Mercurial > repos > melissacline > ucsc_cancer_utilities

diff 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
line wrap: on
line diff
--- a/seg2matrix/mapSegToGeneMatrix.py	Tue Sep 22 15:41:03 2015 -0700
+++ b/seg2matrix/mapSegToGeneMatrix.py	Tue Oct 27 16:07:09 2015 -0700
@@ -48,11 +48,11 @@
         if line[0]=="#":
             continue
         tmp = string.split(line,"\t")
-        if len(tmp)!= 6:
+        if len(tmp)!= 5:
             continue
-        seg = segToProbeMap.probeseg("", tmp[1], int(tmp[2]), int(tmp[3]),tmp[4])
+        seg = segToProbeMap.probeseg("", tmp[1], int(tmp[2]), int(tmp[3]),".")
         sample = tmp[0]
-        value = float(tmp[5])
+        value = float(tmp[4])
         if sample not in samples:
             samples[sample]=len(samples)
             matrix.append(copy.deepcopy(oneSample))