[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 #5 from biopython-bugzilla at maubp.freeserve.co.uk  2009-09-02 12:45 EST -------
(In reply to comment #4)
> 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?).

It now has a first attempt at writing a Roche style SFF index, which my code
will parse back again happily. I have not yet tried the resulting file with
the Roche SFF tools. Note that this does not preserve any Roche XML meta data.
Note also that the index is skipped if any of the record names are not 14 chars
long (which is try on all the Roche indexes I have looked at).


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