-HTML-TableExtract] [www/p5-libwww] [www/p5-HTML-Parser] [graphics/p5-GraphViz] [graphics/p5-GD] [lang/perl5] [net/p5-SOAP-Lite] [math/p5-Spreadsheet-ParseExcel] [devel/p5-Error] [devel/p5-Array-Compare] [devel/p5-List-MoreUtils] [devel/p5-Set-Scalar] [devel/p5-Graph] [devel/p5-IO-String] [devel/p5-Clone] [graphics/p5-SVG] [devel/p5-Sort-Naturally] [biology/p5-Bio-ASN1-EntrezGene] [graphics/p5-SVG-Graph] [print/p5-PostScript] [math/p5-Algorithm-Munkres] [devel/p5-Convert-Binary-C] [devel/p5-Data-Stag]

Required to build:
[textproc/p5-Text-Diff] [devel/p5-Module-Build] [devel/p5-Test-Most] [pkgtools/cwrappers]

Master sites: (Expand)

SHA1: 06a6d7a9faebe6e63c02ba5b31d1f7618289f534
RMD160: 7aa9377f07e6b8fa0095f06898655acc11cfc27e
Filesize: 7356.232 KB

Version history: (Expand)


CVS history: (Expand)


   2020-09-06 22:07:47 by Thomas Klausner | Files touched by this commit (3) | Package updated
Log message:
bioperl: update to 1.7.7.

1.7.7     2019-12-07 13:41:36-06:00 America/Chicago

    * The program bp_chaos_plot has been removed.

    * GD is now no longer a dependency, suggestion or requirement.

    * #321 - GenBank format fix for un-quoted features, text wrapping

    * Bio::DB::Query::WebQuery now includes methods for delay(), delay_policy(),
      and a 'private' _sleep() function that mirror those from
      Bio::DB::WebDBSeqI, primarily for compliance with potential website
      restrictions for the number and frequency of queries (e.g. NCBI eUtils).

    * Fix bug #329, related to Bio::Tree::Statistics::transfer_bootstrap_expectation
      in last release.

1.7.6     2019-08-28 12:37:01+01:00 Europe/London

    * The program bp_classify_hits_kingdom has been removed and is
      now part of the examples documentation instead.

    * GD is now listed as a suggestion instead of a requirement.  The
      bp_chaos_plot program will now work with the GD module.

    * New method Bio::Tree::Statistics::transfer_bootstrap_expectation
      to compute Transfer Bootstrap Expectation (TBE) for internal
      nodes based on the methods outlined in Lemoine et al, Nature,
      2018.

    * New method Bio::SeqIO::fasta::next_seq_fast to retrieve next
      sequence in the stream faster but not perfect.

1.7.5     2019-02-11 14:57:45+00:00 Europe/London

    * The following modules have been removed from the BioPerl
      distribution to be part of a separate distribution with
      independent development:

          Bio::Symbol::*

    * The Bio::Seq::SeqWithQuality module, which was deprecated since
      2001, was finally removed.

    * The deprecated() method has been deprecated.  It is recommended
      to use Carp::carp to warn.

    * The following methods have been deprecated for a long while and
      have now been removed:

          Bio::Align::AlignI->no_residues
          Bio::Align::AlignI->no_sequences
          Bio::LocatableSeq->no_gap
          Bio::LocatableSeq->no_sequences
          Bio::SeqFeature::Generic->slurp_gff_file
          Bio::SimpleAlign->no_residues
          Bio::SimpleAlign->no_sequences

1.7.4     2019-02-05 16:23:53+00:00 Europe/London

    * Fix Bio::Root::Test, and the testuite, to properly check for
      internet connection and the NO_NETWORK_TESTING environment
      variable.  Previously, tests that required internet connection
      were not being skipped, causing tests to fail.

1.7.3     2019-01-30 13:30:34+00:00 Europe/London

    * The following modules have been removed from the BioPerl
      distribution to be part of a separate distribution.  They have
      been integrated into other module distributions for independent
      development:

          Bio::Align::Graphics
          Bio::AlignIO::nexml
          Bio::AlignIO::stockholm
          Bio::Assembly::*
          Bio::Cluster::*
          Bio::ClusterI::*
          Bio::ClusterIO::*
          Bio::DB::Ace
          Bio::DB::BioFetch
          Bio::DB::CUTG
          Bio::DB::EMBL
          Bio::DB::EntrezGene
          Bio::DB::Expression::*
          Bio::DB::GFF
          Bio::DB::GFF::Adaptor::*
          Bio::DB::GFF::Aggregator::*
          Bio::DB::GFF::Featname
          Bio::DB::GFF::Feature
          Bio::DB::GFF::Homol
          Bio::DB::GFF::RelSegment
          Bio::DB::GFF::Segment
          Bio::DB::GFF::Typename
          Bio::DB::GenBank
          Bio::DB::GenPept
          Bio::DB::HIV::*
          Bio::DB::MeSH
          Bio::DB::NCBIHelper
          Bio::DB::Query::GenBank
          Bio::DB::Query::HIVQuery
          Bio::DB::RefSeq
          Bio::DB::SeqFeature::*
          Bio::DB::SeqVersion::*
          Bio::DB::SwissProt
          Bio::DB::TFBS::*
          Bio::DB::Taxonomy::entrez
          Bio::DB::Taxonomy::sqlite
          Bio::DB::Universal
          Bio::Draw::Pictogram
          Bio::Factory::MapFactoryI
          Bio::Index::Hmmer
          Bio::Index::Stockholm
          Bio::LiveSeq::*
          Bio::Map::*
          Bio::MapIO::*
          Bio::MolEvol::CodonModel
          Bio::Nexml::Factory
          Bio::NexmlIO
          Bio::Perl
          Bio::Phenotype::*
          Bio::PhyloNetwork::*
          Bio::PopGen::*
          Bio::Restriction::*
          Bio::Root::Build
          Bio::Search::HSP::HMMERHSP
          Bio::Search::HSP::HmmpfamHSP
          Bio::Search::Hit::HMMERHit
          Bio::Search::Hit::HmmpfamHit
          Bio::Search::Hit::hmmer3Hit
          Bio::Search::Result::HMMERResult
          Bio::Search::Result::HmmpfamResult
          Bio::Search::Result::hmmer3Result
          Bio::SearchDist
          Bio::SearchIO::hmmer
          Bio::SearchIO::hmmer2
          Bio::SearchIO::hmmer3
          Bio::SearchIO::hmmer_pull
          Bio::SeqEvolution::*
          Bio::SeqFeature::SiRNA::*
          Bio::SeqIO::abi
          Bio::SeqIO::agave
          Bio::SeqIO::alf
          Bio::SeqIO::chadoxml
          Bio::SeqIO::chaos
          Bio::SeqIO::chaosxml
          Bio::SeqIO::ctf
          Bio::SeqIO::entrezgene
          Bio::SeqIO::excel
          Bio::SeqIO::exp
          Bio::SeqIO::flybase_chadoxml
          Bio::SeqIO::lasergene
          Bio::SeqIO::nexml
          Bio::SeqIO::pln
          Bio::SeqIO::strider
          Bio::SeqIO::ztr
          Bio::Structure::*
          Bio::Taxonomy::*
          Bio::Tools::AlignFactory
          Bio::Tools::Analysis::* (except SimpleAnalysisBase)
          Bio::Tools::Gel
          Bio::Tools::HMMER::*
          Bio::Tools::Hmmpfam
          Bio::Tools::Phylo::Gumby
          Bio::Tools::Protparam
          Bio::Tools::Run::RemoteBlast
          Bio::Tools::SiRNA::*
          Bio::Tools::dpAlign
          Bio::Tools::pSW
          Bio::Tree::AlleleNode
          Bio::Tree::Draw::Cladogram
          Bio::TreeIO::nexml
          Bio::TreeIO::svggraph
          Bio::Variation::*

    * The following modules are new in the BioPerl distribution.  They
      have been previously released in the BioPerl-Run distribution.
      This will enable smaller distributions that provide a
      Bio::Tool::Run interface, to be only dependent on the BioPerl
      distribution instead of the whole (very large) BioPerl-Run:

          Bio::Tools::Run::Analysis
          Bio::Tools::Run::AnalysisFactory
          Bio::Tools::Run::Phylo::PhyloBase
          Bio::Tools::Run::WrapperBase
          Bio::Tools::Run::WrapperBase::CommandExts

    * The following programs have been removed:

          bp_biofetch_genbank_proxy
          bp_blast2tree
          bp_bulk_load_gff
          bp_composite_LD
          bp_das_server
          bp_download_query_genbank
          bp_fast_load_gff
          bp_flanks
          bp_genbank2gff
          bp_generate_histogram
          bp_heterogeneity_test
          bp_hivq
          bp_hmmer_to_table
          bp_load_gff
          bp_meta_gff
          bp_netinstall
          bp_parse_hmmsearch
          bp_process_wormbase
          bp_query_entrez_taxa
          bp_remote_blast
          bp_seqfeature_delete
          bp_seqfeature_gff3
          bp_seqfeature_load

    * Because of the move of so many modules and programs into
      separate distributions, the following modules are no longer
      prerequisites:

          Ace
          Ace::Sequence::Homol
          Algorithm::Munkres
          Apache::DBI
          Archive::Tar
          Array::Compare
          Bio::ASN1::EntrezGene
          Bio::Expression::Contact
          Bio::Expression::DataSet
          Bio::Expression::Platform
          Bio::Expression::Sample
          Bio::Ext::Align
          Bio::GMOD::CMap::Utils
          Bio::Phylo::Factory
          Bio::Phylo::Forest::Tree
          Bio::Phylo::IO
          Bio::Phylo::Matrices
          Bio::Phylo::Matrices::Datum
          Bio::Phylo::Matrices::Matrix
          Bio::SeqFeature::Annotated
          Bio::SeqIO::staden::read
          Bio::Tools::Run::Alignment::Clustalw
          Bio::Tools::Run::Ensembl
          Bio::Tools::Run::Phylo::Molphy::ProtML
          Bio::Tools::Run::Phylo::Phylip::Neighbor
          Bio::Tools::Run::Phylo::Phylip::ProtDist
          Bio::Tools::Run::Phylo::Phylip::ProtPars
          Bio::Tools::Run::Samtools
          CGI
          CPAN
          Cache::FileCache
          Config
          Convert::Binary::C
          DBD::Pg
          DBD::SQLite
          Data::Stag::XMLWriter
          Encode
          English
          ExtUtils::Install
          ExtUtils::Manifest
          File::Glob
          GD::Simple
          Getopt::Std
          Graph::Undirected
          GraphViz
          HTML::HeadParser
          HTML::TableExtract
          LWP
          LWP::Simple
          MIME::Base64
          Memoize
          PostScript::TextBlock
          SVG
          SVG::Graph
          SVG::Graph::Data
          SVG::Graph::Data::Node
          SVG::Graph::Data::Tree
          Sort::Naturally
          Spreadsheet::ParseExcel
          Term::ReadLine
          Text::NSP::Measures::2D::Fisher2::twotailed
          Text::ParseWords
          Time::Local
          Tree::DAG_Node
          URI::Escape
          WWW::Mechanize
          XML::Simple

    * The following is a new prerequisite:

          Test::RequiresInternet

    * The deobfuscator has been removed.

    * The emacs bioperl minor mode is no longer distributed as part of the
      perl module distributions.  See
      https://github.com/bioperl/emacs-bioperl-mode
   2020-08-31 20:13:29 by Thomas Klausner | Files touched by this commit (3631) | Package updated
Log message:
*: bump PKGREVISION for perl-5.32.
   2019-11-02 23:09:01 by Roland Illig | Files touched by this commit (10)
Log message:
biology: align variable assignments

pkglint -Wall -F --only aligned --only indent -r
   2019-08-11 15:25:21 by Thomas Klausner | Files touched by this commit (3557) | Package updated
Log message:
Bump PKGREVISIONs for perl 5.30.0
   2018-08-22 11:48:07 by Thomas Klausner | Files touched by this commit (3558)
Log message:
Recursive bump for perl5-5.28.0
   2017-09-17 09:48:11 by Thomas Klausner | Files touched by this commit (2) | Package updated
Log message:
bioperl: update to 1.007002.

Add p5-Text-Diff as test dependency.

1.7.2 - "Entebbe"

    [Bugs]

    * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
    * #245 - Code coverage fixes [zmughal,cjfields]
    * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
    * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
    * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as \ 
fh() does not take arguments in [thibauthourlier,bosborne]
    * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
    * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
    * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
    * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
    * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite \ 
[nathanweeks,bosborne]
    * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
    * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]

    [Code changes]

    * PAML-related code from bioperl and bioperl-run are now in a separate \ 
distribution on CPAN [carandraug]
   2016-11-10 15:00:17 by Filip Hajny | Files touched by this commit (1)
Log message:
Give up maintainership.
   2016-11-06 09:05:24 by Wen Heping | Files touched by this commit (3) | Package updated
Log message:
Update to 1.007001

Upstream changes:
1.7.1 - "Election"

    [Bugs]

    * Minor release to incorporate fix for CPAN indexing, which
      prevented proper updates [cjfields]
    * Fix problem in managing Target attribute for gff3 [Jukes34]
    * Minor bug fixes related to NCBI HTTPS support [cjfields]

1.7.0 - "Disney"

    [New site]

    * We have migrated to Github Pages. This was actually planned, but the
      recent OBF server compromise forced our hand.

      Brian Osborne [bosborne] took this under his wing to move docs and has
      done a tremendous amount of work formatting the site and working out some
      of the idiosyncracies with the new Jekyll-based design.  Mark Jensen, Paul
      Cantalupo and Franscison Ossandon also helped.  Kudos!!

    * Similarly, the official issue tracker is now Github Issues.  This has
      been updated in the relevant documentation bits (we hope!)

    [Code changes]

    * Previously deprecated modules removed
      * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
    * Bio::DB::SeqHound has been removed due to the service no longer being
      available
    * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
      reasons due to the server no longer having a valid cert
    * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
    * Bio::Coordinate, Bio::SearchIO::blastxml,
      Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
      added on CPAN

    [New features]

    * Docker instances of tagged releases are available! [hlapp]
    * NCBI HTTPS support [mjohnson and others]
    * Bio::SearchIO::infernal
      - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
    * Bio::Search::HSP::ModelHSP
      - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
        reports [pcantalupo]
    * Bio::Search::Result::INFERNALResult
      - Added new module to represent features of Infernal reports [pcantalupo]
    * Bio::DB::Taxonomy SQLite option [cjfields]
    * WrapperBase quoted option values [majensen]
    * Various documentation fixes and updates [bosborne]

   [Bug Fixes]

    * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing \ 
[cjfields]
    * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
    * NeXML parser fixes [fjossandon]
    * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
    * RT 103272 : SeqFeature database deletion skipped features with a decimal -
      Joshua Fortriede (Xenbase)
    * RT 98374: AlignIO issues with sequence names not correctly parsing - \ 
Xiaoyu Zhuo
    * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
    * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
    * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
    * Issue #81: Small updates to make sure possible memory leaks are detected \ 
[cjfields]
    * Issue #84: EMBL format wrapping problem [nyamned]
    * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
    * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
      or compiled C code (when Inline::C is installed) [rocky]
    * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
    * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements \ 
[fjossandon]
    * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
    * For HMMer report parsing, changed "$hsp->bits" to return 0 \ 
instead of undef
      to be consistent with "$hit->bits" behaviour [fjossandon]
    * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
      aminoacids made "next_seq" confused and broke the parser [fjossandon]
    * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
      Definition, so now "join(complement(C..D),complement(A..B))" is \ 
equivalent
      to "complement(join(A..B,C..D))" [fjossandon]
    * For the many many many fixes that weren't mentioned - blame the release guy!