[Biopython-dev] Draft announcement for Biopython 1.51

[David Winter]

Hi all, here is a draft announcement to go out when 1.51 is built and 
ready to go. Comments and corrections are very welcome (should we keep 
the deprecation paragraph in?)

I've also added a draft post to the OBF blog with this text marked up 
with links and ready to go, hopefully that way whoever builds the 
release can just ask someone with an account there (Brad and Peter at 
least) to push post once everything is ready.

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We are pleased to announce the release of Biopython 1.51.This new stable 
release enhances version 1.50 (released in April) by extending the 
functionality of existing modules, adding a set of application wrappers 
for popular alignment programs and fixing a number of minor bugs.

In particular, the SeqIO module can now write genbank files that include 
features and deal with FASTQ files created by Illumina 1.3+. Support for 
this format allows interconversion between FASTQ files using Sloexa, 
Sanger and Ilumina quality scores and has been validated against the the 
BioPerl and EMBOSS implementations of this format.

Biopython 1.51 is the first stable release to include the 
Align.Applications module which allows users to define command line 
wrappers for popular alignment programs including ClustalW, Muscle and 
T-Coffee.

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This new release also spells the beginning of the end for some of 
Biopython's older tools. Bio.Fasta and the application tools 
ApplicationResult and generic_run() have been marked as deprecated which 
means they can still be imported but doing who warn the user that these 
functions will be removed in the future. Bio.Fasta has been superseded 
by SeqIO's support for the Fasta format while we now suggest using the 
subprocess module from the Python Standard Library to call applications 
- use of this module is extensively documented in section 6.3 of the 
Biopython Tutorial and Cookbook.
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As always the Tutorial and Cookbook has been updated to document the 
other changes made since the last release.

Thank you to everyone who tested our 1.51 beta or submitted bugs since 
out last stable release and to all of our contributors

Sources and Windows Installer for the new release are available from the 
downloads page.
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