Something like this would work:

# I would greatly appreciate any help. The file that I am trying to
# alter is in the format
#     23 SNP_A-4293670 0 2713391
# with separation by tabs. The second file is in the format
#     SNP_A-1780270 ss75925050 rs987435
# with separation by spaces. I want the first file to look like this:
#     23 rs###### 0 2713391
# which means that I want the data in second column of the first
# file to be replaced with the data in the third column of the second
# file if it matches the first column of the second file. Thanks

use File::Slurp qw(read_file);
use Tie::File;

use strict;

my $file1 = 'file1.txt';
my $file2 = 'file2.txt';

my %hash = map {
    chomp;
    my @data = split /\s+/;
    $data[0] => $data[2];
} read_file($file2);

tie my @array, 'Tie::File', $file1 or die "Can't open $file1: $!";

foreach (@array) {
    s{^(\S*\s+)(\S+)}{
        if (exists $hash{$2}) {
            print "Replacing $2 with $hash{$2}\n";
            $1 . $hash{$2};
        } else {
            print "Can't find $2, not changing\n";
            $1 . $2;
        }
    }e;
}
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- Miller