[Biopython-dev] [Bug 2837] Reading Roche 454 SFF sequence read files in Bio.SeqIO
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Mon Aug 10 13:43:15 UTC 2009
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
obsolete| |
------- 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This file is already a tiny bit out of date - I've started working on this on a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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