[Biopython-dev] Biopython 1.59 plans

[Peter Cock]

On Fri, Feb 24, 2012 at 2:35 PM, Peter Cock <p.j.a.cock at googlemail.com>
wrote:
>
> I will now prepare a draft announcement for the news blog and emailing...
>

How this look?
Biopython 1.59 released

Source distributions and Windows installers for *Biopython 1.59* are now
available from the downloads page <http://biopython.org/wiki/Download> on
the Biopython website <http://biopython.org/> and from the Python Package
Index (PyPI) <http://pypi.python.org/pypi/biopython>.
Platforms/Deployment

We currently support Python <http://python.org/> 2.5, 2.6 and 2.7 and also
test under Jython <http://jython.org/> 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 <http://numpy.scipy.org/>), and under
PyPy<http://pypy.org/>(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<http://togows.dbcls.jp/site/en/rest.html>,
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<http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetch_help.html>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), however
the NCBI have also changed the retmode default argument so you may need to
make this explicit. e.g. retmode="text"

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)<http://www.sanger.ac.uk/resources/software/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<http://www.reportlab.com/software/opensource/>
.

Bio.Align.Applications now includes a wrapper for command line tool Clustal
Omega <http://www.clustal.org/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<http://biopython.org/DIST/docs/tutorial/Tutorial.html>(
PDF <http://biopython.org/DIST/docs/tutorial/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
   - Joao Rodrigues
   - Konrad Förstner (first contribution)
   - Michiel de Hoon
   - Matej Repič (first contribution)
   - Leighton Pritchard
   - Peter Cock