Mercurial > repos > arkarachai-fungtammasan > str_fm

comparison microsatcompat.py @ 0:07588b899c13 draft

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author arkarachai-fungtammasan
date Wed, 01 Apr 2015 17:05:51 -0400
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-1:000000000000 0:07588b899c13
1 import sys
2 # remove all read that have unmatch microsat
3 # check only one line at a time
4 def complement_base(read):
5 collect=''
6 for i in read:
7 if i.upper()=='A':
8 collect+='T'
9 elif i.upper()=='T':
10 collect+='A'
11 elif i.upper()=='C':
12 collect+='G'
13 elif i.upper()=='G':
14 collect+='C'
15 return collect
16
17 def makeallpossible(read):
18 collect=[]
19 for i in range(len(read)):
20 tmp= read[i:]+read[:i]
21 collect.append(tmp)
22 collect.append(complement_base(tmp))
23 return collect
24
25
26 fd=open(sys.argv[1])
27 lines=fd.xreadlines()
28 firstcolumn=int(sys.argv[2])-1 #4
29 secondcolumn=int(sys.argv[3])-1 # 10
30 for line in lines:
31 temp=line.strip().split('\t')
32 temp=filter(None,temp)
33 micro1=temp[firstcolumn]
34 micro2=temp[secondcolumn]
35 if micro1 in makeallpossible(micro2):
36 print line.strip()