--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/endbias.py	Sat Mar 10 07:59:27 2012 -0500
@@ -0,0 +1,52 @@
+'''
+usage:
+
+python endbias.py utr5-coverage utr3-coverage outputfile
+'''
+import sys,math
+
+def getCoverage(filename):
+    f = open(filename)
+    coverage = {}
+    for line in f:
+        flds = line.strip().split('\t')
+        score = float(flds[4])
+        name = (flds[0].split('utr'))[0].strip('_')
+        if coverage.has_key(name):
+            if score > coverage[name]:
+                coverage[name] = score
+        else:
+            coverage[name] = score
+    return coverage
+
+def endBias(filename,utr5,utr3):
+    out = open(filename,'w')
+    for txpt in utr5.keys():
+        if utr3.has_key(txpt):
+            out.write('\t'.join([txpt,str(utr5[txpt]),str(utr3[txpt]),str(math.log((1+utr5[txpt])/(1+utr3[txpt]),2))])+'\n')
+    out.close()
+   
+   
+utr5 = getCoverage(sys.argv[1])
+utr3 = getCoverage(sys.argv[2])
+endBias(sys.argv[3],utr5,utr3)
+            
+'''
+
+utr5 = getCoverage('hmga2-utr5.coverage')
+utr3 = getCoverage('hmga2-utr3.coverage')
+logratio, cov5,cov3= endBias(utr5,utr3)
+2**pylab.median(logratio.values())
+
+log2utr5 = pylab.log2(pylab.array(cov5)+1)
+log2utr3 = pylab.log2(pylab.array(cov3)+1)
+  
+pylab.plot(log2utr5,log2utr3,'bo')   
+
+pylab.show()               
+
+utr5 = getCoverage('control-utr5.coverage')
+utr3 = getCoverage('control-utr3.coverage')
+logratio, cov5,cov3= endBias(utr5,utr3)
+2**pylab.median(logratio.values())
+'''