BioPerl 1.6.1 released

Posted on September 29, 2009 by Chris Fields

We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl’s core code. You can grab it here:

Via CPAN:

http://search.cpan.org/~cjfields/BioPerl-1.6.1/

Via the BioPerl website:

http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2
http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz
http://bioperl.org/DIST/BioPerl-1.6.1.zip

The PPM for Windows should also finally be available this week, ActivePerl problems permitting (we will post more information when it becomes available).

Tons of bug fixes and changes have been incorporated into this release. For a more complete change list please see the ‘Changes’ file included with the distribution.

A few highlights:

  • FASTQ parsing and interconversion of the three FASTQ variants (Sanger, Illumina, Solexa) now works (a concerted OBF effort!)
  • Significant refactoring of Bio::Restriction methods
  • Complete refactoring of Bio::Search-related tiling code, including HOWTO documentation
  • GBrowse-related fixes:
  • – berkeleydb database now autoindexes wig files and locks correctly
  • – add Pg, SQLite, and faster BerkeleyDB implementations
  • Infernal 1.0 output is now parsed
  • New SearchIO-based parser for gmap -f9 output
  • BLAST XML parsing essentially complete
  • Installation via CPANPLUS should now work
  • For those using Strawberry Perl on Windows, the latest build is expected to pass all tests.
  • ‘raw’ sequence format now parsed by line or optionally as a single sequence
  • SCF parsing/writing now round-trips
  • Demo code for using RPS-BLAST and Bio::Tools::Run::RemoteBlast
  • Bio::Tools::SeqPattern now has a backtranslate() method
  • Bio::Tree::Statistics now has methods to calculate Fitch-based score, internal trait values, statratio(), sum of leaf distances
  • Scripts
  • – update to bp_seqfeature_load for SQLite
  • – hivq.pl – commmand-line interface to Bio::DB::HIV
  • – fastam9_to_table – fix for MPI output
  • – gccalc – total stats
  • – einfo – simple script to find up-to-date NCBI databases, list field and link values for a specific database

We will shortly release updates for BioPerl-db, BioPerl-run, and BioPerl-network. Enjoy!

chris

One thought on “BioPerl 1.6.1 released”

  1. csjewell.comyr.com/ says:
    October 14, 2009 at 5:46 am

    And I will confirm that BioPerl 1.6.1 now passes all tests on Strawberry Perl 5.10.1.0 (tested against the first release candidate) by going “cpan Bio::Perl” – just be prepared for the compiling and testing to take an hour or two!

    This was mentioned above as a “is expected to” – I’m just confirming that it does.

    Do not install either Ace::Browser (Ace itself is no problem, as long as option 3 is not selected) or SOAP::Lite (which does not install on Strawberry Perl at present) when selecting which optional modules to install, and Graphviz will require some additional assistance to install.

    I have not done any testing beyond the fact that CPAN.pm will test and install BioPerl and all dependencies except those mentioned above.

    –Curtis Jewell

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