[Bioperl-announce-l] Release Announcement: Bioperl 1.2.3

Jason Stajich jason at cgt.duhs.duke.edu
Wed Sep 17 23:22:39 EDT 2003

Bioperl 1.2.3

On behalf of the Bioperl developers, I am pleased to announce the 
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 
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

   As well as from mirrors generously provided by Don Gilbert at Indiana

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/


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 
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 
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 
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 
  http://bioperl.org/DIST, and http://cvs.open-bio.org/.

Another recent project which has not been released yet, but should be 
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 
will be available at http://bioperl.org/DIST.

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 
feedback about the modules to help us improve them. We would like to
welcome several new developers who have joined us recently to provide 
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 
well as users to provide feedback and bug reports.

Bugs should be reported at our bug tracking site

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
     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
     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 
        - 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 
         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 
      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 
         parse in the ORIGIN text.
      o Bio::SeqIO::fasta, a new method called preferred_id_type allows 
        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 at portal.open-bio.org

Assistant Scientist, Global Infectious Diseases
Josephine Bay Paul Center, Marine Biological Laboratory
7 MBL Street, Woods Hole, MA 02543-1015

Assistant Scientist, Global Infectious Diseases
Josephine Bay Paul Center, Marine Biological Laboratory
7 MBL Street, Woods Hole, MA 02543-1015

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