[Biopython-dev] Draft announcement for Biopython 1.51

[Peter]

Thanks for the first draft David,

On Thu, Aug 13, 2009 at 1:32 AM, David
Winter<winda002 at student.otago.ac.nz> wrote:
> 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.

Typo: Sloexa -> Solexa. I would probably rephrase the rest a little, there
are some subtleties with 3 container formats but only 2 scoring systems...

In particular, the SeqIO module can now write GenBank with features, and
deal with FASTQ files created by Illumina 1.3+. Support for this format
allows interconversion between FASTQ files using the Sanger, Solexa
or Illumina 1.3+ FASTQ variants, using conventions agreed with the
BioPerl and EMBOSS projects.

[BioPerl and EMBOSS are still working on the FASTQ variants, so we
haven't actually got everything cross validated yet.]

> ??
> 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 Bio.Fasta has been superseded by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.
> ??

I would omit that, or at least cut it down a lot. It might also be worth
mentioning we no longer include Martel/Mindy, and thus don't have
any dependence on mxTextTools. Also we don't support Python 2.3
anymore.

P.S. I try and avoid referring to sections of the Tutorial by number, as
these often change from release to release.

Thanks,

Peter