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comparison poisson2test.py @ 0:efb54966e923 draft

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Imported from capsule None
author devteam
date Thu, 23 Jan 2014 12:31:05 -0500
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-1:000000000000 0:efb54966e923
1 #!/usr/local/bin/python
2
3 import sys
4 from math import *
5 from rpy import *
6
7
8 if ((len(sys.argv)-1) != 6):
9 print 'too few parameters'
10 print 'usage: inputfile, col1, col2, d-value(not 0), p-val correction method(0 or 1)'
11 sys.exit()
12
13 try:
14 lines_arr = open(sys.argv[1]).readlines()
15 except IOError:
16 print'cannot open',sys.argv[1]
17 sys.exit()
18
19 try:
20 i = int(sys.argv[2]) #first column to compare
21 j = int(sys.argv[3]) #second colum to compare
22 d = float(sys.argv[4]) #correction factor
23 k = int(sys.argv[5]) #p-val correction method
24 outfile = open(sys.argv[6],'w') # output data
25
26 if (i>j):
27 print 'column order not correct col1 < col2'
28 print 'usage: inputfile, col1, col2, d-value, p-val correction method'
29 sys.exit()
30
31 try:
32 a = 1 / d
33 assert k in [0,1]
34 except ZeroDivisionError:
35 print 'd cannot be 0'
36 print 'usage: inputfile, col1, col2, d-value, p-val correction method'
37 sys.exit()
38 except:
39 print ' p-val correction should be 0 or 1 (0 = "bonferroni", 1 = "fdr")'
40 print 'usage: inputfile, col1, col2, d-value, p-val correction method'
41 sys.exit()
42 except ValueError:
43 print 'parameters are not integers'
44 print 'usage: inputfile, col1, col2, d-value, p-val correction method'
45 sys.exit()
46
47
48 fsize = len(lines_arr)
49
50 z1 = []
51 z2 = []
52 pz1 = []
53 pz2 = []
54 field = []
55
56 if d<1: # Z score calculation
57 for line in lines_arr:
58 line.strip()
59 field = line.split('\t')
60
61 x = int(field[j-1]) #input column 2
62 y = int(field[i-1]) #input column 1
63 if y>x:
64 z1.append(float((y - ((1/d)*x))/sqrt((1/d)*(x + y))))
65 z2.append(float((2*(sqrt(y+(3/8))-sqrt((1/d)*(x+(3/8)))))/sqrt(1+(1/d))))
66 else:
67 tmp_var1 = x
68 x = y
69 y = tmp_var1
70 z1.append(float((y - (d*x))/sqrt(d*(x + y))))
71 z2.append(float((2*(sqrt(y+(3/8))-sqrt(d*(x+(3/8)))))/sqrt(1+d)))
72
73 else: #d>1 Z score calculation
74 for line in lines_arr:
75 line.strip()
76 field = line.split('\t')
77 x = int(field[i-1]) #input column 1
78 y = int(field[j-1]) #input column 2
79
80 if y>x:
81 z1.append(float((y - (d*x))/sqrt(d*(x + y))))
82 z2.append(float((2*(sqrt(y+(3/8))-sqrt(d*(x+(3/8)))))/sqrt(1+d)))
83 else:
84 tmp_var2 = x
85 x = y
86 y = tmp_var2
87 z1.append(float((y - ((1/d)*x))/sqrt((1/d)*(x + y))))
88 z2.append(float((2*(sqrt(y+(3/8))-sqrt((1/d)*(x+(3/8)))))/sqrt(1+(1/d))))
89
90
91
92
93
94 # P-value caluculation for z1 and z2
95 for p in z1:
96
97 pz1.append(float(r.pnorm(-abs(float(p)))))
98
99 for q in z2:
100
101 pz2.append(float(r.pnorm(-abs(float(q)))))
102
103 # P-value correction for pz1 and pz2
104
105 if k == 0:
106 corrz1 = r.p_adjust(pz1,"bonferroni",fsize)
107 corrz2 = r.p_adjust(pz2,"bonferroni",fsize)
108
109
110 else:
111
112 corrz1 = r.p_adjust(pz1,"fdr",fsize)
113 corrz2 = r.p_adjust(pz2,"fdr",fsize)
114
115
116 #printing all columns
117 for n in range(fsize):
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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