[Biopython-dev] [Bug 2837] Reading Roche 454 SFF sequence read files in Bio.SeqIO

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2837


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
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Attachment #1303 is|0                           |1
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------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2009-08-10 09:43 EST -------
(From update of attachment 1303)
This file is already a tiny bit out of date - I've started working on this on a
git branch.

http://github.com/peterjc/biopython/commits/sff

See also James Casbon's parser, also on github:

http://lists.open-bio.org/pipermail/biopython-dev/2009-July/006456.html

http://github.com/jamescasbon/biopython/tree/sff

It looks like we could try and merge the two. James' code looks like it doesn't
need seek/tell, which means it should work on any input handle (not just an
open file).

Note neither parser yet copes with paired end data (and I have not yet found
any test files to work on).


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