Difference between revisions of "Build mutation Script"
From Bioinformatikpedia
(Created page with " #! /usr/bin/env python import sys sequence_fasta = sys.argv[1] mutation_file = sys.argv[2] f = open (sequence_fasta, 'r') sequence = "" sequence = f.read() sequ…") |
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| + | Usage: ./script.py file.fasta mutation.file |
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#! /usr/bin/env python |
#! /usr/bin/env python |
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f.write(tmp[i] + str(i+1) + "S\n") |
f.write(tmp[i] + str(i+1) + "S\n") |
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f.write(tmp[i] + str(i+1) + "T\n") |
f.write(tmp[i] + str(i+1) + "T\n") |
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| + | f.write(tmp[i] + str(i+1) + "W\n") |
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| + | f.write(tmp[i] + str(i+1) + "Y\n") |
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| + | f.write(tmp[i] + str(i+1) + "V\n") |
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| + | |||
| + | f.close() |
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Latest revision as of 16:44, 11 June 2012
Usage: ./script.py file.fasta mutation.file
#! /usr/bin/env python
import sys
sequence_fasta = sys.argv[1]
mutation_file = sys.argv[2]
f = open (sequence_fasta, 'r')
sequence = ""
sequence = f.read()
sequence = sequence.split('\n')
header = sequence[0]
tmp = ""
for i in range(1,len(sequence)):
tmp += sequence[i]
f.close()
f = open(mutation_file, 'wb')
for i in range(len(tmp)):
f.write(tmp[i] + str(i+1) + "A\n")
f.write(tmp[i] + str(i+1) + "R\n")
f.write(tmp[i] + str(i+1) + "N\n")
f.write(tmp[i] + str(i+1) + "D\n")
f.write(tmp[i] + str(i+1) + "C\n")
f.write(tmp[i] + str(i+1) + "E\n")
f.write(tmp[i] + str(i+1) + "Q\n")
f.write(tmp[i] + str(i+1) + "G\n")
f.write(tmp[i] + str(i+1) + "H\n")
f.write(tmp[i] + str(i+1) + "I\n")
f.write(tmp[i] + str(i+1) + "L\n")
f.write(tmp[i] + str(i+1) + "K\n")
f.write(tmp[i] + str(i+1) + "M\n")
f.write(tmp[i] + str(i+1) + "F\n")
f.write(tmp[i] + str(i+1) + "P\n")
f.write(tmp[i] + str(i+1) + "S\n")
f.write(tmp[i] + str(i+1) + "T\n")
f.write(tmp[i] + str(i+1) + "W\n")
f.write(tmp[i] + str(i+1) + "Y\n")
f.write(tmp[i] + str(i+1) + "V\n")
f.close()
