[Biopython-dev] Draft announcement for Biopython 1.51
David Winter
winda002 at student.otago.ac.nz
Thu Aug 13 00:32:55 UTC 2009
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.
++
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.
??
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 Bio.Fasta has been superseded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.
??
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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