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
|
#!/usr/bin/python
import os
import sys
import subprocess
def searchPattern(pos, pattern):
#print('Search, pos: '+str(i)+', '+pattern)
subprocess.check_call(['../bin/cassiopee', '-p', pattern,
'-s', 'test2.fasta.cass',
'-o', 'test.out',
'-r'
])
results = None
with open('test.out', 'r') as res:
results = res.readlines()
if not results:
return False
match = False
for result in results:
elts = result.split('\t')
if str(pos) == elts[0]:
match = True
break
if not match:
return False
return True
sequence = ''
with open('test2.fasta.cass', 'r') as seq:
sequence = seq.read()
for i in range(0, len(sequence) - 1):
for j in range(1, len(sequence) - i ):
found = searchPattern(i, sequence[i:i+j])
if not found:
print('Not found: pos: '+str(i)+', '+sequence[i:i+j])
sys.exit(1)
|
