my %fnameof;
my %valueof;

my @relation;
my @second;

my $mainfile;
my $subfiles;
{
  open ($testdataset, "datasetnew.txt") or die "Cannot open file";
  @testdataset =  <$testdataset>;
  close ($testdataset);

  open (STDOUT, ">>result.txt");

    $fcount = 1;
    
    $secondcount = 0;
    
 
    @testdataset = grep { $_ ne '' } @testdataset;
    @testdataset = grep /\S/, @testdataset;
  
    foreach $dataline (@testdataset) {
        ($mainfile, $subfiles) = GetFileName($dataline);
        
        for ($mainfile) {
            $mainfile =~ s/^\s+//;
            $mainfile =~ s/\s+$//;
        }
        addtoHash($mainfile);
        
        @subfiles = @keywords = split(/;/, $subfiles);
        @subfiles = grep { $_ ne '' } @subfiles;
        @subfiles = grep /\S/, @subfiles;

        foreach $subfile (@subfiles) {
            $subfile =~ s/^\s+//;
            $subfile =~ s/\s+$//;
            addtoHash($subfile) unless ($_ ne '');
        }

        #defining the relation of mainfile with subfiles. Each mainfil
+e has relation weight = 1 with subfile.
        foreach $subfile (@subfiles) {
                $relation[$valueof{$mainfile}][$valueof{$subfile}] = 1
+;
                $second[$secondcount] = "$valueof{$mainfile};$valueof{
+$subfile}";
                $secondcount++;
        }
    }
    #creating transitive relationship. ie: if A->B and B->C, then A->C
    foreach  $seconditem (@second) {
            @test = split(/;/, $seconditem);
            $b = $test[0];
            $c = $test[1];

            for ($k = 1; $k<=$secondcount; $k++) {
                if ($relation[$c][$k] gt 0) {
                        $relation[$b][$k] = $relation[$b][$k]+1;
                }
            }
    }
    PrintArray();
}

#get mainfile and subfiles
sub GetFileName{
    my $item = $_[0];
    @datasplit = split(/\t/, $item);
    $mainfile = @datasplit[0];
    $subfiles = @datasplit[1];

    return ($mainfile, $subfiles);
}

sub addtoHash{
    my $file = $_[0];
    $exist = 0;
        for ($i = 0; $i < $fcount; $i++)
    {
                if ($fnameof{$i} eq $file)
                {
                    $exist = $i;
                }
    }
    if ($exist == 0)
    {
        $fnameof{$fcount}= $file;
              $valueof{$file} = $fcount;
              
               $fcount++;
    }
}

sub PrintArray(){

    for($i=1;$i<$fcount; $i++) {
        for($j=1;$j<$fcount;$j++){
            if (defined ($relation[$i][$j])) {
                print $fnameof{$i}."-".$relation[$i][$j]."->".$fnameof
+{$j}."\n";
            }
        }
    }
    print "\n";
}
[download]

 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]

First glance -

• add use strict; use warnings to your code then clean up the errors and warnings.
• don't use $a or $b as variable names - they are reserved for use by sort
• use the three parameter open
• where does $fcount in addtoHash get a value? Make it explicit by passing the value into the sub rather than relying on a global.
• Don't prototype PrintArray - especially after it's first use!
• you probably want chomp @testdataset; before @testdataset = grep { $_ ne '' } @testdataset;
• @testdataset = grep { $_ ne '' } @testdataset; is redundant when followed by @testdataset = grep /\S/, @testdataset;
• what does for ($mainfile) { achieve?
• You test if ($exist == 0), but $i can == 0 and therefore $exist can == 0 (in addtoHash)

You could describe the output you expect. Sometimes knowing what is expected of a piece of code helps understand it - sometimes it helps misunderstand it :)

Update: more items added

---

DWIM is Perl's answer to Gödel

The output of the program with the sample dataset I gave in the previous thread is:

cancer-1->breast cancer
cancer-1->lung cancer
cancer-1->heart cancer
cancer-1->stomach cancer
cancer-4->foot cancer
cancer-1->blood cancer
breast cancer-1->foot cancer
breast cancer-1->some cancer
lung cancer-1->foot cancer
lung cancer-2->some cancer
lung cancer-1->blood cancer
heart cancer-1->foot cancer
heart cancer-1->some cancer
stomach cancer-1->foot cancer
stomach cancer-1->some cancer
foot cancer-1->some cancer
blood cancer-1->some cancer
[download]

As you can see, I am trying to create transitive relationships, ie, If A->B, and B->C, then A->C. But I am also giving weight to the relationships, ie, if A->D, and D->C, then again A->C. So the relation [valueof{A}][valueof{C}]=2---->ie 1+1, because the relation was created twice.

I don't have time to look at it personally, at least not now, but the following will help you greatly. Change

   open ($testdataset, "datasetnew.txt") or die "Cannot open file";
   @testdataset =  <$testdataset>;
   close ($testdataset);

   @testdataset = grep { $_ ne '' } @testdataset;
   @testdataset = grep /\S/, @testdataset;
  
   foreach $dataline (@testdataset) {
[download]

to

   open (my $testdataset, '<', "datasetnew.txt")
      or die "Cannot open input file: $!\n";

   while (my $dataline = <$testdataset>) {
      next if $dataline =~ /^\s*$/;
[download]

You'll have (2 or 3) fewer copies of your file in memory.