[Biopython-dev] [Biopython-announce] Biopython 1.61 released

[Michiel de Hoon]

Thanks Peter!
Great to see this new code out.

Best,
-Michiel.

--- On Tue, 2/5/13, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> From: Peter Cock <p.j.a.cock at googlemail.com>
> Subject: [Biopython-announce] Biopython 1.61 released
> To: biopython-announce at lists.open-bio.org, "Biopython Mailing List" <biopython at lists.open-bio.org>, "Biopython-Dev Mailing List" <biopython-dev at lists.open-bio.org>
> Date: Tuesday, February 5, 2013, 5:05 PM
> 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
> 
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