[BioPython] Loading dbxrefs from a gbk file

Sebastian Bassi sbassi at gmail.com
Sat Oct 25 01:03:43 UTC 2008


I have a genbank file like this one: http://www.pastecode.com.ar/f231664eb
I parse it with SeqIO.parse and the SeqRecord object I get is:

SeqRecord(seq=Seq('GAGAAGGACGCGCGGCCCCCAGCGCCTCTTGGGTGGCCGCCTCGGAGCATGACC...ATA',
IUPACAmbiguousDNA()), id='NM_000208.2', name='NM_000208',
description='Homo sapiens insulin receptor (INSR), transcript variant
1, mRNA.', dbxrefs=[])

If you look at lines 130 to 133 (I highlighted in yellow) of the
genbank sequence, there is cross database information (db_xref), but
it is not associated with the SeqRecord, it is an empty list.
According to http://www.biopython.org/wiki/SeqRecord, this condition
is known, but I don't understand if this is on porpuse or is a bug.
Best,
SB.


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