We are pleased to announce the release of Biopython 1.41. Many improvements were made in Biopython during the eight months since the previous release, and the new release contains lots of bugfixes, improvements, new functionalities, and better documentation. To pick a few, there's the new Bio.MEME module by Jason Hackney, updates to the Blast parser using Bertrand Frottier's NCBIXML code, a BLAT parser by Yair Benita, numerous updates in Bio.PDB, CompareACE support in AlignAce, and improved user-friendliness in Bio.Seq.
Lots of people of contributed to this release, in particular Frank Kauff (Bio.Nexus), Jason Hackney (Bio.MEME), Thomas Hamelryck (Bio.PDB), Frederic Sohm (Bio.Restriction), James Casbon (Bio.SCOP) for bug fixes and updates, Peter (Bio.Blast.NCBIXML test cases), and of course Jeff Chang, Brad Chapman, Andrew Dalke, and Iddo Friedberg for Biopython and the fool-proof instructions on how to roll a release, which made this a lot easier than I anticipated. My apologies if I forgot to thank somebody.
Michiel de Hoon on behalf of the Biopython development team.
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 postfor 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
Release Candidate 4 for bioperl 1.5.1 (Developer release) core, run, and ext packages is available.
Several bug fixes went in last week so I've made what I hope to be
the last release candidate before 1.5.1 goes out.
More Info:
http://portal.open-bio.org/pipermail/bioperl-l/2005-October/019904.html
Files are here:
http://bioperl.org/DIST/bioperl-1.5.1-rc4.tar.gz
http://bioperl.org/DIST/bioperl-1.5.1-rc4.zip
http://bioperl.org/DIST/bioperl-run-1.5.1-rc4.tar.gz
http://bioperl.org/DIST/bioperl-run-1.5.1-rc4.zip
http://bioperl.org/DIST/bioperl-ext-1.5.1-rc4.tar.gz
http://bioperl.org/DIST/bioperl-ext-1.5.1-rc4.zip