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("----------------")
from other_written.matrix import BLOSUM62
import ReadData as rd
__all__ = ["AlignmentResult", "aligner"]
IS_PY2 = False
if sys.version_info.major == 2:
IS_PY2 = True
# Container for alignment result
AlignmentResult = namedtuple('AlignmentResult', [
'seq1', 'seq2', 'start1', 'start2', 'end1', 'end2', 'n_gaps1', 'n_gaps2',
'n_mismatches', 'score'
])
mat, index = rd.Read_BLO_Matrix(file_name="../BLOSUM62.txt")
def aligner(seqj,
seqi,
method='global',
gap_open=-7,
gap_extend=-7,
gap_double=-7,
matrix=BLOSUM62,
max_hits=1):
'''Calculates the alignment of two sequences.
The supported 'methods' are:
* 'global' for a global Needleman-Wunsh algorithm
* 'local' for a local Smith-Waterman alignment
def acc_identity(self):
self.identity += 1
def acc_gap_count(self):
self.gap_count += 1
def set_sequence_final_length(self, length):
self.final_length = length
def __str__(self):
return "gap_count = %d; ideXntity = %d \n" % (self.gap_count,
self.identity)
mat, index = Data.Read_BLO_Matrix()
def global_alignment(seqs=Sequence_Pair(),
score=ScoreParam(-10, -0.5, mat, index),
method="global",
max_hits=1):
assert method == "global" or "local"
seqi = seqs.sequence_A
seqj = seqs.sequence_B
NONE, LEFT, UP, DIAG = range(4) # NONE is 0
GAP_CHAR = '-'
