--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/poisson2test.py	Mon Jan 27 09:26:06 2014 -0500
@@ -0,0 +1,124 @@
+#!/usr/local/bin/python
+
+import sys
+from math import *
+from rpy import *
+
+
+if ((len(sys.argv)-1) != 6):
+    print 'too few parameters' 
+    print 'usage: inputfile, col1, col2, d-value(not 0), p-val correction method(0 or 1)'
+    sys.exit()
+    
+try:
+    lines_arr = open(sys.argv[1]).readlines()
+except IOError:
+    print'cannot open',sys.argv[1]
+    sys.exit()  
+ 
+try:
+    i = int(sys.argv[2]) #first column to compare
+    j = int(sys.argv[3]) #second colum to compare
+    d = float(sys.argv[4]) #correction factor
+    k = int(sys.argv[5]) #p-val correction method
+    outfile = open(sys.argv[6],'w') # output data
+    
+    if (i>j):
+        print 'column order not correct col1 < col2'
+        print 'usage: inputfile, col1, col2, d-value, p-val correction method'
+        sys.exit()      
+        
+    try:
+        a = 1 / d
+        assert k in [0,1]
+    except ZeroDivisionError:
+        print 'd cannot be 0'
+        print 'usage: inputfile, col1, col2, d-value, p-val correction method'
+        sys.exit()
+    except:
+        print ' p-val correction should be 0 or 1 (0 = "bonferroni", 1 = "fdr")'
+        print 'usage: inputfile, col1, col2, d-value, p-val correction method'
+        sys.exit()
+except ValueError:
+    print 'parameters are not integers'
+    print 'usage: inputfile, col1, col2, d-value, p-val correction method'
+    sys.exit()
+   
+
+fsize = len(lines_arr)
+
+z1 = []
+z2 = []
+pz1 = []
+pz2 = []
+field = []
+
+if d<1: # Z score calculation
+    for line in lines_arr:
+        line.strip()
+        field = line.split('\t')
+        
+        x = int(field[j-1]) #input column 2
+        y = int(field[i-1]) #input column 1
+        if y>x:
+            z1.append(float((y - ((1/d)*x))/sqrt((1/d)*(x + y))))
+            z2.append(float((2*(sqrt(y+(3/8))-sqrt((1/d)*(x+(3/8)))))/sqrt(1+(1/d))))
+        else:
+            tmp_var1 = x
+            x = y
+            y = tmp_var1
+            z1.append(float((y - (d*x))/sqrt(d*(x + y))))
+            z2.append(float((2*(sqrt(y+(3/8))-sqrt(d*(x+(3/8)))))/sqrt(1+d)))
+            
+else: #d>1 Z score calculation
+    for line in lines_arr:
+        line.strip()
+        field = line.split('\t')
+        x = int(field[i-1]) #input column 1
+        y = int(field[j-1]) #input column 2
+        
+        if y>x:
+            z1.append(float((y - (d*x))/sqrt(d*(x + y))))
+            z2.append(float((2*(sqrt(y+(3/8))-sqrt(d*(x+(3/8)))))/sqrt(1+d)))
+        else:
+            tmp_var2 = x
+            x = y
+            y = tmp_var2
+            z1.append(float((y - ((1/d)*x))/sqrt((1/d)*(x + y))))
+            z2.append(float((2*(sqrt(y+(3/8))-sqrt((1/d)*(x+(3/8)))))/sqrt(1+(1/d))))
+        
+  
+   
+
+
+# P-value caluculation for z1 and z2
+for p in z1:
+    
+    pz1.append(float(r.pnorm(-abs(float(p)))))
+
+for q in z2:
+    
+    pz2.append(float(r.pnorm(-abs(float(q)))))    
+
+# P-value correction for pz1 and pz2
+
+if k == 0:
+    corrz1 = r.p_adjust(pz1,"bonferroni",fsize)
+    corrz2 = r.p_adjust(pz2,"bonferroni",fsize)
+  
+   
+else:
+  
+    corrz1 = r.p_adjust(pz1,"fdr",fsize)
+    corrz2 = r.p_adjust(pz2,"fdr",fsize)
+    
+
+#printing all columns
+for n in range(fsize):
+    print >> outfile, "%s\t%4.3f\t%4.3f\t%8.6f\t%8.6f\t%8.6f\t%8.6f" %(lines_arr[n].strip(),z1[n],z2[n],pz1[n],pz2[n],corrz1[n],corrz2[n])
+
+
+      
+      
+      
+