If the order of the pair is not important, always store the lesser number first. 
#!/usr/bin/perl
use warnings;
use strict;

my %count;
while (<>) {
    my @F1 = split /\t/;
    my @F2 = split /\t/, <>;

    my ($num, $from, $to) = (@F1[ 1, 2 ], $F2[2] );
    ($from, $to) = ($to, $from) if $from > $to;
    ++$count{$num}{$from}{$to};
}

[download]

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,

[download]

In reply to Re: Tallying co-occurence of numbers by choroba
in thread Tallying co-occurence of numbers by K_Edw

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