[BioPython] Getting the location from a Genbank record
Sebastian Bassi
sbassi at gmail.com
Mon Sep 3 03:25:22 UTC 2007
I can get the "location" of the genes I want, but I have them in a
"print mode" (calling __str__), but I don't see how to get the start
and end position in a way I could use to slice the seq. There are
private attributes _start and _end but I don't know if using them if
the "right" way to do it.
from Bio import SeqIO
mr = SeqIO.parse(open("MTtabaco.gbk"), "genbank").next()
targets=(['cox2'],['atp6'],['atp9'],['cob'])
for x in mr.features:
if x.qualifiers.get('gene') in targets:
print x.location
#print mr.seq
Get the slice I am looking for:
>>> mr.seq[x.location._start.position:x.location._end.position]
Seq('ATGAATGTTATAACTCCTAATTCTTTGGTAGCGGACCTCTTTGATAGTTCGACCCTTATCCCCCGTCTAACTCAACTATTCGACTGTACGGCTATTGTGATTGCGAGAGAAAGGAGGGATGGCGCCTTCCTTTACCATCTGGCGGTTGAAAACAAAAGTGCTTCCAGGTACACGGCTGTTAGGCTCATCCAAGGCGTATTTACGGAAGTAGCAGGGAACTTGACCGTCAAGTTTGAAAAAAGCTGGCCAAGCCTGTGTCACTTTCTTACGTCAGGAGAAAGGGAGATCAAAGAAGTATGGGGCCGATACGCGAAGGATCAAATCATAGAGATAGCGGATCTTAAGAGGCGGAAGAAAAGGAACCTCGGCGACCCAGAGATCGCGGAGTCCGCGCCCGTGCCGAAAGTGAAGAAGCTTTCCTCTCCTTTCAGTCGAGCATGCCCGCCCTTTAGCACTTCCCTTCCCGAAGTGGGAGTAGGAGAAAGGAAAGCGCACTCGATCAATTACCATGCCGTGTCGTAA',
IUPACAmbiguousDNA())
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