use Modern::Perl;

# Process the second file only once
my @alleles;
{
    open my $secondfile, '<', './secondfile.txt' or die "Could not open second file. $!";
    while (<$secondfile>) {
        chomp;
        my ($minor, $major) = split;
        push @alleles, {
            "$minor$minor" => 0,
            "$minor$major" => 1,
            "$major$minor" => 1,
            "$major$major" => 2,
            '00'           => -1,
        }
    }
}

#Process the first file
open my $firstfile, '<', './firstfile.txt' or die "Could not open first file. $!";
while (<$firstfile>) {
    chomp;
    say "Working on $_";
    my @snps = split;
    my $index;
    my @results;
    while (@snps) {
        my $marker = shift(@snps) . shift(@snps);
        push @results, ($alleles[$index])->{$marker};
        $index++;
    }
    say join ',', @results;
}