[Biopython] gff3: feature.location.end problem
Mic
mictadlo at gmail.com
Tue May 28 01:49:30 UTC 2013
Hi,
When parsing this gff3 file:
##gff-version 3
##sequence-region ID1 1 20
ID1 prediction gene 1 20 10.0 + .
other=Some,annotations;ID=gene1
ID1 prediction exon 1 5 . + .
Parent=gene1
ID1 prediction exon 16 20 . + .
Parent=gene1
with this code:
from BCBio import GFF # handles GFF files
with open("test.gff3") as file:
for rec in GFF.parse(file):
annotations = rec.annotations['sequence-region'][0]
id = annotations[0]
start = int(annotations[1])
end = int(annotations[2])
print id, start, end
for feature in rec.features:
contig_id = feature.qualifiers['ID'][0]
print contig_id, int(feature.location.start),
int(feature.location.end)
I get the following output:
ID1 1 20
gene1 0 20
Why is it not "gene1 0 19" and "ID1 0 19"?
Thank you in advance.
Mic
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