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gcon.py
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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
with open("rosalind_gcon.txt") as file:
dna_list = parse_FASTA(file)
a, b = [x.content for x in dna_list]
score_mat = [ # substitution penalty
[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]
]
score_mat_map = {'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6, 'I': 7, 'K': 8, 'L': 9,
'M': 10, 'N': 11, 'P': 12, 'Q': 13, 'R': 14, 'S': 15, 'T': 16, 'V': 17, 'W': 18, 'Y': 19}
# g(k) = alpha + beta * k
alpha = -5 # Gap initial penalty.
beta = 0 # 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)]
D[0][0], P[0][0], Q[0][0] = 0, 0, 0
for i in range(1, len(b)+1):
D[i][0] = alpha + i * beta
Q[i][0] = -sys.maxsize
for j in range(1, len(a)+1):
D[0][j] = alpha + j * beta
P[0][j] = -sys.maxsize
for i in range(1, len(b)+1):
for j in range(1, len(a)+1):
P[i][j] = max(D[i-1][j] + alpha + beta, P[i-1][j] + beta)
Q[i][j] = max(D[i][j-1] + alpha + beta, Q[i][j-1] + beta)
D[i][j] = max(P[i][j], Q[i][j], D[i-1][j-1] + score_mat[score_mat_map[a[j-1]]][score_mat_map[b[i-1]]])
print(D[-1][-1])