[Biopython-dev] Biopython 1.61 release

[Peter Cock]

On Tue, Feb 5, 2013 at 6:57 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Hi all,
>
> The Biopython 1.61 release files are live, http://biopython.org/DIST/
> and this its tagged on GitHub now, i.e. this commit:
> https://github.com/biopython/biopython/commit/d372e59b3d9147cd9855feb6e3b90ff523f539b5
>
> I've not yet pushed this to PyPI, nor done the announcement.
>
> If anyone would like to write a draft based on the NEWS file
> and the previous announcements during the next hour or two,
> that would be great. Otherwise I'll do this after dinner...
>
> Thanks,
>
> Peter

Draft text below, based heavily on the NEWS file - any comments?

I'll post the new Tutorial online now, and then update the
Downloads page on the wiki before posting this.

Peter

--

Biopython 1.61 released

Source distributions and Windows installers for Biopython 1.61 are now
available from the downloads page on the Biopython website and from
the Python Package Index (PyPI).

The updated Biopython Tutorial and Cookbook is online (PDF).

Platforms/Deployment

We currently support Python 2.5, 2.6 and 2.7 and also test under
Python 3.1, 3.2 and 3.3 (including modules using NumPy), and Jython
2.5 and PyPy 1.9 (Jython and PyPy do not cover NumPy or our C
extensions). We are still encouraging early adopters to help test on
these platforms, and have included a ‘beta’ installer for Python 3.2
(and Python 3.3 too follow soon) under 32-bit Windows.

Please note we are phasing out support for Python 2.5. We will
continue support for at least one further release (Biopython 1.62).
This could be extended given feedback from our users. Focusing on
Python 2.6 and 2.7 only will make writing Python 3 compatible code
easier.

Features

GenomeDiagram has three new sigils (shapes to illustrate features).
OCTO shows an octagonal shape, like the existing BOX sigil but with
the corners cut off. JAGGY shows a box with jagged edges at the start
and end, intended for things like NNNNN regions in draft genomes.
Finally BIGARROW is like the existing ARROW sigil but is drawn
straddling the axis. This is useful for drawing vertically compact
figures where you do not have overlapping genes.

New module Bio.Graphics.ColorSpiral can generate colors along a spiral
path through HSV color space. This can be used to make arbitrary
‘rainbow’ scales, for example to color features or cross-links on a
GenomeDiagram figure.

The Bio.SeqIO module now supports reading sequences from PDB files in
two different ways. The “pdb-atom” format determines the sequence as
it appears in the structure based on the atom coordinate section of
the file (via Bio.PDB,
so NumPy is currently required for this). Alternatively, you can use
the “pdb-seqres” format to read the complete protein sequence as it is
listed in the PDB header, if available.

The Bio.SeqUtils module how has a seq1 function to turn a sequence
using three letter amino acid codes into one using the more common one
letter codes. This acts as the inverse of the existing seq3 function.

The multiple-sequence-alignment object used by Bio.AlignIO etc now
supports an annotation dictionary. Additional support for per-column
annotation is planned, with addition and splicing to work like that
for the SeqRecord per-letter annotation.

The Bio.Motif module has been updated and reorganized. To allow for a
clean deprecation of the old code, the new motif code is stored in a
new module Bio.motifs, and a PendingDeprecationWarning was added to
Bio.Motif.

Experimental Code – SearchIO

This release also includes Bow’s Google Summer of Code work writing a
unified parsing framework for NCBI BLAST (assorted formats including
tabular and XML), HMMER, BLAT, and other sequence searching tools.
This is currently available with the new BiopythonExperimentalWarning
to indicate that this is still somewhat experimental. We’re bundling
it with the main release to get more public feedback, but with the big
warning that the API is likely to change. In fact, even the current
name of Bio.SearchIO may change since unless you are familiar with
BioPerl its purpose isn’t immediately clear.

Contributors

Brandon Invergo
Bryan Lunt (first contribution)
Christian Brueffer (first contribution)
David Cain
Eric Talevich
Grace Yeo (first contribution)
Jeffrey Chang
Jingping Li (first contribution)
Kai Blin (first contribution)
Leighton Pritchard
Lenna Peterson
Lucas Sinclair (first contribution)
Michiel de Hoon
Nick Semenkovich (first contribution)
Peter Cock
Robert Ernst (first contribution)
Tiago Antao
Wibowo ‘Bow’ Arindrarto