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import csv
import sys
def main():
# TODO: Check for command-line usage
if len(sys.argv) < 1 or len(sys.argv) > 2:
print("Oopsie you used the wrong number of arguments D: you should use two next time :3")
return
# check to see if arg 0 is a csv file
if not sys.argv[0].endswith('.csv'):
print("Oh no, that isn't a csv file :( that won't work can you fix that please?")
return
# check to see if arg 1 is a txt file
if not sys.argv[1].endswith('.txt'):
print("Oh no, that isn't a txt file :( that won't work can you fix that please?")
return
# TODO: Read database file into a variable
rows = []
with open(argv[0]) as file:
reader = csv.DictReader(file)
for row in reader:
rows.append(row)
# TODO: Read DNA sequence file into a variable
sequence = ''
with open(argv[1]) as file:
sequence = sequence.join(file.readlines())
# TODO: Find longest match of each STR in DNA sequence
#
# TODO: Check database for matching profiles
return
# Given entire DNA sequence and an STR (ACTG) as inputs, outputs the longest repitition
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()
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