Tag: Biopython

Biopython 1.53 released

December 15, 2009 :

We are pleased to announce the availability of Biopython 1.53, a new stable release of the Biopython library, three months […]

Interleaving paired FASTQ files with Biopython

December 14, 2009 :

This post is about paired end data (FASTA or FASTQ) and manipulating it with Biopython’s Bio.SeqIO module (see also FASTQ […]

Working with FASTQ files in Biopython when speed matters

September 25, 2009 :

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.

Biopython CVS to git migration

September 24, 2009 :

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.

Biopython 1.52 released

September 22, 2009 :

We are pleased to announce the availability of Biopython 1.52, a new stable release of the Biopython library. It may […]

Simpler, optimized format conversion with Biopython

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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.

Indexing sequence files with Biopython

September 21, 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.

Biopython 1.51 released

August 17, 2009 :

We are pleased to announce the release of Biopython 1.51.This new stable release enhances version 1.50 (released in April) by […]

Biopython 1.51 beta released

June 23, 2009 :

A beta release for Biopython 1.51 is now available for download and testing. In the two months since Biopython 1.50 […]

Clever tricks with NCBI Entrez EInfo (& Biopython)

June 21, 2009 :

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.

Dropping Python 2.3 Support

May 6, 2009 :

As announced here, any last minute requests to postpone dropping support for Python 2.3 from the next release of Biopython […]

Introducing (and expanding) the Biopython Cookbook

April 29, 2009 :

Hi all, You may have noticed we’re trying out using the wiki for Biopython cookbook entries. It’s a new idea […]

Biopython projects chosen for Google Summer of Code

April 27, 2009 :

Congratulations to Nick Matzke and Eric Talevich who have had Biopython projects accepted for this year’s Google Summer of Code. […]

Biopython release 1.50

April 20, 2009 :

We are pleased to announce Biopython release 1.50, featuring some significant additions since Biopython 1.49 was released late last year. […]

Biopython 1.50 beta released

April 3, 2009 :

We are pleased to announce a beta release of Biopython 1.50 for public testing. There have been some significant changes […]

Biopython on twitter

March 27, 2009 :

Just to let you all know, Biopython is now on twitter. And in case you missed the OBF announcement last […]

Biopython and next generation sequencing

March 26, 2009 :

Those of you doing next generation sequencing may be pleased to know that the next release of Biopython is expected […]

Biopython paper published

March 22, 2009 :

An Application Note describing Biopython has recently been accepted for publication in the Oxford Journal Bioinformatics. An advance copy of […]