Tag: Biopython
Making Biopython SeqIO and AlignIO easier
April 5, 2010 :
One of the small changes coming in Biopython 1.54 (which you can try out already using the Biopython 1.54 beta) […]
Biopython 1.54 beta released
April 2, 2010 :
A beta release for Biopython 1.54 is now available for download and testing.
Sanger FASTQ format and the Solexa/Illumina variants
December 17, 2009 :
I’m delighted to announce an open access publication in Nucleic Acids Research describing the FASTQ file format based on the […]
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
September 22, 2009 :
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 […]