Mercurial > repos > tyty > structurefold
comparison upload/reactivity_cal/react_cal.py @ 34:d74ed492efdd draft
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author | tyty |
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date | Mon, 20 Oct 2014 14:55:16 -0400 |
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33:1a92d934f8d1 | 34:d74ed492efdd |
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1 #!/usr/bin/env python | |
2 # -*- coding: utf-8 -*- | |
3 import sys | |
4 from Bio import SeqIO | |
5 import math | |
6 from parse_dis_react import * | |
7 from react_norm_function import * | |
8 import os | |
9 | |
10 | |
11 dist_file1 = sys.argv[1] #plus library | |
12 dist_file2 = sys.argv[2] #minus library | |
13 seq_file = sys.argv[3] #Reference library(genome/cDNA) | |
14 nt_spec = sys.argv[4] #only show reactivity for AC or ATCG | |
15 flag_in = sys.argv[5] # perform 2-8% normalization (1) or not (0) | |
16 threshold = sys.argv[6] #Threshold to cap the reactivities | |
17 output_file = sys.argv[7] | |
18 | |
19 | |
20 distri_p = parse_dist(dist_file1) | |
21 distri_m = parse_dist(dist_file2) | |
22 threshold = float(threshold) | |
23 | |
24 | |
25 ospath = os.path.realpath(sys.argv[0]) | |
26 ost = ospath.split('/') | |
27 syspath = "" | |
28 for i in range(len(ost)-1): | |
29 syspath = syspath+ost[i].strip() | |
30 syspath = syspath+'/' | |
31 | |
32 h = file(syspath+"react.txt",'w') | |
33 flag_in = int(flag_in) | |
34 | |
35 seqs = SeqIO.parse(open(seq_file),'fasta'); | |
36 nt_s = set() | |
37 for i in range(len(nt_spec)): | |
38 nt_s.add(nt_spec[i]) | |
39 | |
40 flag = 0 | |
41 trans = [] | |
42 distri_p = distri_p[1] | |
43 distri_m = distri_m[1] | |
44 | |
45 #thres = int(threshold) | |
46 | |
47 | |
48 transcripts = {} | |
49 for seq in seqs: | |
50 n = seq.id | |
51 trans.append(n) | |
52 transcripts[n] = seq.seq.tostring() | |
53 | |
54 | |
55 #print(distri_p) | |
56 | |
57 | |
58 for i in range(0, len(trans)): | |
59 h.write(trans[i]) | |
60 h.write('\n') | |
61 for j in range(len(distri_p[trans[i]])): | |
62 distri_p[trans[i]][j] = math.log((int(distri_p[trans[i]][j])+1),math.e) | |
63 for j in range(len(distri_m[trans[i]])): | |
64 distri_m[trans[i]][j] = math.log((int(distri_m[trans[i]][j])+1),math.e) | |
65 s_p = sum(distri_p[trans[i]]) | |
66 s_m = sum(distri_m[trans[i]]) | |
67 length = len(distri_p[trans[i]]) | |
68 if s_p!= 0 and s_m!= 0: | |
69 r = [] | |
70 for j in range(0, len(distri_p[trans[i]])): | |
71 f_p = (float(distri_p[trans[i]][j]))/float(s_p)*length | |
72 f_m = (float(distri_m[trans[i]][j]))/float(s_m)*length | |
73 raw_react = f_p-f_m | |
74 r.append(max(0, raw_react)) | |
75 | |
76 if s_p!= 0 and s_m!= 0: | |
77 for k in range(1,(len(r)-1)): | |
78 if transcripts[trans[i]][k-1] in nt_s: | |
79 h.write(str(r[k])) | |
80 h.write('\t') | |
81 else: | |
82 h.write('NA') | |
83 h.write('\t') | |
84 k = k+1 | |
85 if transcripts[trans[i]][k-1] in nt_s: | |
86 h.write(str(r[k])) | |
87 h.write('\n') | |
88 else: | |
89 h.write('NA') | |
90 h.write('\n') | |
91 | |
92 | |
93 h.close() | |
94 | |
95 if flag_in: | |
96 react_norm((syspath+"react.txt"),output_file, threshold) | |
97 else: | |
98 h_o = file(output_file, 'w') | |
99 f_i = open(syspath+"react.txt") | |
100 for aline in f_i.readlines(): | |
101 h_o.write(aline.strip()) | |
102 h_o.write('\n') | |
103 os.system("rm -f "+syspath+"react.txt") | |
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