def degenerate_dna_pairwise_aligner(seq1, seq2: str, substitution_matrix):
with warnings.catch_warnings():
warnings.filterwarnings('ignore', category=EfficiencyWarning)
forward = DegenerateDNA(seq2)
lpa1 = local_pairwise_align(seq1, forward, 3, 1, substitution_matrix)
reverse = DegenerateDNA(reverse_complement(seq2))
lpa2 = local_pairwise_align(seq1, reverse, 3, 1, substitution_matrix)
if lpa1[1] >= lpa2[1]:
return lpa1[0], lpa1[1] # TabularMSA, score
return lpa2[0], lpa2[1]
def proteinAlign(seq1,
seq2,
gap_open_penalty,
gap_extend_penalty,
local=False):
seq1 = seq1.upper()
seq2 = seq2.upper()
if local:
aln, score, _ = local_pairwise_align(Protein(seq1), Protein(seq2),
gap_open_penalty,
gap_extend_penalty, blosum50)
else:
aln, score, _ = global_pairwise_align(Protein(seq1),
Protein(seq2),
gap_open_penalty,
gap_extend_penalty,
blosum50,
penalize_terminal_gaps=True)
response = {
'aln1':
str(aln[0]),
'aln2':
str(aln[1]),
'score':
score,
'similarity':
float('{:.2f}'.format(aln[0].match_frequency(aln[1], relative=True) *
100))
}
return response
def test_local_pairwise_align_custom_alphabet(self):
custom_substitution_matrix = make_identity_substitution_matrix(
5, -4, alphabet=CustomSequence.definite_chars)
custom_msa, custom_score, custom_start_end = local_pairwise_align(
CustomSequence("YWXXZZYWXXWYYZWXX"),
CustomSequence("YWWXZZZYWXYZWWX"), 5.0, 0.5,
custom_substitution_matrix)
# Expected values computed by running an equivalent alignment using the
# DNA alphabet with the following mapping:
#
# W X Y Z
# | | | |
# A C G T
#
self.assertEqual(
custom_msa,
TabularMSA([CustomSequence('WXXZZYWXXWYYZWXX'),
CustomSequence('WXZZZYWX^^^YZWWX')]))
self.assertEqual(custom_score, 41.0)
self.assertEqual(custom_start_end, [(1, 16), (2, 14)])
def sw_calc_best_x(comb):
best = -99999999999
target = list_to_str(y)
for i in list(comb):
x = list_to_str(i)
# print(x)
# print(target)
alignment, score, pos = local_pairwise_align(
SyscallSequence(list_to_str(i)),
SyscallSequence(target),
gap_open_penalty=-2,
gap_extend_penalty=-0.01,
substitution_matrix=matrix)
print(alignment)
print(score)
if score > best:
best = score
best_alignment = alignment
_best_x = x
print("----- Best alignment: -----")
print("score: ", best)
print(best_alignment)
return _best_x
def test_local_pairwise_align_type_mismatch(self):
with self.assertRaisesRegex(TypeError,
"same type: 'DNA' != 'RNA'"):
local_pairwise_align(DNA('ACGT'), RNA('ACGU'), 1.0, 1.0, {})
def test_local_pairwise_align_invalid_type(self):
with self.assertRaisesRegex(TypeError,
'GrammaredSequence.*Sequence'):
local_pairwise_align(DNA('ACGT'), Sequence('ACGT'), 1.0, 1.0, {})
def test_local_pairwise_align_invalid_type(self):
with six.assertRaisesRegex(self, TypeError, 'IUPACSequence.*Sequence'):
local_pairwise_align(DNA('ACGT'), Sequence('ACGT'), 1.0, 1.0, {})
