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SENDU / bioperl-1.5.2_005-RC / t / InterProParser.t 

            

              
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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $GNF: projects/gi/symgene/src/perl/seqproc/t/InterProParser.t,v 1.7 2003/02/07 22:05:58 pdimitro Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
my $error;
use lib '..','.','./blib/lib';
use vars qw($NUMTESTS $DEBUG $HAVEGRAPHDIRECTED $errmsg);
$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
BEGIN {
        $errmsg = 'Unable to run Interpro Tests';
   # to handle systems with no installed Test module
   # we include the t dir (where a copy of Test.pm is located)
   # as a fallback
   eval { require Test; };
   $error = 0;
   if( $@ ) {
      use lib 't';
   }
   use Test; 
   $NUMTESTS = 47;
   plan tests => $NUMTESTS;
   eval {
      require XML::Parser::PerlSAX;
   };
   if ( $@ ) {
      warn( "XML::Parser::PerlSAX not installed. This means that InterPro Ontology Parsing module is not usable. Skipping tests.\n") if $DEBUG;
      $errmsg .= ', XML::Parser::PerlSAX not installed';
      $error = 1;
   }
   eval {
      require XML::Parser;
   };
   if( $@ ) {
      warn "XML::Parser not installed. This means that InterPro Ontology Parsing module is not usable. Skipping tests.\n" if $DEBUG;
      $error = 1;
      $errmsg .= ', XML::Parser not installed';
   }
        eval {require Graph::Directed; 
                        $HAVEGRAPHDIRECTED=1;
                };
        if ($@) {
                $errmsg .= ', Graph::Directed not installed';
                $HAVEGRAPHDIRECTED = 0;
                $error = 1;
        }
}
END {
   foreach ( $Test::ntest..$NUMTESTS) {
      skip($errmsg,1);
   }
}
if ( $error ) {
    exit(0);
}
require Bio::OntologyIO;
require Bio::Root::IO;
my $io = Bio::Root::IO->new();
ok (1);
my $ipp = Bio::OntologyIO->new( -format => 'interpro',
                                                                                  -file =>
                                                                                  $io->catfile('t','data','interpro_short.xml'),
                                                                                  -ontology_engine => 'simple' );
ok ($ipp);
my $ip;
while(my $ont = $ipp->next_ontology()) {
    # there should be only one ontology
    ok ($ip, undef);
    $ip = $ont;
}
#print $ip->to_string."\n";
my @rt = sort { $a->name cmp $b->name; } $ip->get_root_terms();
# there should be 4 root terms: InterPro Domain, InterPro Family,
# InterPro Repeat, and InterPro PTM (Post Translational Modification)
#
# I added 2 more terms, Active_site and Binding_site. -Juguang
ok (scalar(@rt), 6);
# every InterPro term should have an ontology,
foreach ($ip->get_leaf_terms, @rt) {
        ok ($_->ontology);
        ok ($_->ontology->name, "InterPro",
                 "term ".$_->name." not in ontology InterPro");
}
# there are 6 fully instantiated InterPro terms in total, which should be returned as the leafs
ok (scalar($ip->get_leaf_terms()), 8);
# roots and leafs together:
ok (scalar($ip->get_all_terms()), 13);
# descendants and children (synonymous here because of depth 1)
# note that the sort should have placed Domain first and Family second
ok (scalar($ip->get_descendant_terms($rt[2])), 4); # 4 InterPro Domains
ok (scalar($ip->get_child_terms($rt[2])), 4);      # dto.
ok (scalar($ip->get_descendant_terms($rt[3])), 3); # 3 Interpro Family
ok (scalar($ip->get_child_terms($rt[3])), 3);      # dto.
# test for ancestors and parents (synonymous here because of depth 1)
foreach my $t ($ip->get_leaf_terms) {
        # every InterPro term has exactly one parent - namely either 
        # Domain, Family, Repeat, or PTM(Post Transl. Modification)
        if (!($t->identifier eq "Repeat" || $t->identifier eq "PTM" 
                        || $t->identifier eq'Active_site' || $t->identifier eq'Binding_site')) {
                ok (scalar($ip->get_parent_terms($t)), 1);
                ok (scalar($ip->get_ancestor_terms($t)), 1);
        }
}
# test for secondary accession map
ok(scalar(keys %{$ipp->secondary_accessions_map}), 2);