[BioPython] How is a join stored in the gb_record?

Bonis Sanz, Julio JBonis at imim.es
Mon Nov 29 06:55:05 EST 2004


I have parsed a "genome" genBank record with biopython...

Lets say:

     mRNA            join(1870..1959,2070..2106,8593..8646,9327..9399,

what I need is to retrieve from the gb_record the subsegments (1870 to 1959, 2070 to 2106....)

But I only have realized how to retrieve the start and end points (1870 and 40397) by:


Any idea?


Julio Bonis Sanz

-----Mensaje original-----
De: biopython-bounces at portal.open-bio.org
[mailto:biopython-bounces at portal.open-bio.org]En nombre de Bonis Sanz,
Enviado el: jueves, 25 de noviembre de 2004 16:40
Para: biopython at biopython.org
Asunto: [BioPython] Bug in GenBank.FeatureParser detected


I was trying to parse a genbank record obtained by using eutils:


It means, human chromosome 13, from 46267941 to 46467941. My idea is to give a position and a chromosome and then get the surrounding genes/mRNAs/CDS/SNPs in the area....

Well, I have found that when trying to use GenBank.FeatureParser() it shows an error here:

LOCUS       NC_000013             200001 bp    DNA     linear   CON 25-OCT-2004
DEFINITION  Homo sapiens chromosome 13, complete sequence.
ACCESSION   NC_000013 REGION: 46267941..46467941
VERSION     NC_000013.9  GI:51511729

Specifically in line:

ACCESSION   NC_000013 REGION: 46267941..46467941


If you remove 'REGION: 46267941..46467941' then the parser works fine.

I guess it should be easy to fix in the Biopython code... but I get lost when trying to find where....

Someone can help? I suggest to add the fix as soon as possible...


Julio Bonis Sanz MD http://www.juliobonis.com/portal/

Research Group on Biomedical Informatics http://www.imim.es/grib/
Barcelona - Spain

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