Bioperl 1.2.3 Released

Bioperl 1.2.3

On behalf of the Bioperl developers, we are 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 web-based sequence databases, 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/.


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
databases, 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 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 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 included in the release 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. Information about bugs in the Changes are also available from this site.
http://bugzilla.bioperl.org

A synopsis of changes from the Changes file


1.2.3 Stable release update

  • Bug #1475 – Fix and add speedup to spliced_seq for remote location
    handling.

  • Bug #1477 – Sel –> Sec abbreviation fixed
  • Fix bug #1487 where paring in-between locations when
    end < start caused the FTLocationFactory logic to fail.
  • 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).

  • 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.

  • 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.
  • 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.
  • Bio::DB::GFF
    • Update for GFF3 compatibility.
    • Added scripts for importing from UCSC and GenBank.
    • Added a 1.2003 version number.
  • Bio::Graphics
    • Updated tutorial.
    • Added a 1.2003 version number.
  • SeqIO::swiss Bug #1504 fixed with swiss writing which was not
    properly writing keywords out.

  • 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.
  • 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.

  • 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

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