O|B|F News

Source distributions and Windows installers for Biopython 1.59 are now available from the downloads page on the Biopython website and from the Python Package Index (PyPI).

Platforms/Deployment

We currently support Python 2.5, 2.6 and 2.7 and also test under Jython 2.5 (which does not cover NumPy). Please note that this release will not work on Python 2.4

Most functionality is also working under Python 3.1 and 3.2 (including modules using NumPy), and under PyPy (excluding our NumPy dependencies). We are now encouraging early adopters to help beta testing on these platforms.

The installation setup.py now supports ‘install_requires’ when setuptools is installed. This avoids the manual dialog when installing Biopython via easy_install or pip and numpy is not installed. It also allows user libraries that require Biopython to include it in their install_requires and get automatic installation of dependencies.

Features

New module Bio.TogoWS offers a wrapper for the TogoWS REST API, a web service based in Japan offering access to KEGG, DDBJ, PDBj, CBRC plus access to some NCBI and EBI resources including PubMed, GenBank and UniProt. This is much easier to use than the NCBI Entrez API, but should be especially useful for Biopython users based in Asia.

The NCBI Entrez Fetch function Bio.Entrez.efetch has been updated to handle the NCBI’s stricter handling of multiple ID arguments in EFetch 2.0 (released February 2012, see this announcement), however the NCBI have also changed the retmode default argument so you may need to make this explicit. e.g. add retmode="text" to your EFetch calls (see this announcement).

The position objects used in Bio.SeqFeature now act almost like integers, making dealing with fuzzy locations in EMBL/GenBank files much easier. Also the SeqFeature‘s strand and any database reference are now properties of the FeatureLocation object (a more logical placement), with proxy methods for backwards compatibility.

Bio.Graphics.BasicChromosome has been extended to allow simple sub-features to be drawn on chromosome segments, suitable to show the position of genes, SNPs or other loci.

Bio.Graphics.GenomeDiagram has been extended to allow cross-links between tracks, and track specific start/end positions for showing regions. This can be used to imitate the output from the Artemis Comparison Tool (ACT). Also, a new attribute circle_core makes it easier to have an empty space in the middle of a circular diagram (see tutorial).

Note Bio.Graphics requires the ReportLab library.

Bio.Align.Applications now includes a wrapper for command line tool Clustal Omega for protein multiple sequence alignment.

Bio.AlignIO now supports sequential PHYLIP files (as well as interlaced PHYLIP files) as a separate format variant.

Additionally there have been other minor bug fixes and more unit tests, and updates to the documentation including the Biopython Tutorial (PDF).

Contributors

Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:

• Andreas Wilm (first contribution)
• Alessio Papini (first contribution)
• Brad Chapman
• Brandon Invergo
• Connor McCoy
• Eric Talevich
• João Rodrigues
• Konrad Förstner (first contribution)
• Michiel de Hoon
• Matej Repič (first contribution)
• Leighton Pritchard
• Peter Cock

Source distributions and Windows installers for Biopython 1.58 are available from the downloads page on the Biopython website and from the Python Package Index (PyPI).

A new interface and parsers for the PAML (Phylogenetic Analysis by Maximum Likelihood) package of programs, supporting codeml, baseml and yn00 as well as a Python re-implementation of chi2 was added as the Bio.Phylo.PAML module.

Bio.SeqIO now includes read and write support for the SeqXML, a simple XML format offering basic annotation support. See Schmitt et al (2011) in Briefings in Bioinformatics.

Bio.SeqIO now includes read support for ABI files (“Sanger” capillary sequencing trace files, containing called sequence with PHRED qualities).

The Bio.AlignIO “fasta-m10″ parser was updated to cope with the marker lines as used in Bill Pearson’s FASTA version 3.36, without this fix the parser would only return alignments for the first query sequence.

The Bio.AlignIO “phylip” parser and writer now treat a dot/period in the sequence as an error, in line with the official PHYLIP specification. Older verions of our code didn’t do anything special with this character. Also, support for “phylip-relaxed” has been added which allows longer record names as used in RAxML and PHYML.

Of potential interest to anyone subclassing Biopython objects, any remaining “old syle” Python classes have been switched to “new style” classes. This allows things like defining properties.

Bio.HMM’s Viterbi algorithm now expects the initial probabilities explicitly.

Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:

• Aaron Gallagher (first contribution)
• Bartek Wilczynski
• Bogdan T. (first contribution)
• Brandon Invergo (first contribution)
• Connor McCoy (first contribution)
• David Cain (first contribution)
• Eric Talevich
• Fábio Madeira (first contribution)
• Hongbo Zhu
• Joao Rodrigues
• Michiel de Hoon
• Peter Cock
• Thomas Schmitt (first contribution)
• Tiago Antao
• Walter Gillett
• Wibowo Arindrarto (first contribution)