As pg said, use hash refs like so: 
%majCodon = calMajCodon(\%genes, \%codonTotal);

sub calMajCodon {
    # To just use the hash refs (and save memory) ... 
    my ($genes, $codonTotal) = @_;
    print $codonTotal->{startCodon};
    
    # ... or to use as regular hashes.
    my %genes = %{$_[0]};
    my %codonTotal = %{$_[1]};
    print $codonTotal{startCodon};
    
    # And to return a hash...
    return %majCodons;
}

[download]
See perlref.

Update Fixed ambiguous use of shift as pointed out by the anony monk.

In reply to Re: passing two hashs to a subroutine by The Mad Hatter
in thread passing two hashs to a subroutine by Anonymous Monk

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