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
|
import parasail
from unittest import TestCase, main, expectedFailure
class Tests(TestCase):
import pytest
import platform
@pytest.mark.skipif(platform.uname().machine=='aarch64', reason="FIXME: test4 ends up in Segmentation fault on arm64")
def test1(self):
p = parasail.ssw_init("asdf", parasail.blosum62, 1)
r = parasail.ssw_profile(p, "asdf", 10, 1)
print(p.s1)
# print(p.s1Len)
print(r.cigarLen)
print(r.cigar[0])
def test2(self):
r = parasail.sw_trace("asdf", "asdf", 10, 1, parasail.blosum62)
c = r.cigar
print(c.len)
print(c.seq[0])
print(c.decode)
@pytest.mark.skipif(platform.uname().machine=='aarch64', reason="FIXME: test4 ends up in Segmentation fault on arm64")
def test3(self):
p = parasail.profile_create_8("asdf", parasail.blosum62)
r = parasail.sw_trace_striped_profile_8(p, "asdf", 10, 1)
c = r.cigar
print(c.len)
print(c.seq[0])
def test4(self):
r = parasail.sw_trace("asdf", "asdf", 10, 1, parasail.blosum62)
print(r.query)
print(r.ref)
if __name__ == '__main__':
main()
|
