[Biopython-dev] sff file

[Peter]

On Mon, Oct 26, 2009 at 3:53 PM, Sebastian Bassi
<sbassi at clubdelarazon.org> wrote:
> Where I can get an sff to make some tests?

I have some on my SFF branch (under Tests/Roche):
http://github.com/peterjc/biopython/tree/index

(I used to have a branch called "sff", and another "index" for what
ended up on the trunk as the new Bio.SeqIO.index function, but
the two were linked for indexing SFF files).

If you fancy trying the code, it offers reading, writing and indexing of
SFF files, showing the full untrimmed sequence in the SeqRecord.

> Biopython doens't include any sample sff file, I guess this is due to
> file size limitation.

Size isn't an issue - the Roche tools will let you create reduced SFF
files using just some of the records (e.g. a random subset).

> I would be happy if I can download a small (less than 10Mb) sff file.
> I went to ENTREZ Sequence Read Archive, and seems they only provide
> fastq.

I gather the NCBI Short Read Archive used to offer SFF files, but
sadly that do not any more. I am aware of a few projects at Sanger
with public SFF files - but these will all be large files, see:
http://lists.open-bio.org/pipermail/biopython/2009-August/005443.html

Peter