diff seg2matrix/segToMatrixGalaxy.py @ 31:ab20c0d04f4a

add seg2matrix tool

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seg2matrix/segToMatrixGalaxy.py	Fri Jul 24 13:10:11 2015 -0700
@@ -0,0 +1,61 @@
+#!/usr/bin/env python
+
+import sys,os
+import CGData.GenomicSegment
+import CGData.SegToMatrix
+import CGData.RefGene
+import CGData.GeneMap
+
+class matrix_write:    
+    def __init__(self, handle):
+        self.buff = ""
+        self.handle = handle
+        self.probes = []
+    def write(self, s):
+        self.buff += s        
+        if s.endswith("\n"):
+            tmp = self.buff.split("\t")
+            if tmp[0] != "probe":
+                tmp2 = tmp[0].split("_")
+                p = probeseg(tmp[0], tmp2[0], int(tmp2[1]), int(tmp2[2]))
+                self.probes.append(p)
+                
+            self.handle.write(self.buff)
+            self.buff = ""
+
+class probeseg:
+    def __init__(self, name, chrom, chrom_start, chrom_end):
+        self.name = name
+        self.chrom = chrom
+        self.chrom_start = chrom_start
+        self.chrom_end = chrom_end
+        self.strand = "."
+
+
+if __name__ == "__main__":
+    if len(sys.argv[:])!= 5:
+        print "python segToMatrixGalaxy.py inputSegmentFile refGeneFile outputMatrix outputProbeMap\n"
+        sys.exit()
+    seg = CGData.GenomicSegment.GenomicSegment()
+    seg.load(sys.argv[1])
+    
+    refgene = CGData.RefGene.RefGene()
+    refgene.load(os.path.dirname(sys.argv[0])+"/"+sys.argv[2])
+    
+    handle = open(sys.argv[3], "w")
+    m = matrix_write(handle)    
+    CGData.SegToMatrix.seg_to_matrix(seg, m)
+    handle.close()
+    
+    handle = open(sys.argv[4], "w")
+    probeMapper = CGData.GeneMap.ProbeMapper('b')
+    handle.write("%s\t%s\t%s\t%s\t%s\t%s\n" % ("#id", "gene","chrom","chromStart","chromEnd","strand"))
+    for probe in m.probes:
+        hits = []
+        for hit in probeMapper.find_overlap( probe, refgene ):
+            if hit.name not in hits:
+                hits.append(hit.name)
+        handle.write("%s\t%s\t%s\t%s\t%s\t.\n" % (probe.name, ",".join(hits), probe.chrom, probe.chrom_start, probe.chrom_end))
+    handle.close()
+    
+