Category Archives: Biopython

The Biopython Project is an international distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world.

Making Biopython SeqIO and AlignIO easier

Posted on April 5, 2010 by Peter

One of the small changes coming in Biopython 1.54 (which you can try out already using the Biopython 1.54 beta) is to Bio.SeqIO and Bio.AlignIO. Previously the input and output functions had required file handles, but they will now also … Continue reading →

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Biopython 1.54 beta released

Posted on April 2, 2010 by Peter

A beta release for Biopython 1.54 is now available for download and testing.
Continue reading →

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O|B|F in Google Summer of Code

Posted on March 21, 2010 by Robert Buels

O|B|F is in Google Summer of Code, student applications due to Google April 9, 2010. Continue reading →

Posted in BioDAS, BioJava, BioLib, BioMOBY, BioPerl, Biopython, BioRuby, Blipkit, Community, Google Summer of Code, OBDA / BioSQL, OBF, OBF Projects | Tagged , , | Leave a comment

Sanger FASTQ format and the Solexa/Illumina variants

Posted on December 17, 2009 by Peter

I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the conventions agreed by the OBF projects: The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ … Continue reading →

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Biopython 1.53 released

Posted on December 15, 2009 by Peter

We are pleased to announce the availability of Biopython 1.53, a new stable release of the Biopython library, three months after the release of Biopython 1.52. This is our first release since migrating from CVS to git for source code … Continue reading →

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Interleaving paired FASTQ files with Biopython

Posted on December 14, 2009 by Peter

This post is about paired end data (FASTA or FASTQ) and manipulating it with Biopython’s Bio.SeqIO module (see also FASTQ conversions & speeding up FASTQ).

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Working with FASTQ files in Biopython when speed matters

Posted on September 25, 2009 by Peter

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

Posted on September 24, 2009 by Peter

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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Biopython 1.52 released

Posted on September 22, 2009 by davidw

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 →

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Simpler, optimized format conversion with Biopython

Posted on September 22, 2009 by davidw

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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