[Bio info Basics] #Bioinformatics

bioinformatics_basic.py

#PatternCount
def PatternCount(Pattern, Text):
    count = 0
    for i in range(len(Text)-len(Pattern)+1):
        if Text[i:i+len(Pattern)] == Pattern:
            count = count+1
    return count 

#FrequentWords
def CountDict(Text, k):
    Count = {} 
    for i in range(len(Text)-k+1):
        Pattern = Text[i:i+k]
        Count[i] = PatternCount(Pattern, Text)
    return Count
  
  #FrequentPatterns
  def FrequentWords(Text, k):
    FrequentPatterns = []
    Count = CountDict(Text, k)
    m = max(Count.values())
    for i in Count:
        if Count[i] == m:
            FrequentPatterns.append(Text[i:i+k])
    return FrequentPatterns
  
  def FrequentWords(Text, k):
    FrequentPatterns = []
    Count = CountDict(Text, k)
    m = max(Count.values())
    for i in Count:
        if Count[i] == m:
            FrequentPatterns.append(Text[i:i+k])
    FrequentPatternsNoDuplicates = remove_duplicates(FrequentPatterns)
    return FrequentPatternsNoDuplicates 
  
  def remove_duplicates(Items):
    ItemsNoDuplicates = [] # output variable
    for item in Items:
        if item not in ItemsNoDuplicates:
            ItemsNoDuplicates.append(item)
    return ItemsNoDuplicates