From heikki at ebi.ac.uk Wed Oct 1 12:30:47 2003 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Wed Oct 1 18:27:57 2003 Subject: [Bioperl-announce-l] Bioperl Developer snapshot 1.3.01 Message-ID: <1065025847.2553.112.camel@localhost> Bioperl developer snap shot 1.3.01 ----------------------------------- This is the first developer snap shot from the BioPerl CVS head that will eventually lead to release 1.4. Note that this is called snap shot rather than release. Number of things are guarantied to fail. The meaning of the snapshot is get more people to move from 1.2 series into using the latest code base to have enough momentum to put together a solid release. 1.3 series will be available only from the BioPerl FTP site and its mirrors, not from CPAN. Depending on developer activity new snapshots will be made available weekly or forth-nightly. These snap shots will be taken from the CVS head until there is a good reason to branch. http://bioperl.org/DIST/current_core_unstable.tar.gz http://bioperl.org/DIST/bioperl-1.3.01.tar.gz New things is featured for the first time in 1.3 which will be relaesed in 1.4 include: - installable scripts - Bio::Popgen - Bio::Restriction - Bio::Tools::Analysis - web based DNA and Protein analysis tools - Bio::Seq::Meta - per residue annotable sequences - Bio::Matrix::IO - improved Bio::Tools::Genewise - Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA - small inhibitory RNA - Bio::SeqFeature::Tools - seqFeature mapping tools - Bio::Tools::dpAlign - pure perl dynamic programming sequence alignment - new Bio::SearchIO formats - new parsers in Bio::Tools: Blat, Geneid, Lagan, Mdust, Promoterwise,PrositeScan, - hundreds of new and improved files Start these now! All feed back to bioperl-l@bioperl.org -Heikki -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From heikki at ebi.ac.uk Fri Oct 17 06:20:34 2003 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Fri Oct 17 18:34:32 2003 Subject: [Bioperl-announce-l] Bioperl Developer snapshot 1.3.02 Message-ID: <1066386033.2446.128.camel@localhost> Bioperl developer snap shot 1.3.02 --------------------------------- This is the second developer snap shot from the BioPerl CVS head that will eventually lead to release 1.4. http://bioperl.org/DIST/current_core_unstable.tar.gz http://bioperl.org/DIST/bioperl-1.3.02.tar.gz Last fortnight has been dominated by bug fixing (but more is needed; see bugzilla). The only new stuff added has been on comparison matrix modules by Stafan Kirov. The most important fixes have been tweaks in ontology handling, GFF histograms, some Bio::Graphics glyphs, feature table output and Gene/Genomewise parsing. The full list is below. Enjoy, -Heikki NEW DIRECTORIES and FILES ========================= Bio::Matrix::PSM IO InstanceSite InstanceSiteI Psm PsmHeader PsmHeaderI PsmI SiteMatrix SiteMatrixI Added DNA PSM (Position Scoring Matrix) modules This includes meme, mast and transfac parsers examples/rnai_finder.cgi cgi script for RNAi reagent design CHANGES ======= Bio::DB::GFF::Adaptor::dbi fixed bug 1384; histograms not working Bio::DB::GFF::Feature bulk_load_gff.PLS fast_load_gff.PLS load_gff.PLS fixed overly-promiscuous regexp for detecting FASTA files Bio::DB::Query::WebQuery quell undef warnings Bio::DB::WebDBSeqI reset MODVERSION to use Packagewide Version system - change agent string to be 'bioperl-Bio_DB_GenBank/1.3' for example Bio::Graphics::FeatureFile All functionality moved to Bio::DB::GFF->split_group, however still see major perf problems, not sure if this is localized to FeatureFile or not Bio::Graphics::Glyph::Factory fixed implementation of user-defined glyph sort routines Bio::Graphics::Glyph::arrow Bio::Graphics::Glyph partial fix for incorrectly-rendered half-open intervals Bio::Index::Abstract don't warn if we set verbose to -1 Bio::Location::Simple::to_FTstring() was never returning a location of the form "complement(12345) Bio::Ontology::SimpleGOEngine Bio::OntologyIO::dagflat Bio::Expression::FeatureGroup allowing an underscore in ontology IDs. this is necessary to be able to parse cjm's OBO_REL relationship ontology, which otherwise observes DAG-Edit format Bio::Ontology::SimpleGOEngine Bio::OntologyIO::dagflat.pm MPATH ontology doesn't have at least 3 digits in all identifiers Bio::SearchIO::(chado&chadosxpr) removed as redundant Bio::SeqFeature::Tools::TypeMapper updated type sequence_variant to reflect SO Bio::SeqIO::chadoxml fix bug of null srcfeature_id for featureloc when srcfeature is not given on write_seq() invocation; fix bug of not calling unflattener when -seq_so_type is explicitly supplied. fixed bug 1532 with regard to filehandle; modified code to eliminate warnings when run with 'perl -w'. debugging code clean up Bio::SearchIO::wise was swapping query/target improperly Bio::Restriction::IO::base fix suggested in bug report #1538, correctly parse negative cut site locations Bio::Tools::Phylo::PAML::Result doc fixes + several minor fixes to quiet warnings when Test::Harness runs tests with 'use warnings' -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________