Mercurial > repos > arkarachai-fungtammasan > str_fm
comparison microsatpurity.py @ 0:07588b899c13 draft
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| author | arkarachai-fungtammasan |
|---|---|
| date | Wed, 01 Apr 2015 17:05:51 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:07588b899c13 |
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| 1 import sys | |
| 2 # remove all read that have impure microsat | |
| 3 # check only one line at a time | |
| 4 | |
| 5 | |
| 6 fd=open(sys.argv[1]) | |
| 7 lines=fd.xreadlines() | |
| 8 ##motifIx=int(sys.argv[2]) | |
| 9 period=int(sys.argv[2]) | |
| 10 tr_ref_seqIx=int(sys.argv[3])-1 | |
| 11 ##output=(sys.argv[4]) | |
| 12 ##fout=open(output,'w') | |
| 13 for line in lines: | |
| 14 temp=line.strip().split('\t') | |
| 15 temp=filter(None,temp) | |
| 16 #motif=temp[motifIx] | |
| 17 tr_ref_seq=temp[tr_ref_seqIx] | |
| 18 ##period=len(motif) | |
| 19 cand_motif=tr_ref_seq[:period] | |
| 20 len_microsat=len(tr_ref_seq) | |
| 21 expand_microsat_cand=cand_motif*(len_microsat/period) + cand_motif[:(len_microsat%period)] | |
| 22 if tr_ref_seq == expand_microsat_cand: | |
| 23 print line.strip() | |
| 24 ##print line.strip() >> fout |