diff reactivity_cal/react_norm_function.py @ 73:1c325ff557d9 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/react_norm_function.py	Tue Dec 09 03:03:11 2014 -0500
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+import sys
+from Bio import SeqIO
+import math
+from parse_dis_react import *
+
+def cap(a,value):
+    if a>=value:
+        return value
+    else:
+        return a
+
+def react_norm(react_file, result_file, capped_value):
+    print("Normalizing.....")
+    react1 = parse_dist(react_file)
+    react = react1[1]
+    h = file(result_file, 'w')
+
+    capped = int(capped_value)
+
+    all_react = []
+
+
+    for t in react:
+        if react[t]!='null':
+            for i in range(len(react[t])):
+                if react[t][i]!='NA':                   
+                    all_react.append(float(react[t][i]))
+
+
+    all_react.sort(reverse = True)
+
+
+    eight = all_react[int(len(all_react)*0.02):int(len(all_react)*0.1)]
+    meight = sum(eight)/len(eight)
+
+    for t in react:
+        h.write(t)
+        h.write('\n')
+        if react[t]!='null':
+            for i in range((len(react[t])-1)):
+                if react[t][i]!='NA':
+                    h.write(str(cap((float(react[t][i])/meight),capped)))
+                else:
+                    h.write('NA')
+                h.write('\t')
+            if react[t][i+1]!='NA':
+                h.write(str(cap((float(react[t][i+1])/meight),capped)))
+            else:
+                h.write('NA')
+            h.write('\n')
+
+    h.close()
+        
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