Mercurial > repos > arkarachai-fungtammasan > microsatellite_ngs
view microsatpurity.py @ 3:7cc220e8c2ac
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author | arkarachai-fungtammasan |
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date | Fri, 24 Oct 2014 15:45:00 -0400 |
parents | 20ab85af9505 |
children |
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import sys # remove all read that have impure microsat # check only one line at a time fd=open(sys.argv[1]) lines=fd.xreadlines() ##motifIx=int(sys.argv[2]) period=int(sys.argv[2]) tr_ref_seqIx=int(sys.argv[3])-1 ##output=(sys.argv[4]) ##fout=open(output,'w') for line in lines: temp=line.strip().split('\t') temp=filter(None,temp) #motif=temp[motifIx] tr_ref_seq=temp[tr_ref_seqIx] ##period=len(motif) cand_motif=tr_ref_seq[:period] len_microsat=len(tr_ref_seq) expand_microsat_cand=cand_motif*(len_microsat/period) + cand_motif[:(len_microsat%period)] if tr_ref_seq == expand_microsat_cand: print line.strip() ##print line.strip() >> fout