def nw_bio(seq1, seq2, cost_table):
aligner = PairwiseAligner(alphabet=list(set(seq1 + seq2)))
aligner.match_score = cost_table[0]
aligner.mismatch_score = cost_table[1]
aligner.gap_score = cost_table[2]
alignments = aligner.align(seq1, seq2)
formated_alignments = []
for i in range(len(alignments)):
als = str(alignments[i]).split("\n")
formated_alignments.append([als[0], als[2], int(alignments[i].score)])
return formated_alignments
def nw_bio_mat(seq1, seq2, cost_mat, key):
aligner = PairwiseAligner(alphabet=key)
matrix = {}
for i in range(len(key)):
for j in range(0, len(key)):
matrix[(key[i], key[j])] = cost_mat[i * len(key) + j]
aligner.substitution_matrix = substitution_matrices.Array(data=matrix)
aligner.gap_score = cost_mat[len(key)**2]
alignments = aligner.align(seq1, seq2)
formated_alignments = []
for i in range(len(alignments)):
als = str(alignments[i]).split("\n")
formated_alignments.append([als[0], als[2], int(alignments[i].score)])
return formated_alignments