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1 #!/usr/bin/env python
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2 # -*- coding: utf-8 -*-
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3 import sys
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4 from Bio import SeqIO
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5 import math
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6 from parse_dis_react import *
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7
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8 def cap(a,value):
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9 if a>=value:
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10 return value
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11 else:
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12 return a
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13
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14 def react_norm(react_file, result_file, capped_value):
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15 print("Normalizing.....")
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16 react1 = parse_dist(react_file)
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17 react = react1[1]
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18 h = file(result_file, 'w')
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19
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20 capped = int(capped_value)
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21
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22 all_react = []
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23
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24
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25 for t in react:
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26 if react[t]!='null':
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27 for i in range(len(react[t])):
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28 if react[t][i]!='NA':
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29 all_react.append(float(react[t][i]))
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30 # except:
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31 # print(react[t][i])
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32 # print(t)
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33 # print(i)
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34
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35 all_react.sort(reverse = True)
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36 #print((all_react))
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37 #print(all_react[int(len(all_react)*0.02)])
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38 #print(all_react[int(len(all_react)*0.03)])
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39 #print(all_react[int(len(all_react)*0.025)])
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40 #print(all_react[int(len(all_react)*0.04)])
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41 #print(all_react[int(len(all_react)*0.05)])
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42 '''
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43 mean = sum(all_react)/len(all_react)
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44 print(mean)
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45 temp = 0
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46
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47 for i in range(len(all_react)):
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48 temp = temp+all_react[i]*all_react[i]
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49 temp = temp/len(all_react)
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50 sd = math.sqrt(temp-mean*mean)
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51 '''
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52 eight = all_react[int(len(all_react)*0.02):int(len(all_react)*0.1)]
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53 meight = sum(eight)/len(eight)
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54
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55 for t in react:
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56 h.write(t)
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57 h.write('\n')
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58 if react[t]!='null':
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59 if (t.find('AT1G29930')==-1) and (t.find('At1g29930')==-1):
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60 for i in range((len(react[t])-1)):
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61 if react[t][i]!='NA':
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62 h.write(str(cap((float(react[t][i])/meight),capped)))
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63 else:
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64 h.write('NA')
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65 h.write('\t')
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66 if react[t][i+1]!='NA':
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67 h.write(str(cap((float(react[t][i+1])/meight),capped)))
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68 else:
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69 h.write('NA')
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70 h.write('\n')
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71 else:
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72 for i in range((len(react[t])-1)):
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73 if react[t][i]!='NA':
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74 h.write(str(float(react[t][i])*2.6))
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75 else:
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76 h.write('NA')
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77 h.write('\t')
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78 if react[t][i+1]!='NA':
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79 h.write(str(float(react[t][i])*2.6))
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80 else:
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81 h.write('NA')
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82 h.write('\n')
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83
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84
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85
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86 h.close()
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