From jason.stajich at duke.edu Thu Oct 13 21:00:38 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Thu Oct 13 21:10:52 2005 Subject: [Bioperl-announce-l] bioperl 1.5.1 release Message-ID: <99C2FCCA-9282-43B0-8C0A-2DA3495DDFF1@duke.edu> I am EXTREMELY pleased to announce the release of Bioperl 1.5.1. http://bioperl.org/DIST/bioperl-1.5.1.tar.gz http://bioperl.org/DIST/bioperl-1.5.1.tar.bz2 http://bioperl.org/DIST/bioperl-1.5.1.zip http://bioperl.org/DIST/bioperl-run-1.5.1.tar.gz http://bioperl.org/DIST/bioperl-run-1.5.1.tar.bz2 http://bioperl.org/DIST/bioperl-run-1.5.1.zip http://bioperl.org/DIST/bioperl-ext-1.5.1.tar.gz http://bioperl.org/DIST/bioperl-ext-1.5.1.tar.bz2 http://bioperl.org/DIST/bioperl-ext-1.5.1.zip MD5sums are here for those who like that sort of thing: http://bioperl.org/DIST/SIGNATURES.md5 This release represents a developer release which has been thoroughly tested and is very much a warm up for a bioperl 1.6.0 release. This release replaces bioperl 1.5.0 which had several bugs that made it incompatible with several bioperl-1.4.0 scripts. The current release should reverse these incompatibilities as well fix several outstanding bugs (See Changelog below and Changes file in the distribution for more information. We also re-sync things with the NCBI RemoteBlast server so the SearchIO blast parser and RemoteBlast client so this should work now. This has been tested on the latest Gbrowse candidate and it all works great. Please see the HOWTO documents provided in doc/howto/pdf or on the website http://bioperl.org/HOWTOs/ for information on using the modules as well as the API documentation http://doc.bioperl.org. The code from this release is currently provided as an ever updating link under the bioperl-live and bioperl-run and bioperl-ext links under the Active Code link. We will make another doc package for the 1.6 release. I am also releasing bioperl-run, bioperl-ext packages labeled with the 1.5.1 version as these should all be used in sync. I have not released bioperl-db (bioperl BioSQL implementation) at this time but I expect with Hilmar's help we will do that release in the next few weeks. Some thank yous: Heikki Lehvaslaiho and Brian Osborne for many helpful last minute bug fixes, POD fixes, and generally finding and keeping things consistent. Brian also was instrumental in getting the Docbook to work properly and converting us over to XML from my initial SGML template. I also want to thank several new developers who have pitched in lately to both help with the details and give big picture views on things: Albert Villa, Stefan Kirov, George Hartzell. Thanks to Koen van der Drift for providing the OSX port of bioperl on fink and to George and Mauricio for working to support bioperl on freebsd. I hope the linux aficionados will also continue to help put RPMs up for the toolkit. Also thanks to Sean Davis, Barry Moore, and Marc Logghe who have been extremely helpful at answering questions on the list. We are grateful to all the bug-reports that have come in as well this has continued to make this a more robust and tested release. Would you like to see your name in lights (or at least in the thank you above; I'm sure this email is forwarded around the world...=)? Consider helping out the development team. We need help adding information to the FAQ. If you read the mailing list YOU can help with the FAQ distilling the various Q & A on the list into useful questions in the FAQ. On behalf of Bioperl developers, Jason Stajich 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 -- Jason Stajich Duke University http://www.duke.edu/~jes12