t/Interaction.t

   1 # This is -*-Perl-*- code#
   2 # Bioperl Test Harness Script for Modules
   3
   4 use strict;
   5
   6 BEGIN {
   7         use Bio::Root::Test;
   8         test_begin(-tests => 23,
   9                            -requires_module => 'Graph');
  10
  11         use_ok('Bio::Network::ProteinNet');
  12         use_ok('Bio::Network::Interaction');
  13         use_ok('Bio::Network::Node');
  14         use_ok('Bio::Seq');
  15         use_ok('Bio::Annotation::Comment');
  16         use_ok('Bio::Annotation::Collection');
  17         use_ok('Bio::Annotation::OntologyTerm');
  18 }
  19
  20 my $verbose = test_debug();
  21
  22 my $g = Bio::Network::ProteinNet->new();
  23
  24 my $seq1 = Bio::Seq->new(-seq => "aaaaaaa");
  25 my $seq2 = Bio::Seq->new(-seq => "ttttttt");
  26 my $seq3 = Bio::Seq->new(-seq => "ccccccc");
  27
  28 my $node1 = Bio::Network::Node->new(-protein => $seq1);
  29 my $node2 = Bio::Network::Node->new(-protein => [($seq2,$seq3)]);
  30
  31 my $interx = Bio::Network::Interaction->new(-weight => 2,
  32                                                                                                                   -id => "A");
  33 $g->add_interaction(-nodes => [($node1,$node2)],
  34                                                   -interaction => $interx);
  35
  36 $interx = Bio::Network::Interaction->new(-weight => 3,
  37                                                                                                                 -id => "B");
  38 $g->add_interaction(-nodes => [($node1,$node2)],
  39                                                   -interaction => $interx);
  40
  41 $interx = $g->get_interaction_by_id("A");
  42
  43 ok $interx->primary_id eq "A";
  44 ok $interx->object_id eq "A";
  45 ok $interx->weight == 2;
  46 my @nodes = $interx->nodes;
  47 ok $#nodes == 1;
  48 my @proteins = $nodes[0]->proteins;
  49 ok $proteins[0]->seq eq "aaaaaaa";
  50 @proteins = $nodes[1]->proteins;
  51 ok $proteins[0]->seq eq "ttttttt";
  52
  53 my $nodes = $interx->nodes;
  54 ok $nodes == 2;
  55 #
  56 # set values
  57 #
  58 $interx->primary_id("B");
  59 ok $interx->primary_id eq "B";
  60 $interx->weight(7);
  61 ok $interx->weight == 7;
  62 #
  63 # check that Bio::Seq objects are automatically converted to Nodes
  64 #
  65 $interx = Bio::Network::Interaction->new(-weight => 2,
  66                                                                                                           -id => "C");
  67 $g->add_interaction(-nodes => [($seq1,$seq2)],
  68                                                   -interaction => $interx);
  69
  70 $interx = $g->get_interaction_by_id("C");
  71 ok $interx->primary_id eq "C";
  72 #
  73 # add and remove Annotations
  74 #
  75 my $comment = Bio::Annotation::Comment->new;
  76 $comment->text("Reliable");
  77 my $coll = Bio::Annotation::Collection->new();
  78 $coll->add_Annotation('comment',$comment);
  79 ok $interx->annotation($coll);
  80 my @anns = $coll->get_Annotations('comment');
  81 ok scalar @anns == 1;
  82 ok $anns[0]->as_text, "Comment: Reliable";
  83 my @keys = $coll->get_all_annotation_keys;
  84 ok $keys[0] eq 'comment';
  85 $coll->remove_Annotations('comment');
  86 @anns = $coll->get_Annotations('comment');
  87 ok scalar @anns == 0;
  88
  89 my $term = Bio::Annotation::OntologyTerm->new
  90 (-term => "",
  91  -name => "N-acetylgalactosaminyltransferase",
  92  -label => "test",
  93  -identifier => "000045",
  94  -definition => "Catalysis of galactossaminylation",
  95  -ontology => "GO",
  96  -tagname => "cellular component");
  97 $coll->add_Annotation($term);
  98 ok $interx->annotation($coll);
  99
 100
 101 __END__