This is my go at your questions. For the first one:

#!/usr/bin/perl -w

use strict;
use warnings;

my %hash;
while (<DATA>) {
    my ($coord, $dist) = split;
    $hash{$coord} = $dist 
        unless defined $hash{$coord} && $dist > $hash{$coord};
}

print "$_\t$hash{$_}\n" foreach (sort { $a <=> $b } keys %hash);


__DATA__
567         344  
1345        567
2346        78   
3456        67 
3456        789
4678        45    
5349        6
6700        124 
6700        50
8964        560

[download]

What's important to notice here is that the distance for the coordinate is saved every time except when the coordinate already has a distance and the new distance is larger than the one already saved.

For the second question, where you add more columns... well, you need either a hash or an array to accommodate those. But the idea is the same:

#!/usr/bin/perl -w

use strict;
use warnings;

my %hash;

while (<DATA>) {
    my ($coord, @cols) = split;
    $hash{$coord} = \@cols
        unless (defined $hash{$coord} && $cols[0] > $hash{$coord}[0]);
}

print join "\t", qw(coord dist chr exons palindromes), "\n";
print join "\t", $_, @{$hash{$_}},"\n" 
    foreach (sort {$a <=> $b} keys %hash);

__DATA__
567         344     5   7     8 
1345        567     5   8     123
2346        78      12  1     567
3456        67      10  1     5
3456        789     10  3     6
4678        45      6   2     0
5349        6       8   2     14
6700        124     13  8     56
6700        50      13  1     4
8964        560     2   18    8

[download]

Here I chose a hash of arrays.

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

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