From jason at cgt.duhs.duke.edu Mon Sep 15 13:05:33 2003 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Mon Sep 15 13:07:36 2003 Subject: [Bioperl-announce-l] bioperl 1.2.3 RC1 Message-ID: Bioperl 1.2.3 Release candidate 1 Available from http://bioperl.org/DIST/bioperl-1.2.3-rc1.tar.gz http://bioperl.org/DIST/bioperl-1.2.3-rc1.tar.bz2 http://bioperl.org/DIST/bioperl-1.2.3-rc1.zip MD5 for these releases e44d4c8b0d3e5aedba8da3f0b6d3d0c3 bioperl-1.2.3-rc1.tar.bz2 d8a3fcf235ed1de67bb50c928d0c6d57 bioperl-1.2.3-rc1.tar.gz 7512abce2dd12950ff74dbd2fba4373f bioperl-1.2.3-rc1.zip This release has been tested and passed on the follow platforms & perl versions: Mac OS X perl 5.6.0 perl 5.8.0 i686-Linux perl 5.6.1 perl 5.8.0 alpha-OSF1 perl 5.6.1 Developers: If you have any last minute changes - you need to get them in by tomorrow or let me know what you still have pending and I can hold up making a final release. Users: We would appreciate you downloading this release candidate, running the test suite on your systems and ideally running some of your existing scripts which depend on Bioperl with the release so that we might find any potential incompatibilities. This release should be completely compatable with any 1.2.x dependent Bioperl scripts. Barring any reports of problems with this release candidate I would like to make the 1.2.3 release on Wed. -jason -- Jason Stajich Duke University jason at cgt.mc.duke.edu From steve_chervitz at affymetrix.com Wed Sep 17 05:04:29 2003 From: steve_chervitz at affymetrix.com (Steve Chervitz) Date: Wed Sep 17 08:19:44 2003 Subject: [Bioperl-announce-l] bioperl 1.2.3 RC1 In-Reply-To: Message-ID: On Monday, Sep 15, 2003, at 10:05 US/Pacific, Jason Stajich wrote: > > Developers: > If you have any last minute changes - you need to get them in by > tomorrow > or let me know what you still have pending and I can hold up making a > final release. I put in a small addition to SeqIO::fasta that allows you to specify which type of identifier to appear after the '>' in the generated fasta output (e.g., accession, accession.version, display, or primary). The new method is called preferred_id_type. This is only applicable to fasta format; other formats have special slots for different types of identifiers, so it didn't make sense to put this in SeqIO.pm. I also added a test for it in SeqIO.t. Jason: Since this was such a trivial addition and doesn't affect existing functionality, I put in on the 1.2 branch as well as bioperl-live. However, since it is new functionality, I should have put it on the main trunk only. Let me know if you want to back it out of the branch. One issue I haven't addressed is how to deal with SeqIO::MultiFile. This module should delegate any method calls it can't handle (such as preferred_id_type) to its current SeqIO object. This would also address other format-specific methods such as SeqIO::fasta::width(). Steve From jason at cgt.duhs.duke.edu Wed Sep 17 23:22:39 2003 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Wed Sep 17 23:20:43 2003 Subject: [Bioperl-announce-l] Release Announcement: Bioperl 1.2.3 Message-ID: Bioperl 1.2.3 ------------- On behalf of the Bioperl developers, I am pleased to announce the release of Bioperl 1.2.3. This is the set of Core libraries which constitutes Bioperl and covers areas like Sequence file parsing, Sequence Feature representations, Database access to flatfile and webbased sequence thadatabases, Alignment parsing and manipulation, parsing of and data representation of output from a majority of standard bioinformatics tools, and many more features. This release constitutes several major bugfixes from the 1.2.2 release earlier this summer and provides some new minor functionality improvements. This release is intended to be compatible with code which has been programmed using the API in the 1.2.x series of releases. The release is available as always from http://bioperl.org/DIST/ http://bioperl.org/DIST/bioperl-1.2.3.tar.bz2 http://bioperl.org/DIST/bioperl-1.2.3.tar.gz http://bioperl.org/DIST/bioperl-1.2.3.zip As well as from mirrors generously provided by Don Gilbert at Indiana University http://iubio.bio.indiana.edu/ MD5 signatures for the release files c64219b6540a722e781a53aea215ebc8 bioperl-1.2.3.tar.bz2 72b4a23f7372e820a7a7d9a72e7a0e76 bioperl-1.2.3.tar.gz e3bef5ca6ec6692bc253b75046100b64 bioperl-1.2.3.zip HTML-ized documentation for the release is available from the documentation website http://doc.bioperl.org/ http://doc.bioperl.org/releases/bioperl-1.2.3/ Related Projects ---------------- The Generic Genome Browser (www.gmod.org) which depends on bioperl will likely release a new version which will utilize features in bioperl 1.2.3. This is coordinated by Lincoln Stein and Scott Cain. Code is available from the project site at http://www.gmod.org. We plan to release a new version of bioperl-run in the coming week. bioperl-run is a package of perl module wrappers around many applications common to bioinformatics analyses. Shawn Hoon is responsible for overseeing this release. Previous and future releases are available at http://bioperl.org/DIST/ and in CPAN and as always from our CVS repository http://cvs.open-bio.org. A brand new package bioperl-microarray will be released this week as well, version 0.1. This is a project headed by Allen Day and he will be announcing a code release shortly. The code will be available from CPAN, http://bioperl.org/DIST, and http://cvs.open-bio.org/. Another recent project which has not been released yet, but should be out this fall is bioperl-pedigree. This will include codes for parsing and representing pedigree data and will interface with genotype parsing and representations already part of the Bioperl Core. This package is overseen by Jason Stajich. Code is available from our CVS repository and will be available at http://bioperl.org/DIST. Contributors ------------ The hard work of many people has gone into this release, please see AUTHORS file for a complete list of individuals who have contributed to the project. We would especially like to thank those who have provided bug reports and feedback about the modules to help us improve them. We would like to welcome several new developers who have joined us recently to provide code improvements and implementations of new areas for Bioperl. Future plans ------------ We intend to focus our energy on the next set of developer's releases in the Fall of 2003 which will be numbered 1.3.x and will lead to the next stable release 1.4 in 2004. We encourage new and old developers to be part of the development cycle as well as users to provide feedback and bug reports. Bugs ---- Bugs should be reported at our bug tracking site http://bugzilla.bioperl.org/ A synopsis of changes from the Changes file ------------------------------------------------------------------------ 1.2.3 Stable release update o Bug #1475 - Fix and add speedup to spliced_seq for remote location handling. o Bug #1477 - Sel --> Sec abbreviation fixed o Fix bug #1487 where paring in-between locations when end < start caused the FTLocationFactory logic to fail. o Fix bug #1489 which was not dealing with keywords as an arrayref properly (this is fixed on the main trunk because keywords returns a string and the array is accessible via get_keywords). o Bio::Tree::Tree memory leak (bug #1480) fixed Added a new initialization option -nodelete which won't try and cleanup the containing nodes if this is true. o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed this was only present on the branch for the 1.2.1 and 1.2.2 series - Also merged main trunk changes to the branch which make newick -> nhx round tripping more effective (storing branch length and bootstrap values in same locate for NodeNHX and Node implementations.) Fixes to TreeIO parsing for labeled internal also required small changes to TreeIO::nhx. Improved tests for this module as well. o Bio::SearchIO - Fixed bugs in BLAST parsing which couldn't parse NCBI gapped blast properly (was losing hit significance values due to the extra unexpeted column). - Parsing of blastcl3 (netblast from NCBI) now can handle case of integer overflow (# of letters in nt seq dbs is > MAX_INT) although doesn't try to correct it - will get the negative number for you. Added a test for this as well. - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report has no top-level family classification scores but does have scores and alignments for individual domains. - Parsing FASTA reports where ungapped percent ID is < 10 and the regular expression to match the line was missing the possibility of an extra space. This is rare, which is why we probably did not catch it before. - BLAST parsing picks up more of the statistics/parameter fields at the bottom of reports. Still not fully complete. - SearchIO::Writer::HTMLResultWriter and TextResultWriter were fixed to include many improvements and added flexiblity in outputting the files. Bug #1495 was also fixed in the process. o Bio::DB::GFF - Update for GFF3 compatibility. - Added scripts for importing from UCSC and GenBank. - Added a 1.2003 version number. o Bio::Graphics - Updated tutorial. - Added a 1.2003 version number. o SeqIO::swiss Bug #1504 fixed with swiss writing which was not properly writing keywords out. o Bio::SeqIO::genbank - Fixed bug/enhancement #1513 where dates of the form D-MMM-YYYY were not parsed. Even though this is invalid format we can handle it - and also cleanup the date string so it is properly formatted. - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed and written with Genbank format. Similarly bug #1515 is fixed to parse in the ORIGIN text. o Bio::SeqIO::fasta, a new method called preferred_id_type allows you to specify the ID type, one of (accession accession.version display primary). See Bio::SeqIO::preferred_id_type method documentation for more information. o Unigene parsing updated to handle file format changes by NCBI Jason Stajich on behalf of the Bioperl developers. -- Jason Stajich Duke University jason at cgt.mc.duke.edu From jason at cgt.duhs.duke.edu Wed Sep 17 23:22:39 2003 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Thu Sep 18 07:41:09 2003 Subject: [Bioperl-announce-l] Release Announcement: Bioperl 1.2.3 Message-ID: Bioperl 1.2.3 ------------- On behalf of the Bioperl developers, I am pleased to announce the release of Bioperl 1.2.3. This is the set of Core libraries which constitutes Bioperl and covers areas like Sequence file parsing, Sequence Feature representations, Database access to flatfile and webbased sequence thadatabases, Alignment parsing and manipulation, parsing of and data representation of output from a majority of standard bioinformatics tools, and many more features. This release constitutes several major bugfixes from the 1.2.2 release earlier this summer and provides some new minor functionality improvements. This release is intended to be compatible with code which has been programmed using the API in the 1.2.x series of releases. The release is available as always from http://bioperl.org/DIST/ http://bioperl.org/DIST/bioperl-1.2.3.tar.bz2 http://bioperl.org/DIST/bioperl-1.2.3.tar.gz http://bioperl.org/DIST/bioperl-1.2.3.zip As well as from mirrors generously provided by Don Gilbert at Indiana University http://iubio.bio.indiana.edu/ MD5 signatures for the release files c64219b6540a722e781a53aea215ebc8 bioperl-1.2.3.tar.bz2 72b4a23f7372e820a7a7d9a72e7a0e76 bioperl-1.2.3.tar.gz e3bef5ca6ec6692bc253b75046100b64 bioperl-1.2.3.zip HTML-ized documentation for the release is available from the documentation website http://doc.bioperl.org/ http://doc.bioperl.org/releases/bioperl-1.2.3/ Related Projects ---------------- The Generic Genome Browser (www.gmod.org) which depends on bioperl will likely release a new version which will utilize features in bioperl 1.2.3. This is coordinated by Lincoln Stein and Scott Cain. Code is available from the project site at http://www.gmod.org. We plan to release a new version of bioperl-run in the coming week. bioperl-run is a package of perl module wrappers around many applications common to bioinformatics analyses. Shawn Hoon is responsible for overseeing this release. Previous and future releases are available at http://bioperl.org/DIST/ and in CPAN and as always from our CVS repository http://cvs.open-bio.org. A brand new package bioperl-microarray will be released this week as well, version 0.1. This is a project headed by Allen Day and he will be announcing a code release shortly. The code will be available from CPAN, http://bioperl.org/DIST, and http://cvs.open-bio.org/. Another recent project which has not been released yet, but should be out this fall is bioperl-pedigree. This will include codes for parsing and representing pedigree data and will interface with genotype parsing and representations already part of the Bioperl Core. This package is overseen by Jason Stajich. Code is available from our CVS repository and will be available at http://bioperl.org/DIST. Contributors ------------ The hard work of many people has gone into this release, please see AUTHORS file for a complete list of individuals who have contributed to the project. We would especially like to thank those who have provided bug reports and feedback about the modules to help us improve them. We would like to welcome several new developers who have joined us recently to provide code improvements and implementations of new areas for Bioperl. Future plans ------------ We intend to focus our energy on the next set of developer's releases in the Fall of 2003 which will be numbered 1.3.x and will lead to the next stable release 1.4 in 2004. We encourage new and old developers to be part of the development cycle as well as users to provide feedback and bug reports. Bugs ---- Bugs should be reported at our bug tracking site http://bugzilla.bioperl.org/ A synopsis of changes from the Changes file ------------------------------------------------------------------------ 1.2.3 Stable release update o Bug #1475 - Fix and add speedup to spliced_seq for remote location handling. o Bug #1477 - Sel --> Sec abbreviation fixed o Fix bug #1487 where paring in-between locations when end < start caused the FTLocationFactory logic to fail. o Fix bug #1489 which was not dealing with keywords as an arrayref properly (this is fixed on the main trunk because keywords returns a string and the array is accessible via get_keywords). o Bio::Tree::Tree memory leak (bug #1480) fixed Added a new initialization option -nodelete which won't try and cleanup the containing nodes if this is true. o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed this was only present on the branch for the 1.2.1 and 1.2.2 series - Also merged main trunk changes to the branch which make newick -> nhx round tripping more effective (storing branch length and bootstrap values in same locate for NodeNHX and Node implementations.) Fixes to TreeIO parsing for labeled internal also required small changes to TreeIO::nhx. Improved tests for this module as well. o Bio::SearchIO - Fixed bugs in BLAST parsing which couldn't parse NCBI gapped blast properly (was losing hit significance values due to the extra unexpeted column). - Parsing of blastcl3 (netblast from NCBI) now can handle case of integer overflow (# of letters in nt seq dbs is > MAX_INT) although doesn't try to correct it - will get the negative number for you. Added a test for this as well. - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report has no top-level family classification scores but does have scores and alignments for individual domains. - Parsing FASTA reports where ungapped percent ID is < 10 and the regular expression to match the line was missing the possibility of an extra space. This is rare, which is why we probably did not catch it before. - BLAST parsing picks up more of the statistics/parameter fields at the bottom of reports. Still not fully complete. - SearchIO::Writer::HTMLResultWriter and TextResultWriter were fixed to include many improvements and added flexiblity in outputting the files. Bug #1495 was also fixed in the process. o Bio::DB::GFF - Update for GFF3 compatibility. - Added scripts for importing from UCSC and GenBank. - Added a 1.2003 version number. o Bio::Graphics - Updated tutorial. - Added a 1.2003 version number. o SeqIO::swiss Bug #1504 fixed with swiss writing which was not properly writing keywords out. o Bio::SeqIO::genbank - Fixed bug/enhancement #1513 where dates of the form D-MMM-YYYY were not parsed. Even though this is invalid format we can handle it - and also cleanup the date string so it is properly formatted. - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed and written with Genbank format. Similarly bug #1515 is fixed to parse in the ORIGIN text. o Bio::SeqIO::fasta, a new method called preferred_id_type allows you to specify the ID type, one of (accession accession.version display primary). See Bio::SeqIO::preferred_id_type method documentation for more information. o Unigene parsing updated to handle file format changes by NCBI Jason Stajich on behalf of the Bioperl developers. -- Jason Stajich Duke University jason at cgt.mc.duke.edu _______________________________________________ Bioperl-announce-l mailing list Bioperl-announce-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-announce-l Assistant Scientist, Global Infectious Diseases Josephine Bay Paul Center, Marine Biological Laboratory 7 MBL Street, Woods Hole, MA 02543-1015 http://jbpc.mbl.edu/mcarthur Assistant Scientist, Global Infectious Diseases Josephine Bay Paul Center, Marine Biological Laboratory 7 MBL Street, Woods Hole, MA 02543-1015 http://jbpc.mbl.edu/mcarthur From allenday at ucla.edu Thu Sep 18 21:12:55 2003 From: allenday at ucla.edu (Allen Day) Date: Thu Sep 18 23:41:54 2003 Subject: [Bioperl-announce-l] Release Announcement: bioperl-microarray 0.1 In-Reply-To: Message-ID: The Bioperl developers are pleased to announce a 0.1 release of bioperl-microarray, a Bioperl extension package dedicated to manipulation of microarray data. The package is implemented using IO conventions Bioperl developers should already be familiar with. Data types currently supported are: Affymetrix GeneChip CEL files (read and write) Affymetrix GeneChip CDF files (read) Affymetrix GeneChip Microarray Suite 5.0 normalized files (read) Affymetrix GeneChip dChip normalized files (read) Data types for which support is planned in a 0.2 release include: Bio::MAGE objects and MAGE-ML (read and write) Affymetrix SNPChip genotype files (read) GenePix GPR files (read) Release packages are available from: http://www.bioperl.org/DIST/ http://www.bioperl.org/DIST/bioperl-microarray-0.1.tar.bz2 http://www.bioperl.org/DIST/bioperl-microarray-0.1.tar.gz http://www.bioperl.org/DIST/bioperl-microarray-0.1.zip as well as from CPAN: http://search.cpan.org/author/ALLENDAY/ Documentation available from: http://doc.bioperl.org/bioperl-microarray/ Subscribe to the bioperl-microarray mailing list at: http://bioperl.org/mailman/listinfo/bioperl-microarray/ Report bugs at: http://bugzilla.bioperl.org/ -Allen -------------------- Allen Day Human Genetics, UCLA