[Bioperl-l] BioPerl 1.6.1 released

[Chris Fields]

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
>> _______________________________________________
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>> 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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