use warnings;
use strict;

open(my $COORD, "<", "coordinate.txt")
  or die("Couldn't read coordinate file - $!");
open(my $DIST, "<", "dist.txt")
  or die("Couldn't read distance file - $!");

my %coord;

until (eof $COORD)
{
    my $c = (split " ", scalar <$COORD>)[0];
    my $d = (split " ", scalar <$DIST>)[0];

    my $p = $coord{$c};
    $coord{$c} = $d
      if !defined($p) || $d < $p;
}

close($COORD);
close($DIST);

print "$_\t$coord{$_}\n"
  for sort { $a <=> $b } keys %coord;

[download]

Update: Better handling of data using split.

In reply to Re: Repeats exclusion by repellent
in thread Repeats exclusion by Grig

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