A little late, but wanted to show a slightly different way. Really, much of it follows liverpole's ideas but saves the data as it's string instead of an array of values.

Chris 

#!/usr/bin/perl
use strict;
use warnings;
use File::Basename;
use Sort::Naturally;

my %data;
my $table;
my %col_cnt;

@ARGV = glob "tab*.txt";

while (<>) {
    next if /^ID/;
    chomp;
    ($table = fileparse $ARGV) =~ s/\.txt$// unless $table;
    $col_cnt{$table} ||=  tr/|//;
    
    my ($gene, $cols) = split /\s*\|\s*/, $_, 2;
    $data{$gene}{$table} = $cols;
    $table = '' if eof;
}

my @tables = nsort keys %col_cnt;

for my $gene (nsort keys %data) {
    print $gene;
    for my $table (@tables) {
        if ($data{$gene}{$table}) {
            print ' | ' . $data{$gene}{$table};
        }
        else {
            print ' | ' . join " | ", ("n.a.") x $col_cnt{$table};
        }
    }
    print "\n";
}

[download]
Update: Changed from storing the output in a string and waiting until the the entire output was stored and then printed to printing as the program proceeds.

Update: Changed from built-in sort to 'nsort' (use Sort::Naturally). If the fields being sorted have part of their name a number exceeding 9,(gene1 gene2 gene9 gene10) or (tab1 tab2...tab11 tab12), they won't sort properly using the default sort.

In reply to Re: Merging/Rearranging Tables by Cristoforo
in thread Merging/Rearranging Tables by homeveg

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