BioPerl
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* 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]
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