I have information of coordinates some genes in the below given form and I intend to use the genome sequence file to get this coordinate using Biopython. The result should be in form of fasta file i.e >Bra000001 .......
Bra000001 A03 8794511 8797095
Bra000002 A03 8797899 8800379
Bra000003 A03 8812470 8813271
Bra000004 A03 8816858 8817232
Bra000005 A03 8818081 8820123
Bra000006 A03 8820739 8821050
Bra000007 A03 8823497 8824207
Bra000008 A03 8829308 8830496
Bra000009 A03 8832800 8836134
Kindly help!
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written
by
imaditi1987 •
Have you looked into pybedtools? Not exactly biopython, but if that is the only task you are trying to achieve it will do it very efficiently. Here is their example:
a = pybedtools.BedTool("""
chr1 1 10
chr1 50 55""", from_string=True)
fasta = pybedtools.example_filename('test.fa')
a = a.sequence(fi=fasta)
print(open(a.seqfn).read())
chr1:1-10
GATGAGTCT
chr1:50-55
CCATC
This can be easily changed to read your bed file and fasta:
import pybedtools
from pybedtools import BedTool
a = BedTool("path_to_coordinates.bed")
fasta = BedTool("path_to_sequence.fasta")
a = a.sequence(fi=fasta)
print(open(a.seqfn).read())
It's untested, but it should work with minor changes.
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written
by
A. Domingues
Try using bedtools getfasta command. If takes as input the FASTA file of sequences and a tab-separated value file of the coordinates you want to retrieve. If you absolutely need to do this in Python, you can always use Python's subproces module to externally call the command and capture the output.
The pybedtools package already wraps most of bedtools functions, so in most cases there is no need to use subproces.
•
written
by
A. Domingues
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