Question

I am new to Perl and have never used a CPAN module before, I need to convert an OWL file to OBO format. I successfully installed the “ONTO-PERL-1.37” module. I want to use the following script:

use Carp;
use strict;
use warnings;

use OBO::Parser::OWLParser;

my $my_parser = OBO::Parser::OWLParser->new();
my $ontology = $my_parser->work(shift(@ARGV));
$ontology->export('obo');

exit 0;

END

My question is do i need to declare the input OWL file, if yes how can that be done for the above script?

Answer 1

This script takes the argument from the command line. This is what the shift(@ARGV) is for. shift removes the first element from a list and @ARGV is a list filled with the filename given as a command line argument, when running the script with perl owl2obo.pl my-ontology.owl.

If it easier, you can modify the script with

 my $ontology = $my_parser->work('/the/path/to/ontology.owl');

or

 my $owlfile = shift(@ARGV) || '/path/to/owlfile.owl';
 my $ontology = $my_parser->work($owlfile);

.