def test1():
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])
r = parasail.sw_trace("asdf", "asdf", 10, 1, parasail.blosum62)
c = r.cigar
print(c.len)
print(c.seq[0])
print(c.decode)
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])
r = parasail.sw_trace("asdf", "asdf", 10, 1, parasail.blosum62)
print(r.query)
print(r.ref)
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])
r = parasail.sw_trace("asdf", "asdf", 10, 1, parasail.blosum62)
c = r.cigar
print(c.len)
print(c.seq[0])
print(c.decode)
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])
r = parasail.sw_trace("asdf", "asdf", 10, 1, parasail.blosum62)
print(r.query)
print(r.ref)
def test(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)
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)
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)
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)
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)
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)
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)
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)
result = parasail.sw_stats_striped_16("asdf", "asdf", 10, 1,
parasail.blosum62)
print(result)
print(result.saturated)
print(result.score)
print(result.matches)
print(result.similar)
print(result.length)
print(parasail.blosum62.name)
print(parasail.blosum62.size)
print(parasail.blosum62.matrix)
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)
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))
def test4():
profile = parasail.profile_create_8("asdf", parasail.blosum62)
result = parasail.sw_striped_profile_8(profile, "asdf", 10, 1)
assert (result.score == 20)
del result
del profile
def test4(self):
profile = parasail.profile_create_8("asdf", parasail.blosum62)
result = parasail.sw_striped_profile_8(profile, "asdf", 10, 1)
self.assertEqual(result.score, 20)
def test():
result = parasail.sw_table("asdf","asdfasdf",10,1,parasail.blosum62)
print result
print result.saturated
print result.score
with pytest.raises(AttributeError):
print result.matches
with pytest.raises(AttributeError):
print result.similar
with pytest.raises(AttributeError):
print result.length
print result.score_table
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
result = parasail.sw_rowcol("asdf","asdfasdf",10,1,parasail.blosum62)
print result
print result.saturated
print result.score
with pytest.raises(AttributeError):
print result.matches
with pytest.raises(AttributeError):
print result.similar
with pytest.raises(AttributeError):
print result.length
print result.score_row
print result.score_col
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
result = parasail.sw("asdf","asdf",10,1,parasail.blosum62)
print result
print result.saturated
print result.score
with pytest.raises(AttributeError):
print result.matches
with pytest.raises(AttributeError):
print result.similar
with pytest.raises(AttributeError):
print result.length
with pytest.raises(AttributeError):
print result.score_table
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
result = parasail.sw_scan_32("asdf","asdf",10,1,parasail.blosum62)
print result
print result.saturated
print result.score
with pytest.raises(AttributeError):
print result.matches
with pytest.raises(AttributeError):
print result.similar
with pytest.raises(AttributeError):
print result.length
result = parasail.sw_scan_16("asdf","asdf",10,1,parasail.blosum62)
print result
print result.saturated
print result.score
with pytest.raises(AttributeError):
print result.matches
with pytest.raises(AttributeError):
print result.similar
with pytest.raises(AttributeError):
print result.length
result = parasail.sw_stats_striped_16("asdf","asdf",10,1,parasail.blosum62)
print result
print result.saturated
print result.score
print result.matches
print result.similar
print result.length
print parasail.blosum62.name
print parasail.blosum62.size
print parasail.blosum62.matrix
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
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)
def test():
result = parasail.sw_table("asdf", "asdfasdf", 10, 1, parasail.blosum62)
print result
print result.saturated
print result.score
with pytest.raises(AttributeError):
print result.matches
with pytest.raises(AttributeError):
print result.similar
with pytest.raises(AttributeError):
print result.length
print result.score_table
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
result = parasail.sw_rowcol("asdf", "asdfasdf", 10, 1, parasail.blosum62)
print result
print result.saturated
print result.score
with pytest.raises(AttributeError):
print result.matches
with pytest.raises(AttributeError):
print result.similar
with pytest.raises(AttributeError):
print result.length
print result.score_row
print result.score_col
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
result = parasail.sw("asdf", "asdf", 10, 1, parasail.blosum62)
print result
print result.saturated
print result.score
with pytest.raises(AttributeError):
print result.matches
with pytest.raises(AttributeError):
print result.similar
with pytest.raises(AttributeError):
print result.length
with pytest.raises(AttributeError):
print result.score_table
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
result = parasail.sw_scan_32("asdf", "asdf", 10, 1, parasail.blosum62)
print result
print result.saturated
print result.score
with pytest.raises(AttributeError):
print result.matches
with pytest.raises(AttributeError):
print result.similar
with pytest.raises(AttributeError):
print result.length
result = parasail.sw_scan_16("asdf", "asdf", 10, 1, parasail.blosum62)
print result
print result.saturated
print result.score
with pytest.raises(AttributeError):
print result.matches
with pytest.raises(AttributeError):
print result.similar
with pytest.raises(AttributeError):
print result.length
result = parasail.sw_stats_striped_16("asdf", "asdf", 10, 1,
parasail.blosum62)
print result
print result.saturated
print result.score
print result.matches
print result.similar
print result.length
print parasail.blosum62.name
print parasail.blosum62.size
print parasail.blosum62.matrix
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
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)
