Here a version if the number of switches is not known upfront. 

use strict;
use warnings;

my $max = 0;
my $data;
while(<DATA>){
        chomp;
        my @array = split /\s/;
        my @line = ( shift @array );
        $line[$_] = 1 for @array;  
        $max = @line > $max ? @line : $max;
        push @$data, \@line;
}
for my $row (@$data) {
        print $row->[$_]//0 ," " for (0..$max-1);
        print "\n";
}

__DATA__
run1 2 4
run2 1 6
run3 1
run4 1 3
run5 2 5

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In reply to Re: generating rows(matrix) based on file content by hdb
in thread generating rows(matrix) based on file content by zing

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