BioPerl
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* [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
o Bio::SeqIO::genbank can parse now NCBI produced genbank database
which include a number of header lines.
o More strict genbank and EMBL format writing (corrected number of
spaces where appropriate).
o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
for related BPlite BUGS that are unresolved in this release.
o Bio::DB::GenBank, Bio::DB::GenPept have less problems
downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
use expasy mirrors or EBI dbfetch cgi-script.
o A moderate number of documentation improvements were made as
well to provide a better code synopsis in each module.
0.7 Large number of changes, including refactoring of the
Object system, new parsers, new functionality and
all round better system. Highlights are:
o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
Bio::Root::IO for I/O and file/handle capabilities.
o Imported BPlite modules from Ian Korf for BLAST
parsing. This is considered the supported BLAST parser;
Bio::Tools::Blast.pm will eventually phase out due to lack of support.
o Improved Sequence Feature model. Added complete location
modelling (with fuzzy and compound locations). See
Bio::LocationI and the modules under Bio/Location. Added
support in Genbank/EMBL format parsing to completely parse
feature tables for complex locations.
o Moved special support for databanks etc to specialized modules under
Bio/Seq/. One of these supports very large sequences through
a temporary file as a backend.
o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
CDS retrieval and exon shuffling.
o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
DB/GDB (the latter has platform-specific limitations).
o New analysis parser framework for HT sequence annotation (see
Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
o New Alignment IO framework
o New Index modules (Swissprot)
o New modules for running Blast within perl
(Bio::Tools::Run::StandAloneBlast). Added modules for running
Multiple Sequence Alignment tools ClustalW and TCoffee
(Bio::Tools::Run::Alignment).
o New Cookbook-style tutorial (see bptutorial.pl). Improved
documentation across the package.
o Much improved cross platform support. Many known incompatibilities
have been fixed; however, NT and Mac do not work across the entire
setup (see PLATFORMS).
o Many bug fixes, code restructuring, etc. Overall stability and
maintainability benefit a lot.
o A total of 957 automatic tests
0.6.2
There are very few functionality changes but a large
number of software improvements/bug fixes across the package.
o The EMBL/GenBank parsing are improved.
o The Swissprot reading is improved. Swissprot writing
is disabled as it doesn't work at all. This needs to
wait for 0.7 release
o BLAST reports with no hits are correctly parsed.
o Several other bugs of the BLAST parser (regular expressions, ...)
fixed.
o Old syntax calls have been replaced with more modern syntax
o Modules that did not work at all, in particular the Sim4
set have been removed
o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
have improved compliance with interface specs and documentation
o Mailing list documentation updated throughout the distribution
o Most minor bug fixes have happened.
o The scripts in /examples now work and have the modern syntax
rather than the deprecated syntax
0.6.1 Sun April 2 2000
o Sequences can have Sequence Features attached to them
- The sequence features can be read from or written to
EMBL and GenBank style flat files
o Objects for Annotation, including References (but not
full medline abstracts), Database links and Comments are
provided
o A Species object to represent nodes on a taxonomy tree
is provided
o The ability to parse HMMER and Sim4 output has been added
o The Blast parsing has been improved, with better PSI-BLAST
( run in 0.544 second using v1.01-cache-2.11-cpan-39bf76dae61 )