G'day linseyr,

Welcome to the monastery.

This works with the data you've provided.

#!/usr/bin/env perl

use strict;
use warnings;

my %least_ref;

open my $reference, '<', $ARGV[0] or die "Can't open reference ($ARGV[
+0]): $!";

while (<$reference>) {
    my ($key, $val) = split;

    if (not exists $least_ref{$key} or $val < $least_ref{$key}) {
        $least_ref{$key} = $val;
    }
}

close $reference;

open my $testfile, '<', $ARGV[1] or die "Can't open testfile ($ARGV[1]
+): $!";

while (<$testfile>) {
    my ($key, $val) = split;

    print "$key\t", $least_ref{$key} - $val, "\n";
}

close $testfile;
[download]

Input files:

$ cat > pm_least_diff.ref
chr1    40
chr1    50
chr2    60
chr2    80
chr3    100
[download]

$ cat > pm_least_diff.test
chr1    30
chr2    20
chr2    50
chr3    80
[download]

Script output:

$ pm_least_diff.pl pm_least_diff.ref pm_least_diff.test
chr1    10
chr2    40
chr2    10
chr3    20
[download]