Mercurial > repos > arkarachai-fungtammasan > microsatellite_ngs
view test-data/microsatcompat.py @ 4:ecfc9041bcc5
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author | arkarachai-fungtammasan |
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date | Wed, 01 Apr 2015 14:05:54 -0400 |
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import sys # remove all read that have unmatch microsat # check only one line at a time def complement_base(read): collect='' for i in read: if i.upper()=='A': collect+='T' elif i.upper()=='T': collect+='A' elif i.upper()=='C': collect+='G' elif i.upper()=='G': collect+='C' return collect def makeallpossible(read): collect=[] for i in range(len(read)): tmp= read[i:]+read[:i] collect.append(tmp) collect.append(complement_base(tmp)) return collect fd=open(sys.argv[1]) lines=fd.xreadlines() firstcolumn=int(sys.argv[2])-1 #4 secondcolumn=int(sys.argv[3])-1 # 10 for line in lines: temp=line.strip().split('\t') temp=filter(None,temp) micro1=temp[firstcolumn] micro2=temp[secondcolumn] if micro1 in makeallpossible(micro2): print line.strip()