Thursday, December 17th, 2009
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 variants
Peter J. A. Cock (Biopython), Christopher J. Fields (BioPerl), Naohisa Goto ...
Posted in BioJava, BioPerl, BioRuby, Biopython, Blogroll, Community, Development, Documentation, General, OBF, OBF Projects | No Comments »
Tuesday, December 15th, 2009
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 control.
There have been some additions to our core objects - ...
Posted in Biopython, Code, Development, OBDA / BioSQL, OBF Projects | No Comments »
Monday, December 14th, 2009
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).
Posted in Biopython, Blogroll, Code, Community, Development, Documentation, HOWTO, OBF Projects | No Comments »
Friday, September 25th, 2009
Biopython 1.51 onward includes support for Sanger, Solexa and Illumina 1.3+ FASTQ files in Bio.SeqIO, which allows a lot of neat tricks very concisely. For example, the tutorial (PDF) has examples finding and removing primer or adaptor sequences.
However, because the Bio.SeqIO interface revolves around SeqRecord objects there is often a ...
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Thursday, September 24th, 2009
The release of Biopython 1.52 earlier this week marked the end of an era, it was our last release using CVS for source code control.
As of now, Biopython is using a git repository, hosted on github.com who kindly provide git hosting for open source projects free of charge. The BioRuby ...
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Tuesday, September 22nd, 2009
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 a new release. In particular, Biopython 1.52 includes more substantial support ...
Posted in Biopython, Code, Development, OBF Projects | 2 Comments »
Tuesday, September 22nd, 2009
As per Peter's recent post we are using this space to show of a couple of the new features in Biopython 1.52 before it is released. In this post we'll look at the new convert() function that both Bio.SeqIO and Bio.AlignIO will get in Biopython 1.52.
No one has ever complained ...
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Monday, September 21st, 2009
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. This will of course be covered in the Biopython Tutorial & Cookbook (PDF) once this code is released.
Suppose you have a large sequence ...
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Monday, August 17th, 2009
We are pleased to announce the release of Biopython 1.51.This new stable release enhances version 1.50 (released in April) by extending the functionality of existing modules, adding a set of application wrappers for popular alignment programs and fixing a number of minor bugs.
In particular, the SeqIO module ...
Posted in Biopython, Code, Community, Development, OBF, OBF Projects | 1 Comment »
Tuesday, June 23rd, 2009
A beta release for Biopython 1.51 is now available for download and testing.
In the two months since Biopython 1.50 was released, we have introduced support for writing features in GenBank files using Bio.SeqIO, extended SeqIO's support for the FASTQ format to include files created by Illumina 1.3+, and added a ...
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