59 lines
1.6 KiB
Python
59 lines
1.6 KiB
Python
import csv
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import sys
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def main():
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# TODO: Check for command-line usage
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# TODO: Read database file into a variable
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# TODO: Read DNA sequence file into a variable
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# TODO: Find longest match of each STR in DNA sequence
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# TODO: Check database for matching profiles
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return
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def longest_match(sequence, subsequence):
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"""Returns length of longest run of subsequence in sequence."""
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# Initialize variables
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longest_run = 0
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subsequence_length = len(subsequence)
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sequence_length = len(sequence)
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# Check each character in sequence for most consecutive runs of subsequence
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for i in range(sequence_length):
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# Initialize count of consecutive runs
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count = 0
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# Check for a subsequence match in a "substring" (a subset of characters) within sequence
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# If a match, move substring to next potential match in sequence
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# Continue moving substring and checking for matches until out of consecutive matches
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while True:
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# Adjust substring start and end
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start = i + count * subsequence_length
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end = start + subsequence_length
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# If there is a match in the substring
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if sequence[start:end] == subsequence:
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count += 1
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# If there is no match in the substring
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else:
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break
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# Update most consecutive matches found
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longest_run = max(longest_run, count)
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# After checking for runs at each character in seqeuence, return longest run found
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return longest_run
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main()
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