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
| #!/usr/bin/python
import sys, datetime
from collections import defaultdict
start_time = datetime.datetime.now()
#hash of genome file
genome_hash = defaultdict(list)
genome_file = sys.argv[1]
seq_pos = sys.argv[2]
with open(genome_file) as fd_genome:
for line in fd_genome:
if line.startswith('>'):
chrom = line.strip()[1:]
genome_hash[chrom] = []
else:
seq_eachline = line.strip()
genome_hash[chrom].append(seq_eachline)
with open(seq_pos) as fd:
for line in fd:
chrom = line.split()[0]
start_pos = int(line.split()[1]) - 1
end_pos = int(line.split()[2])
if chrom in genome_hash.keys():
ID = '>' + chrom + '_' + line.split()[1] + '_' + line.split()[2]
chrom_seq = ''.join(genome_hash[chrom])
seq = chrom_seq[start_pos:end_pos]
print ID + '\n' + seq
else:
continue
end_time = datetime.datetime.now()
#print '###############'
#print (end_time - start_time)
|