[2] | 1 | #!/usr/local/bin/python |
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| 2 | |
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| 3 | import sys |
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| 4 | from math import * |
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| 5 | from rpy import * |
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| 6 | |
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| 7 | |
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| 8 | if ((len(sys.argv)-1) != 6): |
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| 9 | print 'too few parameters' |
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| 10 | print 'usage: inputfile, col1, col2, d-value(not 0), p-val correction method(0 or 1)' |
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| 11 | sys.exit() |
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| 12 | |
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| 13 | try: |
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| 14 | lines_arr = open(sys.argv[1]).readlines() |
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| 15 | except IOError: |
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| 16 | print'cannot open',sys.argv[1] |
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| 17 | sys.exit() |
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| 18 | |
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| 19 | try: |
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| 20 | i = int(sys.argv[2]) #first column to compare |
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| 21 | j = int(sys.argv[3]) #second colum to compare |
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| 22 | d = float(sys.argv[4]) #correction factor |
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| 23 | k = int(sys.argv[5]) #p-val correction method |
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| 24 | outfile = open(sys.argv[6],'w') # output data |
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| 25 | |
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| 26 | if (i>j): |
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| 27 | print 'column order not correct col1 < col2' |
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| 28 | print 'usage: inputfile, col1, col2, d-value, p-val correction method' |
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| 29 | sys.exit() |
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| 30 | |
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| 31 | try: |
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| 32 | a = 1 / d |
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| 33 | assert k in [0,1] |
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| 34 | except ZeroDivisionError: |
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| 35 | print 'd cannot be 0' |
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| 36 | print 'usage: inputfile, col1, col2, d-value, p-val correction method' |
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| 37 | sys.exit() |
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| 38 | except: |
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| 39 | print ' p-val correction should be 0 or 1 (0 = "bonferroni", 1 = "fdr")' |
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| 40 | print 'usage: inputfile, col1, col2, d-value, p-val correction method' |
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| 41 | sys.exit() |
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| 42 | except ValueError: |
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| 43 | print 'parameters are not integers' |
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| 44 | print 'usage: inputfile, col1, col2, d-value, p-val correction method' |
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| 45 | sys.exit() |
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| 46 | |
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| 47 | |
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| 48 | fsize = len(lines_arr) |
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| 49 | |
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| 50 | z1 = [] |
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| 51 | z2 = [] |
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| 52 | pz1 = [] |
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| 53 | pz2 = [] |
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| 54 | field = [] |
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| 55 | |
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| 56 | if d<1: # Z score calculation |
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| 57 | for line in lines_arr: |
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| 58 | line.strip() |
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| 59 | field = line.split('\t') |
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| 60 | |
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| 61 | x = int(field[j-1]) #input column 2 |
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| 62 | y = int(field[i-1]) #input column 1 |
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| 63 | if y>x: |
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| 64 | z1.append(float((y - ((1/d)*x))/sqrt((1/d)*(x + y)))) |
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| 65 | z2.append(float((2*(sqrt(y+(3/8))-sqrt((1/d)*(x+(3/8)))))/sqrt(1+(1/d)))) |
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| 66 | else: |
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| 67 | tmp_var1 = x |
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| 68 | x = y |
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| 69 | y = tmp_var1 |
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| 70 | z1.append(float((y - (d*x))/sqrt(d*(x + y)))) |
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| 71 | z2.append(float((2*(sqrt(y+(3/8))-sqrt(d*(x+(3/8)))))/sqrt(1+d))) |
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| 72 | |
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| 73 | else: #d>1 Z score calculation |
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| 74 | for line in lines_arr: |
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| 75 | line.strip() |
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| 76 | field = line.split('\t') |
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| 77 | x = int(field[i-1]) #input column 1 |
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| 78 | y = int(field[j-1]) #input column 2 |
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| 79 | |
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| 80 | if y>x: |
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| 81 | z1.append(float((y - (d*x))/sqrt(d*(x + y)))) |
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| 82 | z2.append(float((2*(sqrt(y+(3/8))-sqrt(d*(x+(3/8)))))/sqrt(1+d))) |
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| 83 | else: |
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| 84 | tmp_var2 = x |
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| 85 | x = y |
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| 86 | y = tmp_var2 |
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| 87 | z1.append(float((y - ((1/d)*x))/sqrt((1/d)*(x + y)))) |
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| 88 | z2.append(float((2*(sqrt(y+(3/8))-sqrt((1/d)*(x+(3/8)))))/sqrt(1+(1/d)))) |
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| 89 | |
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| 90 | |
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| 91 | |
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| 92 | |
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| 93 | |
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| 94 | # P-value caluculation for z1 and z2 |
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| 95 | for p in z1: |
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| 96 | |
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| 97 | pz1.append(float(r.pnorm(-abs(float(p))))) |
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| 98 | |
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| 99 | for q in z2: |
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| 100 | |
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| 101 | pz2.append(float(r.pnorm(-abs(float(q))))) |
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| 102 | |
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| 103 | # P-value correction for pz1 and pz2 |
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| 104 | |
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| 105 | if k == 0: |
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| 106 | corrz1 = r.p_adjust(pz1,"bonferroni",fsize) |
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| 107 | corrz2 = r.p_adjust(pz2,"bonferroni",fsize) |
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| 108 | |
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| 109 | |
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| 110 | else: |
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| 111 | |
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| 112 | corrz1 = r.p_adjust(pz1,"fdr",fsize) |
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| 113 | corrz2 = r.p_adjust(pz2,"fdr",fsize) |
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| 114 | |
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| 115 | |
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| 116 | #printing all columns |
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| 117 | for n in range(fsize): |
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| 118 | 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]) |
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| 119 | |
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| 120 | |
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| 122 | |
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| 123 | |
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| 124 | |
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