Hi guys. I have finally managed to assemble this code with some help. 
my %supermatrix; 
my $list = "LIST.txt";
open my $DATA, '<', $list or die "unable to open my list $list $!\n"; 
print "\nWORKING ON $list\n";
print `head $list`;
while (my $line = <$DATA>)  { 
     chomp $line; 
     
     my $substrate = 1 if $line =~ /substrate.*(\d+)$/;
     print "SUBSTRATE ===$substrate";  
     $line = <DATA>; # fetch next line
     print "PRODUCT====$line"; 
     my @products; 
     (undef, @products) = split / /, $line; 
     foreach my $prod (@products) { 
          $supermatrix{$substrate}{$prod} = 1;
          
          print "combination $substrate $prod exists ! \n" if exists $
+supermatrix{$substrate}{$prod};
     } 
}

[download]

But there are two problems :-

1.] Its not printing any output.

2.] My list would at max be ~5 to 10% smaller than superarrays(whereas this code will handle output data sparsely). Also I need the output in such a format that there are blanks wherever there isnt a "1".

Actually the quality of the output depends on the number of blanks also, because this output will be then compared to other 20 such outputs. So in that sense the position of "blanks" and "1" is equally important.

In reply to Re^2: A complicated file parsing and 2D array/matrix problem. by zing
in thread A file parsing and 2D array/matrix problem. by zing

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