[Bioperl-l] Announcing Bio::SFF

[Peter Cock]

On Mon, Dec 19, 2011 at 3:48 PM, Leon Timmermans
<l.m.timmermans at students.uu.nl> wrote:
> On Mon, Dec 19, 2011 at 3:31 PM, Peter Cock wrote:
>
>> Have you looked at the sample SFF data in Biopython? Please
>> use them for the BioPerl unit tests (we're been talking about a
>> cross project collection of test data files like this), the README
>> file should be self-explanatory:
>> https://github.com/biopython/biopython/tree/master/Tests/Roche
>
> Yeah, I'm using those now
> (https://github.com/Leont/bio-sff/blob/master/t/reader.t).

Could you a link to your /corpus/README.txt file pointing
back to the Biopython original for acknowledgement and
future reference?

>
> I must say there were some interesting corner cases in it.
>

I'm glad you agree - and if you can think of any more special
cases to verify that would be great.

Are you doing just SFF parsing for now? Not writing?

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.

Peter