[Biopython-dev] [Bug 3175] Caret in genbank files leads to GenBank Parser crash in Biopython 1.54

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

http://bugzilla.open-bio.org/show_bug.cgi?id=3175





------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2011-02-04 09:20 EST -------
Hi Aaron,

The example in attachment #1568 from comment #1 is invalid. The feature
location join(16024^16026..16569,1..576) is wrong since the caret should be
used in the form [i]^[i+1], i.e. consecutive numbers. See:
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html

That example should probably be a between location like
join((16024.16026)..16569,1..576)

However, the example in the original bug report, 1000..1001^1002, looks
possible (but unprecedented to my knowledge) and that also fails with the
latest Biopython GenBank parsing code (much changed since Biopython 1.54). I
don't really understand how that usefully differs from 1000..1001 or 1000..1002
though.

Was that from a GenBank file from the NCBI? If so what accession please, or a
URL?

Thanks,

Peter


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