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

Wed Feb 6 02:05:19 UTC 2013

Hi.  

I'm wondering if the MafIO module is going to be included in this release?

-Kieran

On Feb 5, 2013, at 17:03, Michiel de Hoon <mjldehoon at yahoo.com> wrote:

> 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
>> 
>> _______________________________________________
>> Biopython-announce mailing list  -  Biopython-announce at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython-announce
> 
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