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

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





------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2009-09-02 11:24 EST -------
(In reply to comment #3)
> I can now parse the Roche SFF index, allowing fast random access to
> the reads. See:
> 
> http://github.com/peterjc/biopython/commits/index
> http://lists.open-bio.org/pipermail/biopython-dev/2009-August/006603.html
> 
> Peter

That branch now has support for SeqIO parsing, indexing and *writing* of
SFF files. The write support is still very new and needs more testing,
but is looking promising. Note that while currently I read the undocumented
Roche style SFF index block, I have not yet attempted to write out such an
index (probably unwise unless the format does get published?).

Also note that there is still scope for improvement for how the trimming
information is presented in the SeqRecord object (perhaps some kind of
masked SeqRecord/Seq as has been suggested on the mailing lists).

Peter


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