Try using eval() instead, since you are trying to also pass a few arguments to the GraphViz methods:

use GraphViz; 
my $g = GraphViz->new(); 
foreach $command (@commands) {
 eval('$g->'.$command);
 }
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I'm sure this should work as I did try something similar on CGI module. Here's the code that I used to test it on:

use strict;
use CGI;
my @comm = ("header('first')","header('second')");
my $cgi = new CGI;
foreach my $comm (@comm) {
    eval('print $cgi->'.$comm);
}
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The output would be:

Content-Type: first

Content-Type: second
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This also works...

my $comm = "header";
print $cgi->$comm('third');
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however, this won't work:

 my $comm = "header('third')";
 print $cgi->$comm
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Cause the last "'" character in the $comm string is considered by Perl to be equivalent to '::' package separator. Therefore, perl is attempting to locate method ")" via package "header('third')" ;-)

"There is no system but GNU, and Linux is one of its kernels." -- Confession of Faith