def score_nwalign(nwalign_out: list):
align1 = nwalign_out[0]
align2 = nwalign_out[1]
# scoring the alignment #
nwscore = nw.score_alignment(
align1,
align2,
gap_open=10,
gap_extend=5,
matrix=
'/home/saveliy/nwalign3-master/nwalign3-master/nwalign3/matrices/BLOSUM62'
)
return (nwscore)
def evaluation_func(lines):
for i in range(len(lines)):
sum_score = 0
# Compute the pairwise scores
for j in range(len(lines)):
if i != j:
scr = nw.score_alignment(lines[i],
lines[j],
gap_open=-1,
gap_extend=-0.5,
matrix='matrix/BLOSUM62')
sum_score += scr
return sum_score
def _score_alignment(self):
if all(
[self._score_match is not None, self._score_mismatch is not None]):
matrix = self._get_matrix_file(match=self._score_match,
mismatch=self._score_mismatch)
elif self._matrix is not None:
matrix = self._get_matrix_file(matrix=self._matrix)
else:
matrix = self._get_matrix_file(match=self._match,
mismatch=self._mismatch)
gap_open = self._score_gap_open if self._score_gap_open is not None else self._gap_open
gap_extend = self._score_gap_extend if self._score_gap_extend is not None else self._gap_extend
aln = nw.score_alignment(self.aligned_query,
self.aligned_target,
gap_open=gap_open,
gap_extend=gap_extend,
matrix=matrix)
return aln