[Bioperl-l] Announcing Bio::SFF

[Peter Cock]

On Wed, Dec 14, 2011 at 3:43 PM, Leon Timmermans
<l.m.timmermans at students.uu.nl> wrote:
> Hi all,
>
> As already mentioned on IRC, I recently wrote a SFF parser and uploaded it
> to CPAN as Bio::SFF. I haven't written a Bio::SeqIO::sff wrapper yet (SFF
> entries don't map 1:1 with Bio::Seq objects), but if anyone is has the time
> to write one I'd be most grateful.
>
> Leon

Hi Leon,

Have you looked at the index block at all, in order to offer random
access by read ID, or to access the Roche XML manifest? Please
ask if you need more information about this - or if you can read Python:
https://github.com/biopython/biopython/blob/master/Bio/SeqIO/SffIO.py

Is this building on Miguel Pignatelli's work? I don't recall seeing
any follow up posts from him after this one:
http://lists.open-bio.org/pipermail/bioperl-l/2010-November/034239.html

Peter