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
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
|
#!/usr/bin/python3 -O
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
############################################################################
#Calculate coverage from raw file
import sys
def coverage(in_filename, out_filename, maxLen, bar, kmer):
inFile = open(in_filename)
outFile = open(out_filename, 'w')
hist = [0] * (maxLen + 1)
for line in inFile:
coords = line.split()
stpos = int(coords[0])
rlen = int(coords[1])
for i in range(0, rlen - kmer + 1):
cpos = stpos + i
if cpos <= maxLen:
hist[cpos] += 1
covered = 0.0
for i in range(0, maxLen + 1):
if (hist[i] > 0):
covered += 1.0
# print("Coverage: " + str(covered/maxLen) + "\n")
newHist = [0 for i in range((maxLen + 1) / bar + 2)]
for i in range(maxLen + 1):
newHist[int(i/bar)] += hist[i]
for i in range((maxLen + 1) / bar + 1):
outFile.write(str(i) + ' ' + str(newHist[i] / bar) + '\n')
inFile.close()
outFile.close()
return covered/maxLen
def read_genome(filename):
res_seq = []
seq = ''
for line in open(filename):
if line[0] == '>':
pass
else:
seq += line.strip()
return seq
def write_fasta(data, filename):
outFile = open(filename, 'w')
for seq in data:
outFile.write('>' + seq[0] + '\n');
i = 0
while i < len(seq[1]):
outFile.write(seq[1][i:i+60] + '\n')
i += 60
outFile.close()
def analyze_gaps(in_filename, out_filename, reference, out_ref, kmer):
inFile = open(in_filename)
outFile = open(out_filename, 'w')
gaps_stat = {101:0, 501:0, 1001:0}
chunks_stat = {101:0, 501:0, 1001:0}
current = 0
#[start,end)
gaps = []
chunks = []
line = inFile.readline()
while line:
cov = int(line.split()[1])
end = current
while cov == 0 and line:
end += 1
line = inFile.readline()
if line:
cov = int(line.split()[1])
if end != current:
gaps.append((current, end));
length = end - current
for key in gaps_stat:
if length < key:
gaps_stat[key] += 1
current = end
while cov > 0 and line:
end += 1
line = inFile.readline()
if line:
cov = int(line.split()[1])
if end != current:
chunks.append((current, end + kmer - 1));
length = end - current
for key in chunks_stat:
if length < key:
chunks_stat[key] += 1
current = end
outFile.write("Total chunks: " + str(len(chunks)) + "\n")
for key in chunks_stat:
outFile.write("Chunks < " + str(key) + ": " + str(chunks_stat[key])+ "\n")
outFile.write("Total gaps: " + str(len(gaps)) + "\n")
for key in gaps_stat:
outFile.write("Gaps < " + str(key) + ": " + str(gaps_stat[key])+ "\n")
outFile.write("Gaps:\n")
for gap in gaps:
outFile.write(str(gap[0]) + ' ' + str(gap[1]) + "\n")
outFile.close()
# genome = read_genome(reference, chunks)
genome = read_genome(reference)
ref_chunks = []
i = 0
for chunk in chunks:
ref_chunks.append(("PART_" + str(i) + "_from_" + str(chunk[0]) + "_to_" + str(chunk[1]), genome[chunk[0]:chunk[1]]))
i += 1
write_fasta(ref_chunks, out_ref)
return chunks, gaps
def main():
if len(sys.argv) < 5:
print("Usage: <coverage file> <output> <genome length> <bar width> [k = 1]");
exit(0)
kmer = 1
if len(sys.argv) > 5:
kmer = int(sys.argv[5])
cov = coverage(sys.argv[1], sys.argv[2], int(sys.argv[3]), int(sys.argv[4]), kmer)
print("Coverage: " + str(cov) + "\n")
if __name__ == '__main__':
main()
|
