#!/usr/bin/perl

use strict;

my @files = qw/foo bar/;  # get file names from somewhere
my @matrix;

for my $f ( 0 .. $#files ) {
    open( IN, "<", $files[$f] ) or die "$files[$f]: $!\n";
    while (<IN>) {
        my ( $line, @vals ) = split;
        for my $v ( 0..$#vals ) {
            $matrix[$v][$line][$f] = $vals[$v];
        }
    }
}
for my $v ( 0..$#matrix ) {
    open( OUT, ">", "var.$v" ) or die "var.$v: $!\n";
    for my $line ( @{$matrix[$v]} ) {
        print OUT join( "\t", $line, @{$matrix[$v][$line]} ), "\n";
    }
    close OUT;
}