[Bioperl-l] Re: BioPerl 1.6.1 released

[Siddhartha Basu]

Congrats chris,  really appreciate your time and effort.

-siddhartha

On Tue, 29 Sep 2009, Chris Fields wrote:

> No prob.  Next up is db, run, and network!
>
> chris
>
> On Sep 29, 2009, at 2:56 PM, Hilmar Lapp wrote:
>
> > Congrats from me too - awesome Chris, and thanks on behalf of the project!
> >
> > 	-hilmar
> >
> > On Sep 29, 2009, at 2:01 PM, Chris Fields wrote:
> >
> >> We are pleased to announce the availability of BioPerl 1.6.1, the latest 
> >> release of BioPerl 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 [heikki]
> >> * scripts
> >>  - update to bp_seqfeature_load for SQLite [lstein]
> >>  - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
> >>  - fastam9_to_table - fix for MPI output [jason]
> >>  - gccalc - total stats [jason]
> >>  - einfo  - simple script to find up-to-date NCBI database list, list 
> >> field and link values for a specific database
> >>
> >> We will shortly release updates for BioPerl-db, BioPerl-run, and 
> >> BioPerl-network.  Enjoy!
> >>
> >> chris
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> > -- 
> > ===========================================================
> > : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> > ===========================================================
> >
> >
> >
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