Blogroll

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 project have been using github for some time, so we are in good company. Our existing OBF hosted CVS repository will be maintained in the short to medium term as a backup, but will not be updated. [Read More]

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 that bioinformatics just doesn’t have enough file formats - you probably frequently find yourself converting sequence files to suit particular applications with Bio. [Read More]

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 file with many many individual sequences in it. This could be next generation sequence data for example, maybe a FASTQ, FASTA or QUAL file. [Read More]

Constructing complicated NCBI Entrez searches can be tricky, but it turns out one of the Entrez Programming Utilities called Entrez EInfo can help. For example, suppose you want to search for mitochondrial genomes from a given taxa - either just in the Entrez web interface, for use in a script with EFetch. I knew from past experience about using name[ORGN] in Entrez to search for an organism name - but how would you specify just mitochondria? [Read More]