Biopython 1.57 released

The Biopython community is pleased to announce the release of Biopython 1.57. Source distributions and Windows installers are available from the downloads page on the Biopython website and from the Python Package Index.

Bio.SeqIO now includes an index_db() function which extends the existing

indexing functionality to allow indexing many files, and more importantly

this keeps the index on disk in a simple SQLite3 database rather than in

memory in a Python dictionary.

Bio.Blast.Applications now includes a wrapper for the BLAST+ blast_formatter

tool from NCBI BLAST 2.2.24+ or later. This release of BLAST+ added the

ability to run the BLAST tools and save the output as ASN.1 format, and then

convert this to any other supported BLAST ouput format (plain text, tabular,

XML, or HTML) with the blast_formatter tool. The wrappers were also updated

to include new arguments added in BLAST 2.2.25+ such as -db_hard_mask.

The SeqRecord object now has a reverse_complement method (similar to that of

the Seq object). This is most useful to reversing per-letter-annotation (such

as quality scores from FASTQ) or features (such as annotation from GenBank).

Bio.SeqIO.write’s QUAL output has been sped up, and Bio.SeqIO.convert now

uses an optimised routine for FASTQ to QUAL making this much faster.

Biopython can now be installed with pip. Thanks to David Koppstein and

James Casbon for reporting the problem.

Bio.SeqIO.write now uses lower case for the sequence for GenBank, EMBL and

IMGT output.

The Bio.PDB module received several fixes and improvements, including starting

to merge João’s work from GSoC 2010; consequently Atom objects now know

their element type and IUPAC mass. (The new features that use these

attributes won’t be included in Biopython until the next release, though, so

stay tuned.)

The nodetype hierachy in the Bio.SCOP.Cla.Record class is now a dictionary

(previously it was a list of key,value tuples) to better match the standard.

Many thanks to the Biopython developers and community for making this release

possible, especially the following contributors:

Brad Chapman

Eric Talevich

Erick Matsen (first contribution)

Hongbo Zhu

Jeffrey Finkelstein (first contribution)

Joanna & Dominik Kasprzak (first contribution)

Joao Rodrigues

Kristian Rother

Leighton Pritchard

Michiel de Hoon

Peter Cock

Peter Thorpe (first contribution)

Phillip Garland

Walter Gillett (first contribution)

Feedback is most welcome on the mailing lists, or redmine.