diff seg2matrix/segToMatrixGalaxy.py @ 60:bf57076e27b9 default tip

change genomicSegment input data

--- a/seg2matrix/segToMatrixGalaxy.py	Tue Sep 22 15:41:03 2015 -0700
+++ b/seg2matrix/segToMatrixGalaxy.py	Tue Oct 27 16:07:09 2015 -0700
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-import sys,os
+import sys,os, string
 import CGData.GenomicSegment
 import CGData.SegToMatrix
 import CGData.RefGene
@@ -15,7 +15,7 @@
         self.buff += s        
         if s.endswith("\n"):
             tmp = self.buff.split("\t")
-            if tmp[0] != "probe":
+            if string.strip(tmp[0]) !=  "probe":
                 tmp2 = tmp[0].split("_")
                 p = probeseg(tmp[0], tmp2[0], int(tmp2[1]), int(tmp2[2]))
                 self.probes.append(p)
@@ -31,14 +31,13 @@
         self.chrom_end = chrom_end
         self.strand = "."
 
-
 if __name__ == "__main__":
     if len(sys.argv[:])!= 6:
         print "python segToMatrixGalaxy.py inputSegmentFile refGeneFile outputMatrix outputProbeMap NORMAL_CNV\n"
         sys.exit()
     seg = CGData.GenomicSegment.GenomicSegment()
     seg.load(sys.argv[1])
-    
+
     refgene = CGData.RefGene.RefGene()
     refgene.load(os.path.dirname(sys.argv[0])+"/"+os.path.basename(sys.argv[2]))