It's not entierly clear what you are tryng to achieve. But on the guess that it is something to do with finding transitive relationships in the data, the following may be of use:

use strict;
use warnings;

my %mappings;

while (<DATA>) {
    chomp;
    next if ! /\S/;
    
    s/^\s+//;
    s/\s+$//;
    my ($mainfile, $subfiles) = split /\s*,\s*/;
    my @subfiles = split /\s*;\s*/, $subfiles;
   
    $mappings{$mainfile} = [grep /\S/, @subfiles];
}

# Print transitive relationships. ie: if A->B and B->C, then A->C
for my $A (sort keys %mappings) {
    for my $B (@{$mappings{$A}}) {
        print " $A - $B -> @{$mappings{$B}}\n" if exists $mappings{$B}
+;
    }
}

__DATA__
 cancer,breast cancer; lung cancer; heart cancer; stomach cancer;
 breast cancer,foot cancer;
 foot cancer,some cancer;
 lung cancer,blood cancer; foot cancer;
 heart cancer,foot cancer;
 stomach cancer,foot cancer;
 blood cancer,some cancer;

[download]

Prints:

 breast cancer - foot cancer -> some cancer
 cancer - breast cancer -> foot cancer
 cancer - lung cancer -> blood cancer foot cancer
 cancer - heart cancer -> foot cancer
 cancer - stomach cancer -> foot cancer
 heart cancer - foot cancer -> some cancer
 lung cancer - blood cancer -> some cancer
 lung cancer - foot cancer -> some cancer
 stomach cancer - foot cancer -> some cancer

[download]
DWIM is Perl's answer to Gödel

In reply to Re: out of memory problem by GrandFather
in thread out of memory problem by perlbeginner10

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