Category Archives: Documentation

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

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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

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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

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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

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Clever tricks with NCBI Entrez EInfo (& Biopython)

Constructing complicated Entrez searches can be tricky, but it turns out one of the Entrez Programming Utilities called Entrez EInfo can help. This can tell you all the searchable fields available for each of the Entrez databases. Continue reading

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Introducing (and expanding) the Biopython Cookbook

Hi all, You may have noticed we’re trying out using the wiki for Biopython cookbook entries. It’s a new idea so at the moment there are only a few ‘recipes’ on offer. If you have some tricks you find yourself … Continue reading

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Biopython paper published

An Application Note describing Biopython has recently been accepted for publication in the Oxford Journal Bioinformatics. An advance copy of the Open Access article is available online: P.J.A. Cock, T. Antao, J.T. Chang, B.A. Chapman, C.J. Cox, A. Dalke, I. … Continue reading

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Google Summer of Code: Project ideas page

A wiki page for collecting ideas, possible projects, prerequisites, possible solution approaches, mentors, other people or channels to contact for more information or to bounce ideas off of, etc. has been setup: http://open-bio.org/wiki/Google_Summer_Code_2009

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Release 1.6 of BioPerl-run, BioPerl-db, BioPerl-network

All, I am proud to announce that the 1.6 release for BioPerl-run, BioPerl- db, and BioPerl-network are now available by direct download and via CPAN. These are designated as 1.006000, with a requirement for BioPerl 1.6 and higher (1.006000). FIXED: … Continue reading

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BioRuby 1.3.0 is released

Hi all, We are pleased to announce the release of BioRuby 1.3.0. The archive is available at: http://bioruby.org/archive/bioruby-1.3.0.tar.gz Web page: http://bioruby.org/ http://bioruby.open-bio.org/ API documentation: http://bioruby.org/rdoc/ Bug report: http://rubyforge.org/projects/bioruby/ (Updating of http://bioruby.rubyforge.org/ is still in progress. Please wait for a moment.) … Continue reading

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