[Biopython-dev] Biopython 1.62 released

[Peter Cock]

Dear Biopythoneers,

Source distributions and Windows installers for Biopython 1.62 are now
available from the downloads page on the official Biopython website
and (soon) from the Python Package Index (PyPI).

Python support

This is our first release of Biopython which officially supports
Python 3. Specifically, this is supported under Python 3.3. Older
versions of Python 3 may still work albeit with some issues, but are
not supported.

We still fully support Python 2.5, 2.6, and 2.7. Support under Jython
is available for versions 2.5 and 2.7 and under PyPy for versions 1.9
and 2.0. However, unlike CPython, Jython and PyPy support is partial:
NumPy and our C extensions are not covered.

Please note that this release marks our last official for support
Python 2.5. Beginning from Biopython 1.63, the minimum supported
Python version will be 2.6.

Highlights

The translation functions will give a warning on any partial codons
(and this will probably become an error in a future release). If you
know you are dealing with partial sequences, either pad with “N” to
extend the sequence length to a multiple of three, or explicitly trim
the sequence.

The handling of joins and related complex features in Genbank/EMBL
files has been changed with the introduction of a CompoundLocation
object. Previously a SeqFeaturefor something like a multi-exon CDS
would have a child SeqFeature (under thesub_features attribute) for
each exon. The sub_features property will still be populated for now,
but is deprecated and will in future be removed. Please consult the
examples in the help (docstrings) and Tutorial.

Thanks to the efforts of Ben Morris, the Phylo module now supports the
file formats NeXML and CDAO. The Newick parser is also significantly
faster, and can now optionally extract bootstrap values from the
Newick comment field (like Molphy and Archaeopteryx do). Nate Sutton
added a wrapper for FastTree toBio.Phylo.Applications.

New module Bio.UniProt adds parsers for the GAF, GPA and GPI formats
from UniProt-GOA.

The BioSQL module is now supported in Jython. MySQL and PostgreSQL
databases can be used. The relevant JDBC driver should be available in
the CLASSPATH.

Feature labels on circular GenomeDiagram figures now support the
label_positionargument (start, middle or end) in addition to the
current default placement, and in a change to prior releases these
labels are outside the features which is now consistent with the
linear diagrams.

The code for parsing 3D structures in mmCIF files was updated to use
the Python standard library’s shlex module instead of C code using
flex.

The Bio.Sequencing.Applications module now includes a BWA command line wrapper.
Bio.motifs supports JASPAR format files with multiple
position-frequence matrices.

Additionally there have been other minor bug fixes and more unit tests.

Contributors

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

Alexander Campbell (first contribution)
Andrea Rizzi (first contribution)
Anthony Mathelier (first contribution)
Ben Morris (first contribution)
Brad Chapman
Christian Brueffer
David Arenillas (first contribution)
David Martin (first contribution)
Eric Talevich
Iddo Friedberg
Jian-Long Huang (first contribution)
Joao Rodrigues
Kai Blin
Lenna Peterson
Michiel de Hoon
Matsuyuki Shirota (first contribution)
Nate Sutton (first contribution)
Peter Cock
Petra Kubincová (first contribution)
Phillip Garland
Saket Choudhary (first contribution)
Tiago Antao
Wibowo ‘Bow’ Arindrarto
Xabier Bello (first contribution)

Thank you all.

Release announcement here (RSS feed available):
http://news.open-bio.org/news/2013/08/biopython-1-62-released/

P.S. You can follow @Biopython on Twitter
https://twitter.com/Biopython