scripts/biosql/load_interpro.pl

   1 # $Id$
   2 #
   3 # Cared for by Juguang Xiao, juguang@tll.org.sg
   4 #
   5 # Copyright Juguang Xiao
   6 #
   7 # You may distribute this script under the same terms as perl itself
   8
   9 #
  10 # Note that the functionality of using the SAX event handler for
  11 # parsing InterPro should by now be integrated into the main
  12 # load_ontology.pl script. Let me know if that doesn't work for you
  13 # for some reason.
  14 #
  15 # I'll leave this script here around for a while until there is enough
  16 # evidence that it all works through load_ontology.pl as well, so don't be
  17 # confused.
  18 #
  19 # -Hilmar, hlapp at gmx.net
  20 #
  21 use strict;
  22 use Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler;
  23 use XML::Parser::PerlSAX;
  24 use Bio::DB::EasyArgv;
  25 use Getopt::Long;
  26
  27
  28 my $db = get_biosql_db_from_argv;
  29 my ($file, $version);
  30 GetOptions(
  31     'file=s' => \$file,
  32     'version=s' => \$version
  33 );
  34
  35 my $handler = Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler->new(
  36     -db => $db,
  37     -version => "version $version"
  38 );
  39 my $parser = XML::Parser::PerlSAX->new(Handler=>$handler);
  40 my $ret = $parser->parse(Source=>{SystemId=>$file});