Presumably you are calling your sub like this:

versatility( %hash1, %hash2 );
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That doesn't work. All the keys and values will be assigned to %genome1 inside the subroutine and %genome2 will get nothing.

You need to re-write your subroutine to take hash references:

sub versatility {
    my( $genome1, $genome2 ) = @_;
    
    for my $key ( keys %{ $genome1 } ) {
        my @genome1 = $genome1->{ $key } =~ /(\d+)/g;
        my @genome2 = $genome2->{ $key } =~ /(\d+)/g;
        my $m = ( $genome1[1] - $genome2[1] ); 
        my $n = ( $genome1[0] - $genome2[0] );
        if( $n == 0 ){
            print "number of occurance for $key in two genome are same
+\n";
        } 
        else{
            my $slope = $m / $n;
            print "domain versatility= $slope\n";
        } 
    }
}
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And then call it like this:

versatility( \%hash1, \%hash2 );
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(BTW: Do start adding some horizontal whitespace into your code. It makes it so much more readable. Maybe then people would recognise your subroutine as a subroutine :)

I don't see any subroutine in your code, so I don't know how it relates to your problem. Update: That's because I I can't read, but the advice stays the same.

But judging from the text you'll likely need to pass the hashes as references. perlreftut teaches you how.

hi mortiz, you always adress me to that page and i always read that but still i ahve problem.:-(

this is my main script that i used this subroutine

#!/usr/bin/perl -w
use strict;

my %genome1;
my %genome2;
my @files;
my $file;
#input first genome file name.
print "Enter the first genome fasta file=\n";
my $filename=<>;
#analyze the genome.getting domains,number of domains and their combin
+ations.
analyze_genome($filename);
%genome1=n_nn();
for my $key (keys %genome1){
print "$genome1{$key}\n";
}
#delet useless files.
@files = ("domainlist","result","first");
for my $file (@files) {
    unlink $file
       or warn "Couldn't remove '$file': $!";
};



#input second genome file name.
print"Enter the second genome fasta file=\n";
$filename=<>;
analyze_genome($filename);
%genome2=n_nn();
#delet usless files.
@files = ("domainlist","result","first");
for my $file (@files) {
   unlink $file
       or warn "Couldn't remove '$file': $!";
};

#calculate domain versatility for each domain in the genomes.
versatility(%genome1,%genome2);
exit;
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