[Biopython-dev] EMBOSS format name "fastq-sanger" in Biopython?

[Peter]

On Fri, Jul 24, 2009 at 11:48 AM, Peter<biopython at maubp.freeserve.co.uk> wrote:
>
> To be more precise, it looks like "fastq" as an output format in
> EMBOSS is an alias for "fastq-sanger" (to be confirmed), see:
> http://lists.open-bio.org/pipermail/emboss-dev/2009-July/000599.html

Confirmed,
http://lists.open-bio.org/pipermail/emboss-dev/2009-July/000602.html

> In any case, it would still make sense to include "fastq-sanger" as
> an alias for the Sanger standard FASTQ files in Biopython's SeqIO,
> especially if BioPerl is also going to use that name (to be confirmed):
> http://lists.open-bio.org/pipermail/bioperl-l/2009-July/030688.html

Confirmed, BioPerl will support "fastq" or "fastq-sanger" to mean the
Sanger standard FASTQ files:
http://lists.open-bio.org/pipermail/bioperl-l/2009-July/030691.html

I've updated Biopython's SeqIO in CVS to support "fastq-sanger" as
an alias for "fastq".

Peter