-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathlaff.py
202 lines (180 loc) · 8.32 KB
/
laff.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
import string
import sys
VALID_CHARS = set([c for c in string.ascii_letters] + [c for c in string.digits])
class DNA():
def __init__(self, name='', info='', content=None):
self.name = name
self.info = info
self.content = content
def __repr__(self):
return "name: {}\ninfo: {}\ncontent: {}".format(self.name, self.info, self.content)
def add_new_DNA(dna_list, line):
assert line[0] == '>'
first_space_idx = line.find(' ')
if first_space_idx != -1:
dna_name = line[1:first_space_idx]
dna_info = line[first_space_idx:].strip()
else:
dna_name = line[1:]
dna_info = ''
dna_list.append(DNA(name=dna_name, info=dna_info, content=[]))
def add_line_to_DNA(cur_DNA, line):
for x in line:
if x in VALID_CHARS:
cur_DNA.content.append(x)
elif x == ' ':
continue
else:
raise Exception()
def parse_FASTA(file):
"""
Basic state machine for parsing.
0 = Expecting '>' or empty line.
1 = Expecting valid string for current DNA or empty line.
2 = Got at least one string for current DNA. Ready for new DNA
or continue current DNA.
"""
state = 0
dna_list = []
for line in file:
line = line.strip()
if state == 0:
if line[0] == '>':
add_new_DNA(dna_list, line)
state = 1
elif line == '':
continue
else:
raise Exception()
elif state == 1:
add_line_to_DNA(dna_list[-1], line)
state = 2
elif state == 2:
if line[0] == '>':
add_new_DNA(dna_list, line)
state = 1
else:
add_line_to_DNA(dna_list[-1], line)
else:
raise Exception()
file.seek(0)
return dna_list
BLOSUM62 = [ # Substitution penalty BLOSUM62
[ 4, 0, -2, -1, -2, 0, -2, -1, -1, -1, -1, -2, -1, -1, -1, 1, 0, 0, -3, -2],
[ 0, 9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -3, -3, -3, -1, -1, -1, -2, -2],
[ -2, -3, 6, 2, -3, -1, -1, -3, -1, -4, -3, 1, -1, 0, -2, 0, -1, -3, -4, -3],
[ -1, -4, 2, 5, -3, -2, 0, -3, 1, -3, -2, 0, -1, 2, 0, 0, -1, -2, -3, -2],
[ -2, -2, -3, -3, 6, -3, -1, 0, -3, 0, 0, -3, -4, -3, -3, -2, -2, -1, 1, 3],
[ 0, -3, -1, -2, -3, 6, -2, -4, -2, -4, -3, 0, -2, -2, -2, 0, -2, -3, -2, -3],
[ -2, -3, -1, 0, -1, -2, 8, -3, -1, -3, -2, 1, -2, 0, 0, -1, -2, -3, -2, 2],
[ -1, -1, -3, -3, 0, -4, -3, 4, -3, 2, 1, -3, -3, -3, -3, -2, -1, 3, -3, -1],
[ -1, -3, -1, 1, -3, -2, -1, -3, 5, -2, -1, 0, -1, 1, 2, 0, -1, -2, -3, -2],
[ -1, -1, -4, -3, 0, -4, -3, 2, -2, 4, 2, -3, -3, -2, -2, -2, -1, 1, -2, -1],
[ -1, -1, -3, -2, 0, -3, -2, 1, -1, 2, 5, -2, -2, 0, -1, -1, -1, 1, -1, -1],
[ -2, -3, 1, 0, -3, 0, 1, -3, 0, -3, -2, 6, -2, 0, 0, 1, 0, -3, -4, -2],
[ -1, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, 7, -1, -2, -1, -1, -2, -4, -3],
[ -1, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -1, 5, 1, 0, -1, -2, -2, -1],
[ -1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -2, 1, 5, -1, -1, -3, -3, -2],
[ 1, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -1, 0, -1, 4, 1, -2, -3, -2],
[ 0, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 1, 5, 0, -2, -2],
[ 0, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -2, -2, -3, -2, 0, 4, -3, -1],
[ -3, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3, 11, 2],
[ -2, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, 2, 7]
]
BLOSUM62_ENTRIES = ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N',
'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y']
BLOSUM62_MAP = dict(zip(BLOSUM62_ENTRIES, range(len(BLOSUM62_ENTRIES))))
PAM250 = [ # Substitution penalty PAM250
[ 2, -2, 0, 0, -3, 1, -1, -1, -1, -2, -1, 0, 1, 0, -2, 1, 1, 0, -6, -3],
[ -2, 12, -5, -5, -4, -3, -3, -2, -5, -6, -5, -4, -3, -5, -4, 0, -2, -2, -8, 0],
[ 0, -5, 4, 3, -6, 1, 1, -2, 0, -4, -3, 2, -1, 2, -1, 0, 0, -2, -7, -4],
[ 0, -5, 3, 4, -5, 0, 1, -2, 0, -3, -2, 1, -1, 2, -1, 0, 0, -2, -7, -4],
[ -3, -4, -6, -5, 9, -5, -2, 1, -5, 2, 0, -3, -5, -5, -4, -3, -3, -1, 0, 7],
[ 1, -3, 1, 0, -5, 5, -2, -3, -2, -4, -3, 0, 0, -1, -3, 1, 0, -1, -7, -5],
[ -1, -3, 1, 1, -2, -2, 6, -2, 0, -2, -2, 2, 0, 3, 2, -1, -1, -2, -3, 0],
[ -1, -2, -2, -2, 1, -3, -2, 5, -2, 2, 2, -2, -2, -2, -2, -1, 0, 4, -5, -1],
[ -1, -5, 0, 0, -5, -2, 0, -2, 5, -3, 0, 1, -1, 1, 3, 0, 0, -2, -3, -4],
[ -2, -6, -4, -3, 2, -4, -2, 2, -3, 6, 4, -3, -3, -2, -3, -3, -2, 2, -2, -1],
[ -1, -5, -3, -2, 0, -3, -2, 2, 0, 4, 6, -2, -2, -1, 0, -2, -1, 2, -4, -2],
[ 0, -4, 2, 1, -3, 0, 2, -2, 1, -3, -2, 2, 0, 1, 0, 1, 0, -2, -4, -2],
[ 1, -3, -1, -1, -5, 0, 0, -2, -1, -3, -2, 0, 6, 0, 0, 1, 0, -1, -6, -5],
[ 0, -5, 2, 2, -5, -1, 3, -2, 1, -2, -1, 1, 0, 4, 1, -1, -1, -2, -5, -4],
[ -2, -4, -1, -1, -4, -3, 2, -2, 3, -3, 0, 0, 0, 1, 6, 0, -1, -2, 2, -4],
[ 1, 0, 0, 0, -3, 1, -1, -1, 0, -3, -2, 1, 1, -1, 0, 2, 1, -1, -2, -3],
[ 1, -2, 0, 0, -3, 0, -1, 0, 0, -2, -1, 0, 0, -1, -1, 1, 3, 0, -5, -3],
[ 0, -2, -2, -2, -1, -1, -2, 4, -2, 2, 2, -2, -1, -2, -2, -1, 0, 4, -6, -2],
[ -6, -8, -7, -7, 0, -7, -3, -5, -3, -2, -4, -4, -6, -5, 2, -2, -5, -6, 17, 0],
[ -3, 0, -4, -4, 7, -5, 0, -1, -4, -1, -2, -2, -5, -4, -4, -3, -3, -2, 0, 10]
]
PAM250_ENTRIES = ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N',
'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y']
PAM250_MAP = dict(zip(PAM250_ENTRIES, range(len(PAM250_ENTRIES))))
############
# GO HERE! #
############
with open("rosalind_laff.txt") as file:
dna_list = parse_FASTA(file)
a, b = [x.content for x in dna_list]
score_mat = BLOSUM62
score_mat_map = BLOSUM62_MAP
mode = 'max'
func = {'max': max, 'min': min}[mode]
sign = {'max': -1, 'min': 1}[mode] # When maximizing, negative is for punishment
comp_op = {'max': lambda x, y: x > y, 'min': lambda x, y: x < y}[mode]
# g(k) := alpha + beta * k
alpha = sign * 11 # Gap initial penalty.
beta = sign * 1 # Gap continuation penalty.
D = [[None for j in range(len(a)+1)] for i in range(len(b)+1)]
P = [[None for j in range(len(a)+1)] for i in range(len(b)+1)]
Q = [[None for j in range(len(a)+1)] for i in range(len(b)+1)]
for i in range(len(b)+1):
D[i][0] = 0
Q[i][0] = sign * sys.maxsize
for j in range(len(a)+1):
D[0][j] = 0
P[0][j] = sign * sys.maxsize
P[0][0], Q[0][0] = 0, 0
best_val = sign * sys.maxsize
best_i, best_j = None, None
for i in range(1, len(b)+1):
for j in range(1, len(a)+1):
P[i][j] = func(D[i-1][j] + alpha, P[i-1][j] + beta)
Q[i][j] = func(D[i][j-1] + alpha, Q[i][j-1] + beta)
match_score = D[i-1][j-1] + score_mat[score_mat_map[a[j-1]]][score_mat_map[b[i-1]]]
D[i][j] = func(0, match_score, P[i][j], Q[i][j])
if comp_op(D[i][j], best_val):
best_val = D[i][j]
best_i, best_j = i, j
print(best_val)
a_alig = []
b_alig = []
cur_i, cur_j = best_i, best_j
cur_mat = 'D'
while comp_op(D[cur_i][cur_j], 0):
if cur_mat == 'D':
match_score = D[cur_i-1][cur_j-1] + score_mat[score_mat_map[a[cur_j-1]]][score_mat_map[b[cur_i-1]]]
if D[cur_i][cur_j] == match_score:
a_alig.append(a[cur_j-1])
b_alig.append(b[cur_i-1])
cur_i -= 1
cur_j -= 1
elif D[cur_i][cur_j] == P[cur_i][cur_j]:
cur_mat = 'P'
elif D[cur_i][cur_j] == Q[cur_i][cur_j]:
cur_mat = 'Q'
else:
raise Exception()
elif cur_mat == 'P':
if P[cur_i][cur_j] != P[cur_i-1][cur_j] + beta:
cur_mat = 'D'
b_alig.append(b[cur_i-1])
cur_i -= 1
elif cur_mat == 'Q':
if Q[cur_i][cur_j] != Q[cur_i][cur_j-1] + beta:
cur_mat = 'D'
a_alig.append(a[cur_j-1])
cur_j -= 1
else:
raise Exception()
print(''.join(a_alig[::-1]))
print(''.join(b_alig[::-1]))