Pythonを使用したKMPアルゴリズム

Question

私はclrsの本を守り、文字列照合のために "kmpアルゴリズム"に出くわしました。私はPythonをそのまま使用して実装しました。しかし、それは何らかの理由でうまくいかないようです。私の欠点はどこですか？

コードは以下のとおりである：

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

はこれを試してみてください：

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) 

Answer 2

これは、私はあなたが後にしているものを含んでいるのCLR KMPアルゴリズムに基づいて書いたクラスです。 DNA "文字"のみがここで受け入れられることに注意してください。

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

あなたは私のコードを実行しようとする場合があります：あなたが読みしようとしている

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