I am pleased to announce the 1.5.1 developer release of Bioperl.
Essential links here Core http://bioperl.org/DIST/bioperl-1.5.1.tar.gz http://bioperl.org/DIST/bioperl-1.5.1.zip http://bioperl.org/DIST/bioperl-1.5.1.tar.bz2
Run http://bioperl.org/DIST/bioperl-run-1.5.1.tar.gz http://bioperl.org/DIST/bioperl-run-1.5.1.zip http://bioperl.org/DIST/bioperl-run-1.5.1.tar.bz2
Ext http://bioperl.org/DIST/bioperl-ext-1.5.1.tar.gz http://bioperl.org/DIST/bioperl-ext-1.5.1.zip http://bioperl.org/DIST/bioperl-ext-1.5.1.tar.bz2
MD5 sum http://bioperl.org/DIST/SIGNATURES.md5
Please see my mailing list post for more information.
I have appended the Change log from Bioperl core compents below 1.5.1 Developer release
o Major problem with how Annotations were written out with Bio::Seq is fixed by reverting to old behavior for Bio::Annotation objects.
o Bio::SeqIO
- genbank.pm \* bug #1871; REFLOOP’ parsing loop, I changed the pattern to expect at l east 9 spaces at the beginning of a line to indicate line wrapping.
\* Treat multi-line SOURCE sections correctly, this defect broke both common_name() and classification()
\* parse swissprot fields in genpept file
\* parse WGS genbank records
- embl.pm \* Changed regexp for ID line. The capturing parentheses are the same, the difference is an optional repeated-not-semi- colon expression following the captured S+. This means the regexp works when the division looks like /PRO;/ or when the division looks like /ANG ;/ - the latter is from EMBL repbase
\* fix ID line parsing: the molecule string can have spaces in it. Like: “genomic DNA”
- swiss.pm: bugs #1727, #1734
- entrezgene.pm \* Added parser for entrezgene ASN1 (text format) files. Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
o Bio::AlignIO
- maf.pm coordinate problem fixed
o Bio::Taxonomy and Bio::DB::Taxonomy
- Parse NCBI XML now so that nearly all the taxonomy up-and-down can be done via Web without downloading all the sequence. o Bio::Tools::Run::RemoteBlast supports more options and complies to changes to the NCBI interface. It is reccomended that you retrieve the data in XML instead of plain-text BLAST report to insure proper parsing and retrieval of all information as NCBI fully expects to change things in the future. o Bio::Tree and Bio::TreeIO
- Fixes so that re-rooting a tree works properly
- Writing out nhx format from a newick/nexus file will properly output bootstrap information. The use must move the internal node labels over to bootstraps. for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) { $node->bootstrap($node->id); $node->id(’’); } - Nexus parsing is much more flexible now, does not care about LF.
- Cladogram drawing module in Bio::Tree::Draw
- Node height and depth now properly calculated
- fix tree pruning algorithm so that node with 1 child gets merged
o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized bugs and improvements were added, see Gbrowse mailing list for most of these.
o Bio::DB::GFF partially supports GFF3. See information about gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
o Better location parsing in Bio::Factory::FTLocationFactory - this is part of the engine for parsing EMBL/GenBank feature table locations. Nested join/order-by/complement are allowed now
o Bio::PrimarySeqI->translate now takes named parameters
o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence reconstruction) is now supported. Parsing different models and branch specific parametes are now supported.
o Bio::Factory::FTLocationFactory - parse hierarchical locations (joins of joins)
o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays for getter/setter functions
o Bio::SearchIO
- blast bug #1739; match scientific notation in score and possible e+ values
- blast.pm reads more WU-BLAST parameters and parameters, match a full database pathname,
- Handle NCBI WEB and newer BLAST formats specifically (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
- psl off-by-one error fixed
- exonerate parsing much improved, CIGAR and VULGAR can be parsed and HSPs can be constructed from them.
- HSPs query/hit now have a seqdesc field filled out (this was always available via $hit->description and $result->query_description
- hmmer.pm can parse -A0 hmmpfam files
- Writer::GbrowseGFF more customizeable.
o Bio::Tools::Hmmpfam make e-value default score displayed in gff, rather than raw score allow parse of multiple records