#!/usr/bin/perl
use warnings;
use strict;

open my $GENES,     '<', 'genes'     or die $!;
open my $LOCATIONS, '<', 'locations' or die $!;

chomp(my @locations = map { (split ' ')[1] } <$LOCATIONS>);
# If IDs are not already sorted, uncomment the following line:
# @locations = sort { $a <=> $b } @locations;

for (<$GENES>) {
    my ($chromosome, $start, $end) = split ' ';
    print "$chromosome\t$start\t$end";
    my $idx = 0;        # For $end, start searching where you left for
+ $start.
    my $correction = 0; # Needed for Start(-) == Start and End(+) == E
+nd.
    for my $pos ($start, $end) {
        $idx++ while $locations[$idx] <= $pos - $correction
                     and $idx <= $#locations;
        die "No numbers around $pos ($idx)\n"
            if $idx == 0 or $idx > $#locations;
        print "\t$locations[$idx-1]\t$locations[$idx]";
        $correction = 1;
    }
    print "\n";
}
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