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Monthly Archives: September 2009
BioPerl 1.6.1 released
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 … Continue reading
Posted in BioPerl, Community, Development, Documentation, General, OBF, OBF Projects
Tagged BioPerl, FASTQ
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Working with FASTQ files in Biopython when speed matters
Biopython’s SeqIO interface revolves around SeqRecord objects which can impose a speed penalty. For FASTQ files the quality string gets turned into a list of integers on parsing, and then re-encoded back to ASCII on writing. Working directly with the raw strings is less flexible, but much faster. Continue reading
Posted in Biopython, Blogroll, Code, Community, Development, Documentation, HOWTO, OBF Projects
Tagged Biopython, FASTQ
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Biopython CVS to git migration
Biopython has now moved from CVS to a git repository, hosted on github.com who kindly provide git hosting for open source projects free of charge. The BioRuby project have been using github for some time, so we are in good company. Continue reading
Posted in Biopython, Blogroll, Code, Community, Development, Documentation, OBF, OBF Projects
Tagged Biopython
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Biopython 1.52 released
We are pleased to announce the availability of Biopython 1.52, a new stable release of the Biopython library. It may only have been one month since the last release, but in that time we’ve added enough useful features to warrant … Continue reading
Simpler, optimized format conversion with Biopython
In this post we’ll look at the new convert() function that both Bio.SeqIO and Bio.AlignIO will get in Biopython 1.52. This allows easier file conversion, and internally provides a mechanism for specific optimisations, such as for FASTQ conversions. Continue reading
Posted in Biopython, Blogroll, Code, Development, Documentation, HOWTO, OBF, OBF Projects
Tagged Biopython, FASTQ
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Indexing sequence files with Biopython
The forthcoming release of Biopython 1.52 will include a couple of nice improvements to the Bio.SeqIO module, and here we’re going to introduce the new index function. Continue reading
Posted in Biopython, Blogroll, Code, Development, Documentation, HOWTO, OBF Projects
Tagged Biopython, FASTQ
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BioRuby 1.3.1 released
We are pleased to announce the release of BioRuby 1.3.1. This new release fixes many bugs existed in 1.3.0. Here is a brief summary of changes. Refactoring of BioSQL support. Bio::PubMed bug fixes. Bio::NCBI::REST bug fixes. Bio::GCG::Msf bug fixes. Bio::Fasta::Report … Continue reading