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I am doing a bioinformatics course and I am trying to write a function to find all occurrences of a substring within a string.
def find_match(s, t):
"""Returns a list of all positions of a substring t in string s.
Takes two arguments: s & t.
"""
occurrences = []
for i in range(len(s)-len(t)+1): # loop over alignment
match = True
for j in range(len(t)): # loop over characters
if s[i+j] != t[j]: # compare characters
match = False # mismatch
break
if match: # allchars matched
occurrences.append(i)
return(occurrences)
print(find_match("GATATATGCATATACTT", "ATAT")) # [1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 9, 9, 9, 9, 11, 11, 11, 13]
print(find_match("AUGCUUCAGAAAGGUCUUACG", "U")) # [1, 4, 5, 14, 16, 17]
The output above should exactly match the following:
[2, 4, 10]
[2, 5, 6, 15, 17, 18]
How can I fix this? Preferably without using regular expressions.
>Solution :
It looks like you badly indented the code, the
if match:
has to be outside of the inner cycle.
def find_match(s, t):
"""Returns a list of all positions of a substring t in string s.
Takes two arguments: s & t.
"""
occurrences = []
for i in range(len(s)-len(t)+1): # loop over alignment
match = True
for j in range(len(t)): # loop over characters
if s[i+j] != t[j]: # compare characters
match = False # mismatch
break
if match: # <--- This shouldn't be inside the inner for cycle
occurrences.append(i + 1)
return occurrences
print(find_match("GATATATGCATATACTT", "ATAT")) # [1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 9, 9, 9, 9, 11, 11, 11, 13]
print(find_match("AUGCUUCAGAAAGGUCUUACG", "U")) # [1, 4, 5, 14, 16, 17]