def __init__(self, seq1: str = "", seq2: str = ""):
# 序列A，序列B
if seq1 == "" and seq2 == "":
pair = Data.Read_Two_Seq()
self.sequence_A: str = pair[0]
self.sequence_B: str = pair[1]
elif seq1 != "" and seq2 != "":
self.sequence_A = seq1
self.sequence_B = seq2
# 统计结果
self.gap_count = 0
self.identity = 0
self.similarity = 0
self.final_length = 0
align_j = ''.join(align_j[::-1])
seq_result_str = ''.join(seq_result[::-1])
if flip:
aln = AlignmentResult(align_i, align_j, seq_result_str , i, j, end_i, end_j,
n_gaps_i, n_gaps_j, n_mmatch, score)
else:
aln = AlignmentResult(align_j, align_i, seq_result_str , j, i, end_j, end_i,
n_gaps_j, n_gaps_i, n_mmatch, score)
results.append(aln)
return results
# ----------------- test -------------------------------------------
mat, ind = rd.Read_BLO_Matrix(file_name="BLOSUM62.txt")
alg = aligner(rd.Read_Two_Seq(), mat, ind, gap_open=-10, gap_extend=-0.5,gap_double=-10,max_hits=2)
for i in alg:
print(i)
alg=[]
alg = aligner(['ARAAV','ARAVVVARAV'], mat, ind, method='local', gap_open=-10,gap_extend=-0.5,gap_double=-10,max_hits=2)
for i in alg:
print(i)
alg = []
alg = aligner(rd.Read_Two_Seq(), mat, ind, method="local", gap_open=-10,gap_extend=-0.5,gap_double=-10,max_hits=5)
for i in alg:
print(i)
#print(len(i.seq1))
print("----------------")
