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dna.py
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dna.py
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import csv
import sys
def main():
# Check for command-line usage
if len(sys.argv) < 3:
print("Usage: python dna.py *.csv *.txt")
sys.exit(1)
# Read database file into a variable
database = []
with open(sys.argv[1], 'r') as file:
reader = csv.DictReader(file)
for row in reader:
database.append(row)
# Read DNA sequence file into a variable
with open(sys.argv[2], 'r') as file:
dna_sequence = file.read()
# List of subsequences to check
subsequences = list(database[0].keys())[1:]
# Find longest match of each STR in DNA sequence
result = {}
for subsequence in subsequences:
result[subsequence] = longest_match(dna_sequence, subsequence)
# Check database for matching profiles
for person in database:
match = 0
for subsequence in subsequences:
if int(person[subsequence]) == result[subsequence]:
match += 1
# If all subsequences matched
if match == len(subsequences):
print(person["name"])
return
print("No match")
return
def longest_match(sequence, subsequence):
"""Returns length of longest run of subsequence in sequence."""
# Initialize variables
longest_run = 0
subsequence_length = len(subsequence)
sequence_length = len(sequence)
# Check each character in sequence for most consecutive runs of subsequence
for i in range(sequence_length):
# Initialize count of consecutive runs
count = 0
# Check for a subsequence match in a "substring" (a subset of characters) within sequence
# If a match, move substring to next potential match in sequence
# Continue moving substring and checking for matches until out of consecutive matches
while True:
# Adjust substring start and end
start = i + count * subsequence_length
end = start + subsequence_length
# If there is a match in the substring
if sequence[start:end] == subsequence:
count += 1
# If there is no match in the substring
else:
break
# Update most consecutive matches found
longest_run = max(longest_run, count)
# After checking for runs at each character in seqeuence, return longest run found
return longest_run
main()