Don't know if it's relevant to your project, but bioperl might be of interest to you

Also, your description implies that there might be spaces in file1 between each character. However, you might've just added them to make your question more readable. Either way, you could use the following code to process each line two characters at a time.

After that it's just doing your comparison and outputting to a new file from what you describe.

while (<DATA>) {
    chomp;
    my @letters = m/(\w)/g;
    while (@letters) {
        my $x = shift @letters;
        my $y = shift @letters;
        
        print "($x, $y) ";
    }
    print "\n";
}

__DATA__
T G T T T G T C A A
C G G C T C T G G C
[download]

use warnings;
use strict;

open my $IN,'<','894013-1' or die "Cannot open file1: $!\n";
open my $AL,'<','894013-2' or die "Cannot open file2: $!\n";

my @alleles = map {chomp; split / /} <$AL>;

while (<$IN>) {
    chomp;
    my @individual = split / /;
    for my $half (0 .. @individual/2-1) {
        my %pair;
        my ($pos1,$pos2) = ($half*2,$half*2+1);
        undef @pair{@individual[$pos1,$pos2]};
        my @pair = keys %pair;
        my ($minor,$major) = @alleles[$pos1,$pos2];
        if (@pair == 1) {
            if ($pair[0] eq $minor) {
                print 0;
            } elsif ($pair[0] eq $major) {
                print 2;
            } else {
                print -1;
            }
        } else {
            if (exists $pair{$minor} and exists $pair{$major}) {
                print 1;
            } else {
                print -1;
            }
        }
        print ' ';
    }
    print "\n";
}
[download]

use Modern::Perl;

# Process the second file only once
my @alleles;
{
    open my $secondfile, '<', './secondfile.txt' or die "Could not ope
+n 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 firs
+t 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;
}
[download]

By the way, when running this script on the data you provided it appears that the data for the second individual is quite wrong: it cannot have these alleles at these places, since they do not match what is in the second file.

Finally, writing the results to a file is left as an exercise for the readers.