[Biopython-dev] Biopython 1.53 released

[Peter]

Dear Biopythoneers,

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.

SQLite support (built into Python 2.5+) was added to our BioSQL
interface. This is still a little experimental as we are using a draft
BioSQL SQLite schema, but this should be merged into the next
BioSQL release.

Biopython now includes wrappers for the new NCBI BLAST C++ tools,
which will be replacing the old NCBI “legacy” BLAST tools written in
C. The plain text BLAST parser has been updated to cope as well.
Nevertheless, we (and the NCBI) still recommend using the XML output
for parsing.

Bio.Entrez includes the new (Jan 2010) DTD files from the NCBI for
parsing MedLine/PubMed data.

The NCBI codon tables have been updated from version 3.4 to 3.9, which
adds a few extra start codons, and a few new tables (Tables 16, 21, 22
and 23).

The restriction enzyme list in Bio.Restriction has been updated to the
Nov 2009 release of REBASE.

The Bio.PDB parser and output code has been updated to understand the
element column in ATOM and HETATM lines, and Bio.PDB.PDBList has been
updated for recent changes to the PDB FTP site.

Finally, support for running Biopython under Jython (using the Java
Virtual Machine) has been much improved. Note that Jython does not
support C code, and currently Jython does not parse DTD files (needed
for the Bio.Entrez XML parser). However, most of the Biopython modules
seem fine from testing Jython 2.5.0 and 2.5.1.

Sources and Windows Installers are available from our downloads page.

Thanks to the Biopython development team and to everyone who has
reported bugs or contributed patches since our last release.

--Peter, on behalf of the Biopython developers

P.S. This news post is online at
http://news.open-bio.org/news/2009/12/biopython-release-153/

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