1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
|
#!/bin/python
# -*- coding: utf-8 -*-
###################################
#Removes extensions in lowercase :
# usage : remove_extensions_disco_file.py <disco_snps_file>.fa
import os
import sys
import getopt
import time
fichier=sys.argv[1]
output=sys.argv[2]
nomFichier=(str(fichier).split('.'))
##Delete extension (lowercase) from disco file
snpfile=open(fichier,"r")
snpDiscobis=open(output, "w")
for line in snpfile:
if ">"==line[0]:
snpDiscobis.write(line)
else:
line=str(line)
line=line.replace('a','')
line=line.replace('g','')
line=line.replace('t','')
line=line.replace('c','')
snpDiscobis.write(line)
snpDiscobis.close()
|
