diff seg2matrix/segToProbeMap.py @ 39:61f03b481b0d

new tool

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seg2matrix/segToProbeMap.py	Fri Jul 31 20:38:27 2015 -0700
@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+
+import sys,string
+sys.path.insert(0,"../CGDataNew")
+
+import CGData.GenomicSegment
+import CGData.SegToMatrix
+import CGData.RefGene
+import CGData.GeneMap
+import optparse
+
+class segs:
+    def __init__(self):
+        self.probes = []
+
+    def load (self, handle): #handle bed6
+        fin =open(handle,'r')
+        while 1:
+            line =string.strip(fin.readline())
+            if line =="":
+                break
+            if line[0]=="#":
+                continue
+            tmp = string.split(line,"\t")
+            if len(tmp)== 5:
+                p = probeseg(tmp[0], tmp[1], int(tmp[3]), int(tmp[4]),tmp[2])
+                self.probes.append(p)
+        fin.close()
+
+
+class probeseg:
+    def __init__(self, name, chrom, chrom_start, chrom_end, strand):
+        self.name = name
+        self.chrom = chrom
+        self.chrom_start = chrom_start
+        self.chrom_end = chrom_end
+        self.strand = strand
+
+
+if __name__ == "__main__":
+    def printUsage():
+        print "python segToProbeMap.py segInput(name,chr,strand,start,end) refGene(eg hg18) probeMapOut --mode=cnv|exp\n"
+
+    if len(sys.argv) != 5:
+        printUsage()
+        sys.exit()
+
+    parser = optparse.OptionParser()
+    parser.add_option("--mode", action="store", type="string", dest="mode")
+    (options, args) = parser.parse_args()
+
+    if (not options.mode) or (options.mode not in ["cnv","exp"]):
+        printUsage()
+        sys.exit()
+
+    probes=segs()
+    probes.load(sys.argv[1])
+
+    refgene = CGData.RefGene.RefGene()
+    refgene.load(sys.argv[2])
+
+    handle = open(sys.argv[3], "w")
+    if options.mode=="cnv":
+        probeMapper = CGData.GeneMap.ProbeMapper('b')
+    if options.mode=="exp":
+        probeMapper = CGData.GeneMap.ProbeMapper('g')
+
+    handle.write("%s\t%s\t%s\t%s\t%s\t%s\n" % ("#id", "gene","chrom","chromStart","chromEnd","strand"))
+    for probe in probes.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%s\n" % (probe.name, ",".join(hits), probe.chrom, probe.chrom_start, probe.chrom_end, probe.strand))
+    handle.close()
+
+