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

[Bonis Sanz, Julio]

hi!

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

Lets say:

     mRNA            join(1870..1959,2070..2106,8593..8646,9327..9399,
                     20023..20132,25649..25786,30723..30800,38444..40397)

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:

gb_record.features[x].location._start.position
gb_record.features[x].location._end.position


Any idea?

regards, 

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,
Julio
Enviado el: jueves, 25 de noviembre de 2004 16:40
Para: biopython at biopython.org
Asunto: [BioPython] Bug in GenBank.FeatureParser detected


Hi, 

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

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=51511729&rettype=gbwithparts&retmode=text&seq_start=46267941&seq_stop=46467941

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
KEYWORDS    HTG.

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...

Regards, 

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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