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
b868df933a