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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("Missing command line arguments!")
sys.exit(1)
file_csv = sys.argv[1]
file_text = sys.argv[2]
# Read database file into a variable
rows = []
with open(file_csv) as file:
reader = csv.DictReader(file)
for row in reader:
rows.append(row)
# Read DNA sequence file into a variable
sequence_file = open(file_text)
sequence = sequence_file.read()
# Find longest match of each STR in DNA sequence
dict = rows[0]
dict_keys = list(dict.keys())
i = 1
counts = []
while i < len(dict_keys):
longest_count = longest_match(sequence, dict_keys[i])
counts.append(longest_count)
i += 1
# Check database for matching profiles
j = 0
name = ""
while j < len(rows):
flag = True
k = 1
u = 0
current = rows[j]
while k < len(dict_keys):
if int(current[dict_keys[k]]) != counts[u]:
flag = False
break
k += 1
u += 1
if (flag):
name = current[dict_keys[0]]
return name
j += 1
return "No match"
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
name = main()
print(name)