Biopython

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 - the Seq (and related UnknownSeq) objects gained upper and lower methods (like the string methods of the same name but alphabet aware) plus a new ungap method. The SeqFeature object now has an extract method to get the region of sequence it describes (useful for getting CDS nucleotide sequences from GenBank files). Also SeqRecord objects now support addition, giving a new SeqRecord with the combined sequence, all the SeqFeatures, and any common annotation.

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.

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.

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 for population genetics, and adds new functions that will be useful for people working with next generation sequencing.

Tiago Antao’s work on the Population Genetics module brings a command line wrapper for GenePop which allows the estimation of F-statistics, null allele frequencies and migration rates as well as tests for isolation by distance (IBD) and deviation from Hardy-Weinberg equilibrium.

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.SeqIO. At the moment this is usually a two step process, something like this:

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. Or, it might be a big annotation rich file, such as the whole of UniProt, or a chunk of GenBank.

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 can now write Genbank files that include features, and deal with FASTQ files created by Illumina 1.3+. Support for this format allows interconversion between FASTQ files using Solexa, Sanger and Ilumina variants using conventions agreed upon with the BioPerl and EMBOSS projects.

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 new set of application wrappers for alignment programs, and made numerous tweaks and bug fixes.

All the new features have been tested by the dev team but it’s possible there are cases that we haven’t been able to foresee and test, especially for the GenBank feature writer (as there as just so many possible odd fuzzy feature locations).

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? I actually worked this out from the NCBI help and exploring the Entrez website’s advanced search - but it took a while.