From heikki at nildram.co.uk Mon Dec 8 15:18:54 2003 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Mon Dec 8 18:55:58 2003 Subject: [Bioperl-announce-l] Bioperl-run Developer snapshot 1.3.01 Message-ID: <200312082018.54358.heikki@nildram.co.uk> Bioperl-run Developer snapshot 1.3.01 ------------------------------------- This is a developer release 1.3.01 of Bioperl-run which contains wrappers for external programs. The stable one will be released together with bioperl core 1.4. http://bioperl.org/DIST/current_run_unstable.tar.gz http://bioperl.org/DIST/bioperl-run-devel-1.3.01.tar.gz Highlights: New wrappers for primer3 and hmmer. There is now a workflow modulue for Pise. Critical fixes for the following wrappers: Neighbor (PHYLIP), Vista, mfold (support for new v. 3.1.2) Enjoy, -Heikki on behalf of the Bioperl core team NEW FILES: + Bio::Tools::Run::Primer3 - Porting Rob Edwards extension of Primer3 wrapper and parser + Bio::Tools::Run::Hmmer - Hmmer wrapper factory, currently supports hmmsearch, hmmalign,hmmpfam, hmmbuild and hmmcalibrate + t/Hmmer.t - test for Hmmer + Bio::Tools::Run::PiseWorkflow - PiseWorkflow is a module for building and running a workflow on top of PiseApplication instances. CHANGED FILES: * Bio::Tools::Run::Phylo::Phylip::Neighbor - properly get the hash value * Bio::Tools::Run::Phylo::Molphy::ProtML - align the code * Bio::Tools::Run::Vista - Added java param to allow setting of java parameters, for example to set higher heap sizes.. - Major bug, need to project aligmnents, basically need to remove position in pairwise aligmnet if both are gap characters, else vista will count wrongly * Bio::Tools::Run::Alignment::Lagan - Allowing of setting of outfile - can't declare and expect a variable at the same time * Bio::Tools::Run::FootPrinter - fix stupidity with tempfilehandle and outfh not being closed properly as reported by Ben Westover * Bio::Tools::Run::EMBOSSApplication - no need for this debugging * Bio::Tools::Run::PiseApplication::mfold - Pise/bioperl module for a recent version of mfold (3.1.2). * Bio::Tools::Run::Phylo::Phylip::Consense - typo * Bio::Tools::Run::Phylo::PAML::Codeml - fix typo reported in bug #1505 - default should be an arrayref - George Hartzell fixes * Bio::Tools::Run::Phylo::PAML::Yn00 - bug #1507, SYNOPSIS is runnable now with API changes - bug #1507 add MSwin .exe extension where appropriate - wait -this isn't necessary , we already pad the PROGRAMNAME with the .exe when appropriate - George Hartzell fixes * Bio::Tools::Run::FootPrinter - POD fixes * Bio::Tools::Run::Alignment::Blat - well, at least it runs the blat program now, although it isn't seemingly able to find the output tempfile to retrieve the results * t/Blat.t - well, at least it runs the blat program now, although it isn't seemingly able to find the output tempfile to retrieve the results - various fixes to get blat runnable in line with bioperl-live 1.2.3 all tests now pass. * t/Mdust.t - typo * Bio::Tools::Run::Mdust - use save_tempfiles, use PROGRAMNAME as a variable, use tempfile instead of randomly generating filename - Modified call to io->tmpfile to get file name as well as handle * Makefile.PL - George Hartzell fixes * scripts/panalysis.PLS - Patched, thank you Albert * AUTHORS - updated using info from maintanence/authors.pl script From heikki at nildram.co.uk Mon Dec 8 15:18:37 2003 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Mon Dec 8 18:55:59 2003 Subject: [Bioperl-announce-l] Bioperl-ext Developer snapshot 1.3.01 Message-ID: <200312082018.37975.heikki@nildram.co.uk> Bioperl-ext Developer snapshot 1.3.01 ------------------------------------- This is a developer release 1.3.01 of Bioperl-Ext which contains C compiled Extensions. The stable one will be released together with bioperl core 1.4. http://bioperl.org/DIST/current_ext_unstable.tar.gz http://bioperl.org/DIST/bioperl-ext-devel-1.3.01.tar.gz Changes since 0.6 ----------------- Yee Man Chan's has written alternative pairwise alignment code into Bio/Ext/Align which is accessed by Bio::Tools::dpAlign in bioperl-live. Read the README for details Enjoy, -Heikki on behalf of the Bioperl core team NEW FILES ========= * Bio/Ext/Align/libs/{dpalign.c dpalign.h linspc.c} incorporate Yee Man Chan's alternative alignment code CHANGES ======= * README updated to include info about dpAlign and common io_lib problems * Bio::Ext::Align {Align.xs Makefile.PL typemap} incorporate Yee Man Chan's alternative alignment code From heikki at nildram.co.uk Wed Dec 17 18:28:59 2003 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Thu Dec 18 07:52:19 2003 Subject: [Bioperl-announce-l] Bioperl Developer snapshot 1.3.04 Message-ID: <200312172328.59980.heikki@nildram.co.uk> Bioperl Developer snapshot 1.3.04 ---------------------------------- This is the fourth and last developer snapshot from the BioPerl CVS head before release 1.4 which is due early next week. Bug fixes are still welcome, but please do not commit anything you do not have time to test well. http://bioperl.org/DIST/current_core_unstable.tar.gz http://bioperl.org/DIST/bioperl-1.3.04.tar.gz Changes since 1.3.04 -------------------- This time I dit not have the time to collect details from all the cvs commits (maybe that level of detail is not necessary? It is all in bioperl-guts, anyway.) The highlights are: * SVG::Graphics fine tuning ; SVG output, * Bio::Tree major changes plus a new howto. There is a new Feature-Annotation howto, too. * Parse more BLAST statistics and lots of BLAST-related fixes * Bio::Restriction::Analysis is now fixed and can handle overlapping and multiple cuts as well as circular sequences. * Bio::SearchIO and Bio::AlignIO can quess the incoming format by looking ahead into stream, thanks to Bio::Tools::GuessSeqFormat. * GenBank and EMBL parsers now tolerate words longer than line width. Also, they parse non-binomial virus names better into Bio::Species objects. EMBL parser now does better roundtrip of files. * New GAME format modules. * last minute fix: scripts/Bio-DB-GFF/bp_genbank2gff.PLS can now write to stdout without depending on mysql. NEW FILES: * Bio/OntologyIO/Handlers::InterPro_BioSQL_Handler.pm * Bio/Restriction/IO::bairoch.pm * Bio/SeqIO::game.pm * Bio::Tools::GuessSeqFormat * doc/howto/sgmlFeature-Annotation.sgml * doc/howto/sgm/Trees.sgml * examples/biographics/all_glyphs.pl Enjoy, -Heikki & the rest of the bioperl core team P.S. The web site was updated over five hours ago when I wrote the first version of this message which seems to have vanished into a black hole, -- ______ _/ _/_____________________________________________________ _/ _/ 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 nildram.co.uk Tue Dec 23 04:11:35 2003 From: heikki at nildram.co.uk (Heikki Lehvaslaiho) Date: Tue Dec 23 10:49:49 2003 Subject: [Bioperl-announce-l] Bioperl Release 1.4 Message-ID: <200312230911.35200.heikki@nildram.co.uk> Bioperl Release 1.4 -------------------- The stable Bioperl release 1.4 is available for immediate use at: http://bioperl.org/DIST We are releasing simultaneously three modules: bioperl-core - core bioperl modules http://bioperl.org/DIST/current_core_stable.tar.gz http://bioperl.org/DIST/current_core_stable.tar.bz2 bioperl-ext - C compiled extensions http://bioperl.org/DIST/current_ext_stable.tar.gz http://bioperl.org/DIST/current_ext_stable.tar.bz2 bioperl-run - wrappers for external programs http://bioperl.org/DIST/current_run_stable.tar.gz http://bioperl.org/DIST/current_run_stable.tar.bz2 They will also appear shortly at IUBIO mirror (later today) and in CPAN . Remember, all the external modules needed by bioperl-core can be installed from CPAN under name Bundle-BioPerl . Changes ------- Over 3000 file changes have gone into this release since the 1.2 development tree was branched off from the main. These are the main feature enhancements: o installable scripts o global module version from Bio::Root:Version o Bio::Graphics - major improvements; added SVG support o Bio::Popgen - population genetics o Bio::Restriction - new restrion analysis modulues o Bio::Tools::Analysis - web based DNA and Protein analysis framework and several implementaions o Bio::Seq::Meta - per residue annotable sequences o Bio::Matrix o Bio::Matrix::PSM - Position Scoring Matrix o Bio::Ontology - major contributions o Bio:Tree o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA - small inhibitory RNA o Bio::SeqFeature::Tools - seqFeature mapping tools, e.g. Bio::SeqFeature::Tools::Unflattener.pm o Bio::Tools::dpAlign - pure perl dynamic programming sequence alignment (needs Bioperl-ext) o new Bio::SearchIO formats o new Bio::SeqIO formats: tab, kegg, tigr, game; important fixes for old modulues o Bio::AlignIO: maf o improved Bio::Tools::Genewise o Bio::SeqIO now can recognize sequence formats automatically from stream o new parsers in Bio::Tools: Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan, o several new HOWTOs: SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat Databases o hundreds of new and improved files For detailed documentation, see individual module documentation in the distribution or in http://doc.bioperl.org/. The tutorials are available at http://bioperl.org/HOWTOs/. This release is a result of hard work by the bioperl core team, nearly hundred developers and countless suggestions and bug reports at the bioperl mailing list (bioperl-l@bioperl.org) or the the bioperl bug tracking system (http://bugzilla.bioperl.org/). Wishing you all Peaceful Christmas, -Heikki and all the bioperl developers