def testLCS(self):
v = "AACCTTGG"
w = "ACACTGTGA"
s,b,ret = lcs(v, w)
out = "AACTGG"
assert len(ret) == len(out)
def globalAlign(v,w,sigma=5):
s,backtrack,r = lcs(v, w, 5, lambda x,y:blosum62[(x,y)])
i = len(v)
j = len(w)
vv = []
ww = []
while i>0 or j >0:
b = backtrack[i][j]
print(b)
if b == 'd':
i = i-1
vv.append(v[i])
ww.append("-")
elif b =='r':
j = j-1
ww.append(w[j])
vv.append("-")
else:
i = i-1
j=j-1
vv.append(v[i])
ww.append(w[j])
return s,''.join(reversed(vv)),''.join(reversed(ww))
#------- Inicializa arquivo de entrada -------#
pathToInput = sys.argv[1]
inputFile = open(pathToInput, 'r')
inputName = pathToInput.split('/')[-1]
#------- leia entradas -------#
genomeA = inputFile.readline().rstrip('\n').split()
genomeB = inputFile.readline().rstrip('\n').split()
#------- driver HYB -------#
startTime = time.time()
gatherMatches = []
#lcs stands for longest common substring
matchData = lcs(genomeA, genomeB)
aux1, aux2 = genomeA, genomeB
lisRemoved1, lisRemoved2 = [], []
while(matchData):
aux1, aux2, matches = mark(aux1, aux2, matchData)
matches = fixMatches(matches, lisRemoved1, lisRemoved2)
gatherMatches.extend(matches)
#removeUnmatchable is the key difference between ILCS and HYB
aux1, aux2, lisRemoved1, lisRemoved2 = removeUnmatchable(aux1, aux2)
#print '\ng1: %s\ng2: %s\nmatches: %r\n\n' % (aux1, aux2, matches)
matchData = lcs(aux1, aux2)
if not HYB_Condition(matchData):
print 'Entrei no hyb_condition'
if __name__ == '__main__':
#------- Inicializa arquivo de entrada -------#
pathToInput = sys.argv[1]
inputFile = open(pathToInput, 'r')
inputName = pathToInput.split('/')[-1]
#------- leia entradas -------#
genomeA = inputFile.readline().rstrip('\n').split()
genomeB = inputFile.readline().rstrip('\n').split()
#------- Processo - ILCS -------#
startTime = time.time()
gatherMatches = []
#lcs stands for longest common substring
matchData = lcs(genomeA, genomeB)
auxGenome1, auxGenome2 = genomeA, genomeB
while (matchData):
auxGenome1, auxGenome2, matches = mark(auxGenome1, auxGenome2,
matchData)
#print '\ng1: %s\ng2: %s\nmatches: %r\n\n' % (auxGenome1, auxGenome2, matches)
gatherMatches.extend(matches)
matchData = lcs(auxGenome1, auxGenome2)
# recstrings retorna uma lista de chrs unicos
# recstrings soh recupera os mapeaveis, logo, exclui imapeaveis
genomeA, genomeB = recStrings(gatherMatches) #-> imprime na saida:
genomeA = [str(ord(item)) for item in genomeA]
def add_for_palindrome_LCS(string):
LCS = lcs(string, string[::-1])
return len(string) - LCS
def lis(l):
s1 = ''.join(str(i) for i in l)
s2 = ''.join(sorted(s1))
return lcs(s1, s2)