t/Ensembl.t

   1 # -*-Perl-*-
   2 ## Bioperl Test Harness Script for Modules
   3
   4 use strict;
   5
   6 BEGIN {
   7     use Bio::Root::Test;
   8     test_begin(-tests => 7,
   9                -requires_networking => 1);
  10     use_ok('Bio::Tools::Run::Ensembl');
  11 }
  12
  13 my $setup_ok = Bio::Tools::Run::Ensembl->registry_setup();
  14
  15 # test database access
  16 SKIP: {
  17     test_skip(-tests => 6, -requires_module => 'Bio::EnsEMBL::Registry');
  18     skip("There was some problem contacting the EnsEMBL database?", 6) unless $setup_ok;
  19
  20     # get an adaptor
  21     ok my $adaptor = Bio::Tools::Run::Ensembl->get_adaptor('human', 'Exon');
  22     isa_ok $adaptor, 'Bio::EnsEMBL::DBSQL::ExonAdaptor';
  23     if ($adaptor->can('species_id')) {
  24         is $adaptor->species_id, 1;
  25     }
  26     else {
  27         ok 1;
  28     }
  29
  30     # get an 'easy' gene - one that is in Ensembl
  31     ok my $gene = Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human',
  32                                                              -name => 'BRCA2');
  33     isa_ok $gene, 'Bio::EnsEMBL::Gene';
  34     is $gene->external_name, 'BRCA2';
  35
  36
  37     #*** don't know suitable gene names to test the following, to be completed...
  38
  39     # get one that isn't in human, but is in an orthologue
  40     my $orth_only = '??';
  41     #ok ! Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human',
  42     #                                                -name => $orth_only);
  43     #ok $gene = Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human',
  44     #                                                      -use_orthologues => 'Mus musculus',
  45     #                                                      -name => $orth_only);
  46     #is $gene->external_name, $orth_only;
  47
  48     # get one that isn't in Ensembl but is in Swissprot
  49     my $swiss_only = '??';
  50     #ok ! Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human',
  51     #                                                -use_orthologues => 'Mus musculus',
  52     #                                                -name => $swiss_only);
  53     #ok $gene = Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human',
  54     #                                                      -use_orthologues => 'Mus musculus',
  55     #                                                      -use_swiss_lookup => 1,
  56     #                                                      -name => $swiss_only);
  57     #is $gene->external_name, $swiss_only;
  58
  59     # get one that isn't in Swissprot either, but is in NCBI
  60     my $ncbi_only = '??';
  61     #ok ! Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human',
  62     #                                                -use_orthologues => 'Mus musculus',
  63     #                                                -use_swiss_lookup => 1,
  64     #                                                -name => $ncbi_only);
  65     #ok $gene = Bio::Tools::Run::Ensembl->get_gene_by_name(-species => 'human',
  66     #                                                      -use_orthologues => 'Mus musculus',
  67     #                                                      -use_swiss_lookup => 1,
  68     #                                                      -use_entrez_lookup => 1,
  69     #                                                      -name => $ncbi_only);
  70     #is $gene->external_name,  $ncbi_only;
  71 }