Mercurial > repos > melissacline > ucsc_cancer_utilities

comparison seg2matrix/mapSegToGeneMatrix.py @ 60:bf57076e27b9 default tip

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change genomicSegment input data
author jingchunzhu@gmail.com
date Tue, 27 Oct 2015 16:07:09 -0700
parents 59dbe857f5d4
children
comparison
equal deleted inserted replaced
59:b88b95642f59 60:bf57076e27b9
46 if line == "": # empty line 46 if line == "": # empty line
47 continue 47 continue
48 if line[0]=="#": 48 if line[0]=="#":
49 continue 49 continue
50 tmp = string.split(line,"\t") 50 tmp = string.split(line,"\t")
51 if len(tmp)!= 6: 51 if len(tmp)!= 5:
52 continue 52 continue
53 seg = segToProbeMap.probeseg("", tmp[1], int(tmp[2]), int(tmp[3]),tmp[4]) 53 seg = segToProbeMap.probeseg("", tmp[1], int(tmp[2]), int(tmp[3]),".")
54 sample = tmp[0] 54 sample = tmp[0]
55 value = float(tmp[5]) 55 value = float(tmp[4])
56 if sample not in samples: 56 if sample not in samples:
57 samples[sample]=len(samples) 57 samples[sample]=len(samples)
58 matrix.append(copy.deepcopy(oneSample)) 58 matrix.append(copy.deepcopy(oneSample))
59 59
60 hits={} 60 hits={}