[Bioperl-l] Announcing Bio::SFF

[Chris Fields]

On 12/19/2011 10:47 AM, Leon Timmermans 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.
>
> 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.
>
> 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.
>
> Leon
This is already implemented in Bio::SeqIO I believe.  This is the same 
line of thinking with the FASTQ format, that one can have a 
'format-variant' combination that (as one might guess) indicates to the 
parser any variation of the parser so logic within the parser can deal 
with it.  You can also pass the '-variant => "foo"' parameter as well 
IIRC.  You would just check the variant with the variant() method.

chris