[Biopython-dev] [Bug 2425] Fasta ID parsing error

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Feb 25 20:46:57 UTC 2008


------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2008-02-25 15:46 EST -------
I haven't got round to addressing this issue yet - currently the BioSQL with
SeqIO unit test (which I added relatively recently) deliberately avoids using
any FASTA files because of this problem.

We may want to try and do something intelligent with the version field if
present in the annotation dictionary, which should be more robust than simply
checking the record.id format.

I assume in your example you expected "region1.fasta.screen.Contig1" to be used
as the record key in BioSQL?  There is a 40 character limit on this field,
which should be fine for most FASTA identifiers.

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