[Biopython-dev] CVS freeze for Biopython 1.50

[Peter]

On Mon, Apr 20, 2009 at 1:11 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> That just leaves the official announcement on the news page (which
> will be echoed onto twitter automatically) and to the mailing lists.
> I'll circulate a draft after lunch, unless one of our news coordinator
> volunteers wants to write something?  I realize I should have
> suggested this earlier as this is short notice, and you are in
> different time zones, but its worth a try.

And here is my draft - the HTML is just for the links on the news
site.  Should we add something about the Entrez EFetch change
("genbank" to "gb")?

Peter

--

We are pleased to announce Biopython release 1.50, featuring some
significant additions since Biopython 1.49 was released late last
year.

<a href="http://bioinf.scri.ac.uk/lp/programs.php#genomediagram">GenomeDiagram</a>
by Leighton Pritchard has been integrated into Biopython as the
Bio.Graphics.GenomeDiagram module.

A new module Bio.Motif has been added, which is intended to replace
the existing Bio.AlignAce and Bio.MEME modules. Also have a look at
Bio.ExPASy and the revised Prosite and Enzyme parsers.

As noted in a previous news posting, <a
href="http://biopython.org/wiki/SeqIO">Bio.SeqIO</a> can now read and
write <a href="http://news.open-bio.org/news/2009/03/biopython-next-gen-sequencing/">FASTQ
and QUAL files</a> used in second generation sequencing work. In
connection with this, our <a
href="http://biopython.org/wiki/SeqRecord">SeqRecord</a> object has a
new dictionary attribute, letter_annotations, for
per-letter-annotation information like sequence quality scores or
secondary structure predictions. Also, the SeqRecord object can now be
sliced to give a new SeqRecord covering just part of the sequence.

Biopython 1.50 supports Python 2.3, 2.4, 2.5 and 2.6. However, this is
expected to be the final version to support Python 2.3 (see this <a
href="http://news.open-bio.org/news/2009/04/2008/11/biopython-and-python-26-and-python-23/">previous
announcement</a>). Also, Biopython 1.50 should be the last release to
include our old deprecated parsing infrastructure (Martel and
Bio.Mindy).

We’ve also updated the <a title="Biopython Tutorial and Cookbook
(HTML)" href="http://biopython.org/DIST/docs/tutorial/Tutorial.html">Biopython
Tutorial and Cookbook</a> (also available in <a title="Biopython
Tutorial and Cookbook (PDF)"
href="http://biopython.org/DIST/docs/tutorial/Tutorial.pdf">PDF</a>),
and not just by adding <a title="About the Biopython logo"
href="http://biopython.org/wiki/Logo">our logo</a> to the cover ;)

Thank you to everyone who tested the <a
href="http://news.open-bio.org/news/2009/04/biopython-150-beta-released/">Biopython
1.50 beta release</a>, and to all our contributors.

Source distributions and Windows installers are available from the <a
href="http://biopython.org/wiki/Download">downloads</a> page on the <a
href="http://biopython.org/">Biopython website (biopython.org)</a>.

-Peter on behalf of the Biopython developers