def main():
A, B = (X for _, X in rosalib.parse_fasta())
T, pred = global_score(A, B)
print(T[-1][-1])
SA, SB = solution(A, B, pred)
print(SA)
print(SB)
def main():
A,B = (X for _,X in rosalib.parse_fasta())
T,pred = global_score(A,B)
print(T[-1][-1])
SA,SB = solution(A,B,pred)
print(SA)
print(SB)
def main():
for _,DNA in rosalib.parse_fasta():
S = sign(DNA)
if S in DBC:
continue
elif S in DBI:
del DBI[S]
DBC.add(S)
else:
DBI[S] = DNA
for S in DBI:
DNA = DBI[S]
print('%s->%s' % (DNA,correct(DNA)))
def main():
for _, DNA in rosalib.parse_fasta():
S = sign(DNA)
if S in DBC:
continue
elif S in DBI:
del DBI[S]
DBC.add(S)
else:
DBI[S] = DNA
for S in DBI:
DNA = DBI[S]
print('%s->%s' % (DNA, correct(DNA)))
def main():
DNAS = [DNA for _, DNA in rosalib.parse_fasta()]
Succ = [None] * len(DNAS)
Start = set(range(len(DNAS)))
for i in range(len(DNAS)):
for j in range(len(DNAS)):
if i == j:
continue
e = edge(DNAS[i], DNAS[j])
if e != None:
assert (Succ[i] == None)
Succ[i] = (j, e)
assert (j in Start)
Start.remove(j)
assert (len(Start) == 1)
s = Start.pop()
res = [DNAS[s]]
while Succ[s] != None:
t, e = Succ[s]
res.append(DNAS[t][e:])
s = t
print(''.join(res))
def main():
L = rosalib.parse_fasta()
for i in range(len(L)):
print(' '.join(str(pdist(L[i][1],L[j][1])) for j in range(len(L))))
def main():
A,B = (S for _,S in rosalib.parse_fasta())
s,la,ra,lb,rb = local_score(A,B)
print(s)
print(A[la:ra])
print(B[lb:rb])
#!/usr/bin/env python3
import rosalib
# NB: the statement explains "Why Are We Counting Modulo 134,217,727?
# (...) however, if we count modulo a large prime number"
# yet 2^27-1 = 134217727 is not prime... (-_-)
def Levenstein_align(u,v):
m,n = len(u),len(v)
T = [[max(i,j) for j in range(n+1)] for i in range(m+1)]
Nb = [[int(i==0 or j==0) for j in range(n+1)] for i in range(m+1)]
for i in range(1,m+1):
for j in range(1,n+1):
T[i][j] = min(T[i-1][j]+1,T[i][j-1]+1,T[i-1][j-1]+int(u[i-1]!=v[j-1]))
if T[i-1][j]+1==T[i][j]:
Nb[i][j] += Nb[i-1][j]
if T[i][j-1]+1==T[i][j]:
Nb[i][j] += Nb[i][j-1]
if T[i-1][j-1]+int(u[i-1]!=v[j-1])==T[i][j]:
Nb[i][j] += Nb[i-1][j-1]
return (T[m][n],Nb[m][n])
L = rosalib.parse_fasta()
_,cpt = Levenstein_align(L[0][1],L[1][1])
print(cpt % (2**27-1))
#!/usr/bin/env python3
from itertools import *
import rosalib
DNAS = [DNA for _,DNA in rosalib.parse_fasta()]
n = len(DNAS)
# dp((i1,i2,...,in)) = score max d'un alignement des DNAS[k][:ik] pour tout k
memo,pred = {(0,)*n:0},{}
def dp(I):
if I in memo:
return memo[I]
res = float('-inf')
for D in product(*(range(2 if I[k]>0 else 1) for k in range(n))):
if max(D)==0:
continue
J = tuple(I[k]-D[k] for k in range(n))
C = [DNAS[k][I[k]-1] if D[k]==1 else '-' for k in range(n)]
s = dp(J) + sum(-int(C[k]!=C[l]) for k,l in combinations(range(n),2))
if s>res:
res = s
# on retient le predecesseur pour faciliter la reconstruction
# de la solution
pred[I] = J
memo[I] = res
return res
def solution(I):
Sol = [[] for _ in range(n)]
while I in pred:
J = pred[I]
#!/usr/bin/env python3
import rosalib
_, RNA = rosalib.parse_fasta()[0]
pair = {'A': 'U', 'U': 'A', 'C': 'G', 'G': 'C'}
memo = {}
# nb de planar matchings de RNA[i:j+1]
def planar_match(i, j):
if i > j:
return 1
if (i, j) in memo:
return memo[i, j]
res = planar_match(i + 1, j) # on ne match pas i
for k in range(i + 1, j + 1): # indice avec lequel on match i
if pair[RNA[i]] == RNA[k]:
res += planar_match(i + 1, k - 1) * planar_match(k + 1, j)
memo[i, j] = res
return res
print(planar_match(0, len(RNA) - 1) % 10**6)
def main():
A, B = (S for _, S in rosalib.parse_fasta())
M, SA, SB = fitting_score(A, B)
print(M)
print(SA)
print(SB)
def main():
A, B = (S for _, S in rosalib.parse_fasta())
s, M = align_matrix(A, B)
print(s)
print(sum(sum(L) for L in M))
def main():
L = rosalib.parse_fasta()
_,DNA = L[0]
for (p,s) in rev_pal(DNA):
print(p,s)
#!/usr/bin/env python3
import rosalib
# pretty naive and lazy approach here, yet good enough
# (for sure there are more efficient and still relatively simple
# approaches using string hashing)
# see also https://en.wikipedia.org/wiki/Longest_common_substring_problem
# for a really good approach using suffix trees
def LCSub(DNAS):
L0 = len(DNAS[0])
for k in range(L0,-1,-1):
for i in range(L0-k+1):
P = DNAS[0][i:i+k]
if all(DNAS[j].find(P)>=0 for j in range(1,len(DNAS))):
return P
DNAS = sorted((DNA for _,DNA in rosalib.parse_fasta()), key=len)
print(LCSub(DNAS))
def main():
A,B = (S for _,S in rosalib.parse_fasta())
s,M = align_matrix(A,B)
print(s)
print(sum(sum(L) for L in M))
#!/usr/bin/env python3
import rosalib
def fact(n):
return 1 if n<=1 else n*fact(n-1)
_,RNA = rosalib.parse_fasta()[0]
print(fact(RNA.count('A'))*fact(RNA.count('C')))
def main():
L = rosalib.parse_fasta()
_, DNA = L[0]
for (p, s) in rev_pal(DNA):
print(p, s)
#!/usr/bin/env python3
import rosalib
def subseq(S, T):
P = []
i = j = 0
while i < len(S) and j < len(T):
if S[i] == T[j]:
P.append(i + 1)
j += 1
i += 1
return P if j == len(T) else None
L = rosalib.parse_fasta()
S, T = L[0][1], L[1][1]
print(' '.join(map(str, subseq(S, T))))
def main():
A, B = (S for _, S in rosalib.parse_fasta())
M, SA, SB = semi_global_score(A, B)
print(M)
print(SA)
print(SB)
