Thanks a lot, that's what I need, and this tutorial is very hepfull too.
Hi,
I'm trying to parse GenBank file and extract the genes sequences, but I didn't find how to detect the complement sequences. I tried regex by searching "complenent" in "feature.location" but that didn't work.
If you are some ideas you're welcome :)
1 answer
Each feature object has a .strand (actually an alias for the feature's location's strand, .location.strand), e.g.
from Bio import SeqIO
for record in SeqIO.parse(filename, "embl"):
print(record.id)
for feature in record.features:
print(feature.strand)
print(feature.extract(record.seq))
The last line of the example shows how to get the sequence associated with the feature.
See also the SeqFeature built in documentation, also available at http://biopython.org/DIST/docs/api/Bio.SeqFeature-module.html
As explained there and in the Biopython Tutorial http://biopython.org/DIST/docs/tutorial/Tutorial.html the .strand will be -1 for features on the complement strand.
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