FASTA_search_pattern--allow_2_mismatches

#For Coursera - Genomic Data Science Specialization - Python course
#FIND A PARTICULAR PATTERN IN A FASTA FILE; ALLOW UP TO 2 MISMATCHES
#Read a fasta file
def readGenome(filename):
    genome = ''
    with open(filename, 'r') as f:
        for line in f:
            # ignore header line with genome information
            if not line[0] == '>':
                genome += line.rstrip()
    return genome
#Find how many times a pattern is found in a string
def naive_2mm(p, t):
    occurrences = []
    for i in range(len(t) - len(p) + 1):  # loop over alignments
        match = True
        count=0
        for j in range(len(p)):  # loop over characters
            if t[i+j] != p[j]:  # compare characters
                count+=1
                if count==3:
                    match = False
                    break
        if match:
            occurrences.append(i)  # all chars matched; record
    return occurrences
#Enter the pattern and find the reverse complement
pattern=input("Enter the pattern:")
print("searching for ", pattern)
file=input("Enter the file name:")
sequence=readGenome(file)
result=naive_2mm(pattern, sequence)
print("Number of occurrances: ", len(result), "\n", result)