Documentation

We are pleased to announce the immediate availability of BioPerl 1.6.1, the latest release of BioPerl’s core code. You can grab it here: Via CPAN: http://search.cpan.org/~cjfields/BioPerl-1.6.1/ Via the BioPerl website: http://bioperl.org/DIST/BioPerl-1.6.1.tar.bz2 http://bioperl.org/DIST/BioPerl-1.6.1.tar.gz http://bioperl.org/DIST/BioPerl-1.6.1.zip The PPM for Windows should also finally be available this week, ActivePerl problems permitting (we will post more information when it becomes available). Tons of bug fixes and changes have been incorporated into this release. For a more complete change list please see the ‘Changes’ file included with the distribution. [Read More]

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 speed penalty. For example for FASTQ files, the quality string gets turned into a list of integers on parsing, and then re-encoded back to ASCII on writing. [Read More]

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]

Hi all, You may have noticed we’re trying out using the wiki for Biopython cookbook entries. It’s a new idea so at the moment there are only a few ‘recipes’ on offer. If you have some tricks you find yourself using time and again to solve a problem why not share them? Similarly, if you find yourself coming up against a problem you can’t seem to solve easily with Biopython’s tools send a message to one of the mailing lists proposing it as a cookbook example and someone just might solve it for you! [Read More]

All, I am proud to announce that the 1.6 release for BioPerl-run, BioPerl- db, and BioPerl-network are now available by direct download and via CPAN. These are designated as 1.006000, with a requirement for BioPerl 1.6 and higher (1.006000). FIXED: Bio::Tools::Run::Primer3 now accepts primer3 or primer3_core as executable names Bio::Tools::Run::Vista tests now pass if Vista.jar is installed. bug fix in bioperl-network What remains for the 1.6 release series: \* Documentation, Documentation, and Documentation. [Read More]