[Bioperl-l] Announcing Bio::SFF

[Peter Cock]

On Mon, Dec 19, 2011 at 4:47 PM, Leon Timmermans
<l.m.timmermans at students.uu.nl> wrote:
> On Mon, Dec 19, 2011 at 5:15 PM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
>>
>> Could you a link to your /corpus/README.txt file pointing
>> back to the Biopython original for acknowledgement and
>> future reference?
>
> I forgot about that, I will add it to the next release.

Thanks.

>> Are you doing just SFF parsing for now? Not writing?
>
>
> I haven't written the writer yet (haven't needed it so far). I'd rather
> release working code early instead of waiting until everything is complete.

I understand - but make sure you've designed the data structures
in the parser so as to allow the original record to be re-built as SFF.

>> Now, as to Bio::SeqIO integration, Biopython's SeqIO uses
>> format name "sff" to mean the full read sequence (with mixed
>> case, upper case for the good sequence, lower cases for any
>> left/right clipping - as in the Roche tools), and "sff-trim" to mean
>> the trimmed sequences. I would encourage you to do the
>> same, as part of the general aim of having consistent
>> sequence format names between BioPerl, Biopython, and
>> EMBOSS, where possible.
>
> I agree, consistency is good.

Great. I'd guess Bio::SeqIO integration would be more important
that SFF output initially.

Peter