[Bioperl-l] Announcing Bio::SFF

[Fields, Christopher J]

Leon, 

Nice!  Definitely a good idea to have the lower-level parser and the BioPerl-bridging code separate, one of my concerns with the various parsers we have right now which hard-wire BioPerl classes in with the parser (makes it hard for optimization).

Chris

PS- Peter, I don't think the two projects are related, but I suppose Leon is the best to answer that.

Sent from my stupid iPad, now my laptop's on the fritz

On Dec 14, 2011, at 10:04 AM, "Peter Cock" <p.j.a.cock at googlemail.com> wrote:

> 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
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