1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
|
#!/usr/bin/python3
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
############################################################################
#add some contamination for meta-genomic simulation
import sys
import os
import random
import sets
def read_contigs(filename):
res_seq = {}
seq =''
cont_name = ''
for line in open(filename):
if line[0] == '>':
if cont_name != '':
res_seq[cont_name] = seq
seq = ''
cont_name = line[1:33].strip()
else:
seq += line.strip()
if cont_name != '':
res_seq[cont_name] = seq
return res_seq
def write_fasta(data, filename):
outFile = open(filename, 'w')
for seq in data:
outFile.write('>' + seq[0].strip() + '\n' );
i = 0
while i < len(seq[1]):
outFile.write(seq[1][i:i+60] + '\n')
i += 60
outFile.close()
if len(sys.argv) < 1 :
print("Usage: " + sys.argv[0] + " <first_snps_file> <second_snps_file>")
sys.exit()
infile = open(sys.argv[1],'r');
outfile = open(sys.argv[1]+"_processed",'w');
first = 1
for line in infile:
arr = (line.strip()).split('\t')
if len(arr) > 4:
new_line = ""
interesting_indexes = [0,11,15,19,21,22,23,24]
for i in interesting_indexes:
tmp = arr[i].split('+')[0]
if i == 15 and not first:
tmp = int(tmp) + int(arr[i+1].split('+')[0])
new_line += str(tmp)
if i != 24:
new_line += ' &\t'
else:
new_line += '\\\\\n'
first = 0
outfile.write(new_line)
else:
outfile.write(line)
|
