--- a/endbias.py	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
-'''
-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())
-'''