[Biopython] Biopython 1.61 released

[Wibowo Arindrarto]

Hi Peter,

> Dear Biopythoneers,
>
> 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 to 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.
>
> New 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
>
> Thank you all.
>
> Release announcement here (RSS feed available):
> http://news.open-bio.org/news/2013/02/biopython-1-61-released/
>
> P.S. You can follow @Biopython on Twitter
> https://twitter.com/Biopython

Thanks for doing the release! It feels exciting to see SearchIO code
finally live in the distributions :). Hopefully this will result in
more feedback (and then more improvements ~ likewise for the whole
Biopython as well).

Also, thank you as well to everyone who has criticized / commented /
contributed code to the module :).

cheers,
Bow