diff reactivity_cal/react_norm_function.py @ 5:7a8ddf1819b1 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reactivity_cal/react_norm_function.py	Mon Sep 15 14:52:52 2014 -0400
@@ -0,0 +1,114 @@
+#!/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]))
+#                    except:
+#                        print(react[t][i])
+#                        print(t)
+#                        print(i)
+
+    all_react.sort(reverse = True)
+    #print((all_react))
+    #print(all_react[int(len(all_react)*0.02)])
+    #print(all_react[int(len(all_react)*0.03)])
+    #print(all_react[int(len(all_react)*0.025)])
+    #print(all_react[int(len(all_react)*0.04)])
+    #print(all_react[int(len(all_react)*0.05)])
+    '''
+    mean = sum(all_react)/len(all_react)
+    print(mean)
+    temp = 0
+
+    for i in range(len(all_react)):
+        temp = temp+all_react[i]*all_react[i]
+    temp = temp/len(all_react)
+    sd = math.sqrt(temp-mean*mean)
+    '''
+    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':
+            if (t.find('AT1G29930')==-1) and (t.find('At1g29930')==-1):
+                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')
+            else:
+                for i in range((len(react[t])-1)):
+                    if react[t][i]!='NA':
+                        h.write(str(float(react[t][i])*2.6))
+                    else:
+                        h.write('NA')
+                    h.write('\t')
+                if react[t][i+1]!='NA':
+                    h.write(str(float(react[t][i])*2.6))
+                else:
+                    h.write('NA')
+                h.write('\n')
+                
+                
+
+    h.close()
+        
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