This is a bug fix release from the stable branch.
The Bioperl release 1.2.2 is available at http://www.bioperl.org/DIST/bioperl-1.2.2.tar.gz and is propagating around CPAN now.
Bioperl-run is a collection of modules that wrap bioinformatics applications to allow running them from bioperl. The release cycle of bioperl-run follows the core. The latest bioperl-run release is therefore at: http://www.bioperl.org/DIST/bioperl-run-1.2.2.tar.gz
The main bug fixes in this release are:
bioperl
OBDA Registry code is up to latest specs and fuly functional
Sequence retrieval from NCBI works again after URL change (Bio::DB::GenBank)
The BLAST output parsed now works on megablast and parses even the last hit
Result writers now correctly report alignment start/end info for translated BLAST/FASTA searches (Bio::SearchIO::Writer::(HTML|Text)ResultWriter)
Improvements in closing and keeping open file handles
Robustness of Bio::Graphics modules have been improved
Other improved modules:
Bio::OntologyIO::dagflat
Bio::Annotation::OntologyTerm
Bio::TreeIO::newick
Bio::Tools::BPbl2seq
Bio::Tools::Genemark
Bio::SeqIO::genbank
bioperl-run
SoapLab and PISE improvements
New wrapper for Vista: http://www-gsd.lbl.gov/vista/ (Bio::Tools::Run::Vista)
Other improved modules:
Bio::Tools::Run::Eponine
Bio::Tools::Run::FootPrinter
Bio::Tools::Run::Genewise
Bio::Tools::Run::Genscan
Bio::Tools::Run::Hmmpfam
Bio::Tools::Run::Mdust
Bio::Tools::Run::Signalp
Bio::Tools::Run::Phylo::Phylip::SeqBoot
Bio::Tools::Run::Phylo::Phylip::Neighbor
Bio::Tools::Run::Alignment::Blat
Bio::Tools::Run::Alignment::Lagan
More details are in distribution file ‘Changes’.
Thank you for all who reported bugs and made this release possible.