[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
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
_______________________________________________
BioPython mailing list - BioPython at biopython.org
http://biopython.org/mailman/listinfo/biopython
More information about the BioPython
mailing list