Mercurial > repos > arkarachai-fungtammasan > microsatellite_ngs

comparison test-data/combinedprobforallelecombination.py @ 4:ecfc9041bcc5

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author arkarachai-fungtammasan
date Wed, 01 Apr 2015 14:05:54 -0400
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3:7cc220e8c2ac 4:ecfc9041bcc5
1 import sys
2 import collections
3 import math
4 SAMPLINGCOL=11
5 ALLELE1COL=7
6 ALLELE2COL=8
7 SIGNCOL=4
8 readprofileCOL=2
9 motifCOL=3
10 filaname=sys.argv[1]
11 fd=open(filaname)
12 lines=fd.readlines()
13 binomialcombine=collections.defaultdict(list)
14 for line in lines:
15 temp=line.strip().split('\t')
16 allelelist=[]
17 allelelist.append(int(temp[ALLELE1COL-1]))
18 allelelist.append(int(temp[ALLELE2COL-1]))
19 allelelist.sort()
20 #allelelist=map(str,allelelist)
21 alleleave=str(allelelist[0])+'_'+str(allelelist[1])
22 #alleleave=str(sum(allelelist)/2.0)
23 ##alleleave=str(allelelist[0])+'_'+str(allelelist[1])
24 totalcov=len(temp[readprofileCOL-1].split(','))
25 motif=temp[motifCOL-1]
26 samplingvalue=float(temp[SAMPLINGCOL-1])
27 SIGN=1
28 binomialcombine[(totalcov,alleleave,motif)].append(SIGN*samplingvalue)
29 allkeys= binomialcombine.keys()
30 allkeys.sort()
31 ##print allkeys
32 print 'read_depth'+'\t'+'allele'+'\t'+'heterozygous_prob'+'\t'+'motif'
33 for key in allkeys:
34 ##templist=[str(key[0]),key[1],str(sum(binomialcombine[key])),key[2],str(map(str,(binomialcombine[key])))]
35 templist=[str(key[0]),key[1],str(sum(binomialcombine[key])),key[2]]
36
37 print '\t'.join(templist)
38 #print allkeys#,binomialcombine
39
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