[Bioperl-l] Announcing Bio::SFF

[Leon Timmermans]

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