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import parasail
from unittest import TestCase, main
import pytest
import platform
class Tests(TestCase):
def test1(self):
result = parasail.sw_table("asdf", "asdfasdf", 10, 1, parasail.blosum62)
print(result)
print(result.saturated)
print(result.score)
with self.assertRaises(AttributeError):
print(result.matches)
with self.assertRaises(AttributeError):
print(result.similar)
with self.assertRaises(AttributeError):
print(result.length)
print(result.score_table)
def test2(self):
result = parasail.sw_stats_table("asdf", "asdfasdf", 10, 1, parasail.blosum62)
print(result)
print(result.saturated)
print(result.score)
print(result.matches)
print(result.similar)
print(result.length)
print(result.score_table)
print(result.matches_table)
print(result.similar_table)
print(result.length_table)
def test3(self):
result = parasail.sw_rowcol("asdf", "asdfasdf", 10, 1, parasail.blosum62)
print(result)
print(result.saturated)
print(result.score)
with self.assertRaises(AttributeError):
print(result.matches)
with self.assertRaises(AttributeError):
print(result.similar)
with self.assertRaises(AttributeError):
print(result.length)
print(result.score_row)
print(result.score_col)
def test4(self):
result = parasail.sw_stats_rowcol("asdf", "asdfasdf", 10, 1, parasail.blosum62)
print(result)
print(result.saturated)
print(result.score)
print(result.matches)
print(result.similar)
print(result.length)
print(result.score_row)
print(result.score_col)
print(result.matches_row)
print(result.matches_col)
print(result.similar_row)
print(result.similar_col)
print(result.length_row)
print(result.length_col)
def test5(self):
result = parasail.sw("asdf", "asdf", 10, 1, parasail.blosum62)
print(result)
print(result.saturated)
print(result.score)
with self.assertRaises(AttributeError):
print(result.matches)
with self.assertRaises(AttributeError):
print(result.similar)
with self.assertRaises(AttributeError):
print(result.length)
with self.assertRaises(AttributeError):
print(result.score_table)
@pytest.mark.skipif(platform.uname().machine=='aarch64', reason="FIXME: test6 ends up in Segmentation fault on arm64")
def test6(self):
result = parasail.sw_stats("asdf", "asdf", 10, 1, parasail.blosum62)
print(result)
print(result.saturated)
print(result.score)
print(result.matches)
print(result.similar)
print(result.length)
@pytest.mark.skipif(platform.uname().machine=='aarch64', reason="FIXME: test7 ends up in Segmentation fault on arm64")
def test7(self):
result = parasail.sw_scan_32("asdf", "asdf", 10, 1, parasail.blosum62)
print(result)
print(result.saturated)
print(result.score)
with self.assertRaises(AttributeError):
print(result.matches)
with self.assertRaises(AttributeError):
print(result.similar)
with self.assertRaises(AttributeError):
print(result.length)
@pytest.mark.skipif(platform.uname().machine=='aarch64', reason="FIXME: test8 ends up in Segmentation fault on arm64")
def test8(self):
result = parasail.sw_scan_16("asdf", "asdf", 10, 1, parasail.blosum62)
print(result)
print(result.saturated)
print(result.score)
with self.assertRaises(AttributeError):
print(result.matches)
with self.assertRaises(AttributeError):
print(result.similar)
with self.assertRaises(AttributeError):
print(result.length)
def test9(self):
result = parasail.sw_stats_striped_16("asdf", "asdf", 10, 1, parasail.blosum62)
print(result)
print(result.saturated)
print(result.score)
if platform.uname().machine != 'aarch64':
print(result.matches)
print(result.similar)
print(result.length)
else:
print("On architecture aarch64 this test runs into: AttributeError: 'Result' object has no stats")
print(parasail.blosum62.name)
print(parasail.blosum62.size)
print(parasail.blosum62.matrix)
if platform.uname().machine != 'aarch64':
profile = parasail.profile_create_8("asdf", parasail.blosum62)
profile = parasail.profile_create_8("asdf", parasail.blosum62)
print(profile)
print(profile.s1)
print(profile.matrix)
result = parasail.sw_striped_profile_8(profile, "asdf", 10, 1)
print(result)
print(result.saturated)
print(result.score)
else:
print("On architecture aarch64 this test runs into: Segmentation fault")
@pytest.mark.skipif(platform.uname().machine=='aarch64', reason="FIXME: test10 ends up in Segmentation fault on arm64")
def test10(self):
profile = parasail.profile_create_sat("asdf", parasail.blosum62)
print(profile)
print(profile.s1)
print(profile.matrix)
print(dir(profile.matrix))
print(profile.matrix.min)
print(profile.matrix.max)
print(profile.matrix.size)
result = parasail.sw_striped_profile_sat(profile, "asdf", 10, 1)
print(result)
print(result.saturated)
print(result.score)
print(type(result.score))
if __name__ == '__main__':
main()
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