def edit_distance(seq_x, seq_y, scoring_matrix):
"""
calculate the edit distance through seq_x, seq_y and scoring matrix
by return |seq_x| + |seq_y| - score of the corresponding global alignment
"""
alignment_matrix = pj4.compute_alignment_matrix(seq_x, seq_y, scoring_matrix, True)
score, align_x, align_y = pj4.compute_global_alignment(seq_x, seq_y, scoring_matrix, alignment_matrix)
return len(seq_x) + len(seq_y) - score
for char in seq_human:
if char != '-':
seq_human_nodash = seq_human_nodash + char
for char in seq_fruitfly:
if char != '-':
seq_fruitfly_nodash = seq_fruitfly_nodash + char
print len(seq_human_nodash)
print len(seq_fruitfly_nodash)
# for human
alignment_matrix = pj4.compute_alignment_matrix(seq_human_nodash, seq_PAX, scoring_matrix, True)
score_human, align_human, align_PAX_1 = pj4.compute_global_alignment(seq_human_nodash, seq_PAX, scoring_matrix, alignment_matrix)
print score_human
print align_human
print align_PAX_1
match_human = 0
for ind in range(len(align_human)):
if align_human[ind] == align_PAX_1[ind]:
match_human += 1
print float(match_human) / len(align_human) * 100.
# for fruit fly
alignment_matrix = pj4.compute_alignment_matrix(seq_fruitfly_nodash, seq_PAX, scoring_matrix, True)
score_fruitfly, align_fruitfly, align_PAX_2 = pj4.compute_global_alignment(seq_fruitfly_nodash, seq_PAX, scoring_matrix, alignment_matrix)
