Perl script to find edit distance between two sequences !

BioStar — Tue, 07 Mar 2023 14:11:00 -0600

#!/usr/bin/perl

use strict;
use warnings;

sub edit_distance {
    my ($s1, $s2) = @_;

    my $len1 = length($s1);
    my $len2 = length($s2);

    my @dp;
    for (my $i = 0; $i <= $len1; $i++) {
        for (my $j = 0; $j <= $len2; $j++) {
            $dp[$i][$j] = 0;
        }
    }

    for (my $i = 0; $i <= $len1; $i++) {
        $dp[$i][0] = $i;
    }

    for (my $j = 0; $j <= $len2; $j++) {
        $dp[0][$j] = $j;
    }

    for (my $i = 1; $i <= $len1; $i++) {
        for (my $j = 1; $j <= $len2; $j++) {
            my $cost = substr($s1, $i-1, 1) eq substr($s2, $j-1, 1) ? 0 : 1;
            $dp[$i][$j] = min($dp[$i-1][$j]+1, $dp[$i][$j-1]+1, $dp[$i-1][$j-1]+$cost);
        }
    }

    return $dp[$len1][$len2];
}

sub min {
    my $min = shift @_;
    foreach (@_) {
        $min = $_ if $_ < $min;
    }
    return $min;
}

# Example usage
my $seq1 = "ACGTAGCTAGCTGACTGAC";
my $seq2 = "CGTAGCTAGCTGACAGCTA";
my $distance = edit_distance($seq1, $seq2);
print "The edit distance between $seq1 and $seq2 is $distance.\n";

BOL: Perl script to find edit distance between two sequences !

Perl script to find edit distance between two sequences !