基于python的KMP算法

Question

我跟随clrs的书，遇到了字符串匹配的“kmp算法”。我用python（按原样）实现了它。然而，由于某种原因，它似乎不起作用。我的错在哪里？在

代码如下：

def kmp_matcher(t,p):
    n=len(t)
    m=len(p)
    # pi=[0]*n;
    pi = compute_prefix_function(p)
    q=-1
    for i in range(n):
        while(q>0 and p[q]!=t[i]):
            q=pi[q]
        if(p[q]==t[i]):
            q=q+1
        if(q==m):
            print "pattern occurs with shift "+str(i-m)
            q=pi[q]


def compute_prefix_function(p):
    m=len(p)
    pi =range(m)
    pi[1]=0
    k=0
    for q in range(2,m):
        while(k>0 and p[k]!=p[q]):
            k=pi[k]
        if(p[k]==p[q]):
            k=k+1
        pi[q]=k
    return pi

t = 'brownfoxlazydog'
p = 'lazy'
kmp_matcher(t,p)

Answer 1

你可能想试试我的代码：

def recursive_find_match(i, j, pattern, pattern_track):

    if pattern[i] == pattern[j]:
        pattern_track.append(i+1)
        return {"append":pattern_track, "i": i+1, "j": j+1}
    elif pattern[i] != pattern[j] and i == 0:
        pattern_track.append(i)
        return {"append":pattern_track, "i": i, "j": j+1}

    else:
        i = pattern_track[i-1]
        return recursive_find_match(i, j, pattern, pattern_track)

def kmp(str_, pattern):

    len_str = len(str_)
    len_pattern = len(pattern)
    pattern_track = []

    if len_pattern == 0:
        return
    elif len_pattern == 1:
        pattern_track = [0]
    else:   
        pattern_track = [0]
        i = 0
        j = 1

        while j < len_pattern:
            data = recursive_find_match(i, j, pattern, pattern_track)

            i = data["i"]
            j = data["j"]
            pattern_track = data["append"]

    index_str = 0
    index_pattern = 0
    match_from = -1

    while index_str < len_str:
        if index_pattern == len_pattern:
            break
        if str_[index_str] == pattern[index_pattern]:
            if index_pattern == 0:
                match_from = index_str

            index_pattern += 1
            index_str += 1
        else:
            if index_pattern == 0:
                index_str += 1
            else:
                index_pattern = pattern_track[index_pattern-1]
                match_from = index_str - index_pattern

Answer 2

这是我基于CLRs-KMP算法编写的一个类，其中包含了您所追求的内容。注意这里只接受DNA“字符”。在

class KmpMatcher(object):
def __init__(self, pattern, string, stringName):
    self.motif = pattern.upper()
    self.seq = string.upper()
    self.header = stringName
    self.prefix = []
    self.validBases = ['A', 'T', 'G', 'C', 'N']

#Matches the motif pattern against itself.
def computePrefix(self):
    #Initialize prefix array
    self.fillPrefixList()
    k = 0

    for pos in range(1, len(self.motif)):
        #Check valid nt
        if(self.motif[pos] not in self.validBases):
            self.invalidMotif()

        #Unique base in motif
        while(k > 0 and self.motif[k] != self.motif[pos]):
            k = self.prefix[k]
        #repeat in motif
        if(self.motif[k] == self.motif[pos]):
            k += 1

        self.prefix[pos] = k

#Initialize the prefix list and set first element to 0
def fillPrefixList(self):
    self.prefix = [None] * len(self.motif)
    self.prefix[0] = 0

#An implementation of the Knuth-Morris-Pratt algorithm for linear time string matching
def kmpSearch(self):
    #Compute prefix array
    self.computePrefix()
    #Number of characters matched
    match = 0
    found = False

    for pos in range(0, len(self.seq)):
        #Check valid nt
        if(self.seq[pos] not in self.validBases):
            self.invalidSequence()

        #Next character is not a match
        while(match > 0 and self.motif[match] != self.seq[pos]):
            match = self.prefix[match-1]
        #A character match has been found
        if(self.motif[match] == self.seq[pos]):
            match += 1
        #Motif found
        if(match == len(self.motif)):
            print(self.header)
            print("Match found at position: " + str(pos-match+2) + ':' + str(pos+1))
            found = True
            match = self.prefix[match-1]

    if(found == False):
        print("Sorry '" + self.motif + "'" + " was not found in " + str(self.header))

#An invalid character in the motif message to the user
def invalidMotif(self):
    print("Error: motif contains invalid DNA nucleotides")
    exit()

#An invalid character in the sequence message to the user
def invalidSequence(self):
    print("Error: " + str(self.header) + "sequence contains invalid DNA nucleotides")
    exit()

Answer 3

试试这个：

def kmp_matcher(t, d):
    n=len(t)
    m=len(d)

    pi = compute_prefix_function(d)
    q = 0
    i = 0
    while i < n:
        if d[q]==t[i]:
            q=q+1
            i = i + 1
        else:
            if q != 0:
                q = pi[q-1]
            else:
                i = i + 1
        if q == m:
            print "pattern occurs with shift "+str(i-q)
            q = pi[q-1]

def compute_prefix_function(p):
    m=len(p)
    pi =range(m)
    k=1
    l = 0
    while k < m:
        if p[k] <= p[l]:
            l = l + 1
            pi[k] = l
            k = k + 1
        else:
            if l != 0:
                l = pi[l-1]
            else:
                pi[k] = 0
                k = k + 1
    return pi

t = 'brownfoxlazydog'
p = 'lazy'
kmp_matcher(t, p)