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Summary of important user-visible changes for BioPerl
-----------------------------------------------------
{{$NEXT}}
* 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::TreeIO::phyloxml
* Add minimum dependency on base.pm v2.18. Fixes bug in some cases when
using SUPER::new() [#307].
* Fix test for BSML SAX by using lax parser XML::SAX::PurePerl since
the external DTD URL now 404s [#376].
* Updated Bio::Tools::CodonTable for the latest version of NCBI
genetic code table (version 4.9). Previously, version 4.2 was
being used. This update changes codon tables 3, 15, 24, 27-30,
32, and 33 [#389, #391].
* Bio::Tools::CodonTable::is_start_codon now returns true when all
possible codons (in the case of ambiguous codons such as NTG)
are start codons. For some recent versions it was return true
if any of the codons was a start codon. This change is
consistent with the behaviour of is_ter_codon and returns to the
(very) old behaviour [#266].
* Requirement of Test::Memory::Cycle changed to "suggestion" to
make BioPerl easier to install (Test::Memory::Cycle requires a
compiler). Test::Memory::Cycle was only used during for testing
during installation.
1.7.8 2021-02-02 23:02:18-06:00 America/Chicago
* Bio::SeqIO::interpro has been moved to a separate repository to
deal with issues with XML::DOM::XPath bitrot [#347]
* Pull requests:
* Adjust Swiss-Prot FT A..B lines [#348] from @smoe
* Update %FTQUAL_NO_QUOTE: List of qualifiers without quote [#339] from
@hdevillers
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
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]
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!
1.6.924
[Significant changes]
* Bug/feature issue tracking has moved to GitHub Issues:
https://github.com/bioperl/bioperl-live/issues
* DB_File has been demoted from "required" to "recommended",
which should make easier for Windows users to install BioPerl
if they don't need that module.
[New features]
* Bio::Search::HSP::GenericHSP
- Bug #3370, added a "posterior_string" method to retrieve the
posterior probability lines (PP) from HMMER3 reports [fjossandon]
- Added a "consensus_string" method to retrieve the consensus
structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
* Bio::SearchIO::hmmer2
- The number of identical and conserved residues are now calculated
directly from the homology line [fjossandon]
- Now the Query Length and Hit Length are reported when the alignment
runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
- Implemented the capture of the consensus structure lines [fjossandon]
* Bio::SearchIO::hmmer3
- The number of identical and conserved residues are now calculated
directly from the homology line [fjossandon]
- Now the Hit Length is reported when the alignment runs until the end
of the sequence/model ('.]' or '[]') [fjossandon]
- Implemented the capture of the consensus structure lines [fjossandon]
- Implemented the capture of the posterior probability lines [fjossandon]
- Completed the development of NHMMER parsing, including alignments [fjossandon]
* Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
- Feature #2615, moved "_init_parse_params", "max_significance, "signif",
"min_score", "min_bits, and "hit_filter" methods from
'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
This means that the Bio::SearchIO->new() parameters '-signif', '-score',
'-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
besides Blast, instead of being ignored. Added tests for all moved methods
using HMMER outputs and run the full test suite and everything pass [fjossandon]
* Bio::SeqIO::MultiFile
- Autodetection of file format [fangly]
* Bio::Tools::GuessSeqFormat:
- Format detection from non-seekable filehandles such as STDIN [fangly]
[Bug fixes]
* Fix problems when using Storable as backend for cloning [v1.6.x branch, tsibley]
* Fix potential problems with Storable in Bio::DB::SeqFeature::Store [tsibley]
* SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." [nathanweeks]
* Abstract: Fixed ActivePerl incapability of removing temporary files
because of problems closing tied filehandles [fjossandon]
* IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
because ActivePerl were producing a ".index.pag" and ".index.dir"
files instead of a single ".index" file (like Strawberry Perl).
Now those temporary files are correctly considered and deleted. [fjossandon]
* Test files: Added missing module requirements (DB_File and Data::Stag)
to several tests files that were failing because those modules were
not present. Now those test files are correctly skipped instead. [fjossandon]
* Blast: Added support to changes in bl2seq from BLAST+ output, which
now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
* Phylip: Return undef in "next_aln" at file end to avoid
an infinite loop [yschensandiego]
* HMMER3: When a hit description is too long, it is truncated in
the Scores table. In those cases, the more complete description from
the Annotation line (>>) will be used [fjossandon]
* GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
since it is now used by HMMER3 format in alignments [fjossandon]
* GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
to return undef if the query/hit length is unknown (like in some
HMMER outputs), to avoid division by 0 crashes. Also "query_length"
now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
* HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
added support to multi-query reports, reduced code redundancy,
and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
* [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
* [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
* [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
* Fixed some Bio::Root::Utilities subroutines [fjossandon]
* Double-quotes on paths are needed in some places [fjossandon]
* [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
* Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
* Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
with the latest changes made in their own repositories [fjossandon]
* General synching of files with the master branch [fjossandon]
* Fixed tests failing in Windows because of using Linux commands [fjossandon]
* Closed many open filehandles that prevented temporary files deletion [fjossandon]
* Fixed broken MeSH parser [fjossandon]
* Fixed missing detection of format in SeqIO when given a -string [fangly]
1.6.923
* Major Windows support updates! [fjossandon]
* MAKER update to allow for stricter standard codon table [cjfields]
* Better support for circular sequences [fjossandon]
* Fixes for some complex location types [fjossandon]
* Address CONTIG bug in GenBank format, bug #3448 [cjfields]
* Fix bug #2978 related to BLAST report type [fjossandon]
* Deobfuscator fixes [DaveMessina]
1.6.922
* Address CPAN test failures [cjfields]
* Add BIOPROJECT support for Genbank files [hyphaltip]
* Better regex support for HMMER3 output [bosborne]
1.6.921
* Minor update to address CPAN test failures
1.6.920
* Remove Bio::Biblio and related files [carandraug]
- this cause version clashes with an independently-released
version of Bio::Biblio
1.6.910
[New features]
* Hash randomization fixes for perl 5.18.x
- Note: at least one module (Bio::Map::Physical) still has a failing test;
this is documented in bug #3446 and has been TODO'd; we will be pulling
Bio::Map and similar modules out of core into separate distributions in the
1.7.x release series [cjfields]
[New features]
* Bio::Seq::SimulatedRead
- New module to represent reads taken from other sequences [fangly]
* Bio::Root::Root
- Support of Clone::Fast as a faster cloning alternative [fangly]
* Bio::Root::IO
- Moved the format() and variant() methods from Bio::*IO modules to
Bio::Root::IO [fangly]
- Can now use format() to get the type of IO format in use [fangly]
* Bio::Tools::IUPAC
- New regexp() method to create regular expressions from IUPAC sequences
[fangly]
* Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
- Code refresh [fangly]
* Bio::DB::Taxonomy
- Added support for the Greengenes and Silva taxonomies [fangly]
* Bio::Tree::TreeFunctionsI
- get_lineage_string() represents a lineage as a string [fangly]
- add_trait() returns instead of reporting an error when the column
number is exceeded in add_trait() [fangly]
- Option to support tree leaves without trait [fangly]
- Allow ID of 0 in trait files [fangly]
* Bio::DB::Taxonomy::list
- Misc optimizations [fangly]
- Option -names of get_taxon() to help with ambiguous taxa [fangly]
* Bio::DB::Taxonomy::*
- get_num_taxa() returns the number of taxa in the database [fangly]
* Bio::DB::Fasta and Bio::DB::Qual
- support indexing an arbitrary list of files [fangly]
- user can supply an arbitrary index file name [fangly]
- new option to remove index file at the end [fangly]
* Bio::DB::Fasta
- now handles IUPAC degenerate residues [fangly]
* Bio::PrimarySeq and Bio::PrimarySeqI
- speed improvements for large sequences [Ben Woodcroft, fangly]
* Bio::PrimaryQual
- tightened and optimized quality string validation [fangly]
* Bio::SeqIO::fasta
- new method and option 'block', to create FASTA output with space
intervaled blocks (similar to genbank or EMBL) has been implemented.
- package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
in favour of the methods 'width' and 'preferred_id_type` respectively.
* Bio::FeatureIO::*
- moved from bioperl-live into the separate distribution Bio-FeatureIO
* Bio::SeqFeature::Annotated
- moved from bioperl-live into the separate distribution Bio-FeatureIO
* Bio::Cluster::SequenceFamily
- improved performance when using get_members with overlapping multiple
criteria
* Bio::SearchIO::hmmer3
- now supports nhmmer [bosborne]
[Bug fixes]
* [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
* [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
* [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
information was lost in a multi-result blast file [Paul Cantalupo]
* [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
total gaps [Paul Cantalupo]
* [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
* [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
when end of domain indicator is split across lines [Paul Cantalupo]
* [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
cjfields]
* [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
instances where blank lines are within sequences [cjfields]
* Bio::DB::Fasta reports correct alphabet for files with multiple sequence
types [fangly]
* Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
* [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
cjfields]
* Various fixes for Stockholm file indexing and processing [bosborne]
* Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
breaks parsing [cjfields]
* Fix case where Bio::Seq::Meta* objects with no meta information could not
be reverse-complemented [fangly]
* Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
* Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
when unsure that values will be numerical [fangly]
* Fix undef warnings in Bio::SeqIO::embl [fangly]
* Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
* Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
* Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
Sallou]
* Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
source_tag and display_name must return a string, not undef [fangly]
* Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
add_SeqFeature takes a single argument [fangly]
* Use cross-platform filenames and temporary directory in
Bio::DB::Taxonomy::flatfile [fangly]
* Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
properly identified as existing taxa in the database [fangly]
* Fix issue where a Bio::DB::Taxonomy::list object could not be created
without also passing a lineage to store [fangly]
* Prevent passing a directory to the gi2taxid option (-g) of
bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
[fangly]
* Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
* Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
* Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
object before trying to access, and no longer returns repeated sequences.
1.6.901 May 18, 2011
[Notes]
* Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
modules using Ace will also be deprecated [lds, cjfields]
* Minor bug fix release
* Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
* Address Build.PL issues when DBI is not present [hartzell]
* Skip gbxml.t and Interpro tests when modules not installed [cjfields]
* Remove deprecated code for perl 5.14.0 compat [cjfields]
* Due to schema changes and lack of support for older versions, support
for NeXML 0.9 is only (very) partially implemented.
See: https://redmine.open-bio.org/issues/3207
[Bug fixes]
* [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
docs [genehack, cjfields]
* $VERSION for CPAN/cpanm-based installs was broken; force setting of
module version from dist_version (probably not the best way to do this,
but it seems to work) [rbuels, cjfields]
1.6.900 April 14, 201
[Notes]
* This will probably be the last release to add significant features to
core modules; subsequent releases will be for bug fixes alone.
We are planning on a restructuring of core for summer 2011, potentially
as part of the Google Summer of Code. This may become BioPerl 2.0.
* Version bump represents 'just prior to v 1.7'. We may have point
releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
This code essentially is what is on the github master branch.
[New features]
* Core code updated for perl 5.12.x [cjfields, Charle Tilford]
* Bio::Tree refactor
- major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
- removal of Scalar::Util::weaken code, which was causing odd headaches
with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
* Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
many others]
* Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
[Warren Kretzschmar]
* Bio::SeqIO::gbxml
- bug 2515 - new contribution [Ryan Golhar, jhannah]
* Bio::Assembly::IO
- support for reading Maq, Sam and Bowtie files [maj]
- support for reading 454 GS Assembler (Newbler) ACE files [fangly]
- bug 2483: support for writing ACE files [Joshua Udall, fangly]
- bug 2599: support DBLINK annotation in GenBank files [cjfields]
- bug 2726: reading/writing granularity: whole scaffold or one contig
at a time [Joshua Udall, fangly]
* Bio::OntologyIO
- Added parsing of xrefs to OBO files, which are stored as secondary
dbxrefs of the cvterm [Naama Menda]
- General Interpro-related code refactors [dukeleto, rbuels, cjfields]
* PAML code updated to work with PAML 4.4d [DaveMessina]
[Bug fixes]
* [3198] - sort tabular BLAST hits by score [DaveMessina]
* [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
* [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
* [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
[cjfields]
* [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
* [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
* [3164] - TreeFunctionsI syntax bug [gjuggler]
* [3163] - AssemblyIO speedup [fangly]
* [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
hyphaltip]
* [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
* [3158] - fix EMBL file mis-parsing [cjfields]
* [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
cjfields]
* [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
* [3148] - URL change for UniProt [cjfields]
* [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
* [3136] - HMMer3 parser fixes [kblin]
* [3126] - catch description [Toshihiko Akiba]
* [3122] - Catch instances where non-seekable filehandles were being
seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
* [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
[dukeleto, rbuels, cjfields]
* [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
jhannah]
* [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
* [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
cjfields]
* [3107] - BLAST alignment column_from_residue_number() [cjfields]
* [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
* [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
* [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
* [3086] - EMBL misparsing long tags [kblin, cjfields]
* [3085] - CommandExts and array of files [maj, hyphaltip]
* [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
for alignment slices [Ha X. Dang, cjfields]
* [3076] - XMFA alignment strand wrong [Ha X., cjfields]
* [3073] - fix parsing of GenBank files from RDP [cjfields]
* [3068] - FASTQ parse failure with trailing 0 [cjfields]
* [3064] - All-gap midline BLAST report issues [cjfields]
* [3063] - BLASt report RID [Razi Khaja, cjfields]
* [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
* [3053] - LOCUS line formatting [M. Wayne, cjfields]
* [3039] - correct Newick output root node branch length [gjuggler,
DaveMessina]
* [3038] - SELEX alignment error [Bernd, cjfields]
* [3033] - PrimarySeq ID setting [Bernd, maj]
* [3032] - Fgenesh errors [Wes Barris, hyphaltip]
* [3034] - AlignIO::clustal output [Bernd, DaveMessina]
* [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
* [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
* [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
* [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
PAML 4.4d [DaveMessina]
* [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
DaveMessina]
* [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
* [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
* [3017] - using threads with Bio::DB::GenBank [cjfields]
* [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
* [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
* [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
* [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
* [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
cjfields]
* [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
* [2977] - TreeIO issues [DaveMessina]
* [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
* [2944] - Bio::Tools::GFF score [cjfields]
* [2942] - correct MapTiling output [maj]
* [2939] - PDB residue insertion codes [John May, maj]
* [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
* [2928] - GuessSeqFormat raw [maj]
* [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
* [2922] - open() directive issue [cjfields]
* [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
* [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
* [2899] - SeqFeature::Store host issues [lstein, dbolser]
* [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
cjfields]
* [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
* [2876] - CDD search with RemoteBlast [Malcolm Cook]
* [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
* [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
* [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
* [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
* [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
* [2758] - Bio::AssemblyIO ace problems [fangly]
* [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
* [2726] - ace file IO [Josh, fangly]
* [2700] - Refactor Build.PL [cjfields]
* [2673] - addition of simple Root-based clone() method [cjfields]
* [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
* [2599] - support for DBLINK annotation in GenBank files [cjfields]
* [2594] - Bio::Species memory leak [cjfields]
* [2515] - GenBank XML parser [jhannah]
* [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
* [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
* [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
cjfields]
* [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
[Deprecated]
* Bio::Expression modules - these were originally designed to go with the
bioperl-microarray suite of tools, however they have never been completed
and so have been removed from the distribution. The original code has
been moved into the inactive bioperl-microarray suite. [cjfields]
[Other]
* Repository moved from Subversion (SVN) to
http://github.com/bioperl/bioperl-live [cjfields]
* Bug database has moved to Redmine (https://redmine.open-bio.org)
* Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
Thieme have been moved to their own distribution (Bio-Microarray).
[cjfields]
1.6.1 Sept. 29, 2009 (point release)
* No change from last alpha except VERSION and doc updates [cjfields]
1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
* Fix for silent OBDA bug related to FASTA validation [cjfields]
1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
* Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
* [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
[cjfields]
* BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
* WinXP test fixes [cjfields, maj]
* BioPerl.pod added for descriptive information, fixes CPAN indexing
[cjfields]
* Minor doc fixes [cjfields]
1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
* Fix tests failing due to merging issues [cjfields]
* More documentation updates for POD parsing [cjfields]
1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
* Bio::Root::Build
- fix YAML meta data generation [cjfields]
1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
* Bio::Align::DNAStatistics
- fix divide by zero problem [jason]
* Bio::AlignIO::*
- bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
* Bio::AlignIO::stockholm
- bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
* Bio::Assembly::Tools::ContigSpectrum
- function to score contig spectrum [fangly]
* Bio::DB::EUtilities
- small updates [cjfields]
* Bio::DB::Fasta
- berkeleydb database now autoindexes wig files and locks correctly
[lstein]
* Bio::DB::HIV
- various small updates for stability; tracking changes to LANL
database interface [maj]
* Bio::DB::SeqFeature (lots of updates and changes)
- add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
- bug 2835 - patch [Dan Bolser]
- bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
* Bio::DB::SwissProt
- bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
* Bio::Factory::FTLocationFactory
- mailing list bug fix [cjfields]
* Bio::LocatableSeq
- performance work on column_from_residue_number [hartzell]
* Bio::Matrix::IO::phylip
- bug 2800 - patch to fix phylip parsing [Wei Zou]
* Bio::Nexml
- Google Summer of Code project from Chase Miller - parsers for Nexml
file format [maj, chmille4]
* Bio::PopGen
- Make Individual, Population, Marker objects AnnotatableI [maj]
- simplify LD code [jason]
* Bio::RangeI
- deal with empty intersection [jason]
* Bio::Restriction
- significant overhaul of Bio::Restriction system: complete support for
external and non-palindromic cutters. [maj]
* Bio::Root::Build
- CPANPLUS support, no automatic installation [sendu]
* Bio::Root::IO
- allow IO::String (regression fix) [cjfields]
- catch unintentional undef values [cjfields]
- throw if non-fh is passed to -fh [maj]
* Bio::Root::Root/RootI
- small debugging and core fixes [cjfields]
* Bio::Root::Test
- bug RT 48813 - fix for Strawberry Perl bug [kmx]
* Bio::Root::Utilities
- bug 2737 - better warnings [cjfields]
* Bio::Search
- tiling completely refactored, HOWTO added [maj]
NOTE : Bio::Search::Hit::* classes do not use this code directly; we
will deprecate usage of the older tiling code in the next BioPerl
release
- small fixes [cjfields]
* Bio::SearchIO
- Infernal 1.0 output now parsed [cjfields]
- new parser for gmap -f9 output [hartzell]
- bug 2852 - fix infinite loop in some output [cjfields]
- blastxml output now passes all TODO tests [cjfields]
- bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
- RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
- bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
* Bio::Seq::LargePrimarySeq
- delete tempdirs [cjfields]
- bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
* Bio::Seq::Quality
- extract regions based on quality threshold value [Dan Bolser, heikki]
- bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
* Bio::SeqFeature::Lite
- various Bio::DB::SeqFeature-related fixes [lstein]
* Bio::SeqFeature::Tools::TypeMapper
- additional terms for GenBank to SO map [scain]
* Bio::SeqIO::chadoxml
- bug 2785 - patch to get this working for bp_seqconvert [cjfields]
* Bio::SeqIO::embl
- support for CDS records [dave_messina, Sylvia]
* Bio::SeqIO::fastq
- complete refactoring to handle all FASTQ variants, perform validation,
write output. API now conforms with other Bio* parsers and the rest of
Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
[cjfields]
* Bio::SeqIO::genbank
- bug 2784 - fix DBSOURCE issue [Phillip Garland]
- bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
* Bio::SeqIO::largefasta
- parser returns a Bio::Seq::LargePrimarySeq [jhannah]
* Bio::SeqIO::raw
- add option for 'single' and 'multiple'
* Bio::SeqIO::scf
- bug 2881 - fix scf round-tripping [Adam Søgren]
* Bio::SeqUtils
- bug 2766, 2810 - copy over tags from features, doc fixes [David
Jackson]
* Bio::SimpleAlign
- bug 2793 - patch for add_seq index issue [jhannah, maj]
- bug 2801 - throw if args are required [cjfields]
- bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
[Tristan Lefebure, maj]
- bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
- fix POD and add get_SeqFeatures filter [maj]
* Bio::Tools::dpAlign
- add support for LocatableSeq [ymc]
- to be moved to a separate distribution [cjfields, rbuels]
* Bio::Tools::EUtilities
- fix for two bugs from mail list [Adam Whitney, cjfields]
- add generic ItemContainerI interface for containing same methods
[cjfields]
* Bio::Tools::HMM
- fix up code, add more warnings [cjfields]
- to be moved to a separate distribution [cjfields, rbuels]
* Bio::Tools::Primer3
- bug 2862 - fenceposting issue fixed [maj]
* Bio::Tools::Run::RemoteBlast