t/Interaction.t

   1 # This is -*-Perl-*- code#
   2 # Bioperl Test Harness Script for Modules
   3 # $Id$
   4
   5 use vars qw($NUMTESTS $DEBUG $ERROR);
   6 use strict;
   7 $DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
   8
   9 BEGIN {
  10         # to handle systems with no installed Test module
  11         # we include the t dir (where a copy of Test.pm is located)
  12         # as a fallback
  13         eval { require Test; };
  14         $ERROR = 0;
  15         if ( $@ ) {
  16                 use lib 't';
  17         }
  18         use Test;
  19         $NUMTESTS = 17;
  20         plan tests => $NUMTESTS;
  21         eval { require Graph; };
  22         if ($@) {
  23                 warn "Perl's Graph needed for the bioperl-network package, skipping tests";
  24                 $ERROR = 1;
  25         }
  26 }
  27
  28 END {
  29         foreach ( $Test::ntest..$NUMTESTS) {
  30                 skip("Missing dependencies. Skipping tests",1);
  31         }
  32 }
  33
  34 exit 0 if $ERROR ==  1;
  35
  36 require Bio::Network::ProteinNet;
  37 require Bio::Network::Interaction;
  38 require Bio::Network::Node;
  39 require Bio::Seq;
  40 require Bio::Annotation::Collection;
  41 require Bio::Annotation::OntologyTerm;
  42
  43 my $verbose = 0;
  44 $verbose = 1 if $DEBUG;
  45
  46 ok 1;
  47
  48 my $g = Bio::Network::ProteinNet->new();
  49
  50 my $seq1 = Bio::Seq->new(-seq => "aaaaaaa");
  51 my $seq2 = Bio::Seq->new(-seq => "ttttttt");
  52 my $seq3 = Bio::Seq->new(-seq => "ccccccc");
  53
  54 my $node1 = Bio::Network::Node->new(-protein => $seq1);
  55 my $node2 = Bio::Network::Node->new(-protein => [($seq2,$seq3)]);
  56
  57 my $interx = Bio::Network::Interaction->new(-weight => 2,
  58                                                                                                                 -id => "A");
  59 $g->add_interaction(-nodes => [($node1,$node2)],
  60                                                   -interaction => $interx);
  61
  62 $interx = Bio::Network::Interaction->new(-weight => 3,
  63                                                                                                                 -id => "B");
  64 $g->add_interaction(-nodes => [($node1,$node2)],
  65                                                   -interaction => $interx);
  66
  67 $interx = $g->get_interaction_by_id("A");
  68
  69 ok $interx->primary_id, "A";
  70 ok $interx->object_id, "A";
  71 ok $interx->weight, 2;
  72 my @nodes = $interx->nodes;
  73 ok $#nodes, 1;
  74 my @proteins = $nodes[0]->proteins;
  75 ok $proteins[0]->seq, "aaaaaaa";
  76 @proteins = $nodes[1]->proteins;
  77 ok $proteins[0]->seq, "ttttttt";
  78
  79 my $nodes = $interx->nodes;
  80 ok $nodes, 2;
  81 #
  82 # set values
  83 #
  84 $interx->primary_id("B");
  85 ok $interx->primary_id, "B";
  86 $interx->weight(7);
  87 ok $interx->weight, 7;
  88 #
  89 # check that Bio::Seq objects are automatically converted to Nodes
  90 #
  91 $interx = Bio::Network::Interaction->new(-weight => 2,
  92                                                                                                           -id => "C");
  93 $g->add_interaction(-nodes => [($seq1,$seq2)],
  94                                                   -interaction => $interx);
  95
  96 $interx = $g->get_interaction_by_id("C");
  97 ok $interx->primary_id, "C";
  98 #
  99 # add and remove Annotations
 100 #
 101 my $comment = Bio::Annotation::Comment->new;
 102 $comment->text("Reliable");
 103 my $coll = Bio::Annotation::Collection->new();
 104 $coll->add_Annotation('comment',$comment);
 105 ok $interx->annotation($coll);
 106 my @anns = $coll->get_Annotations('comment');
 107 ok scalar @anns, 1;
 108 ok $anns[0]->as_text, "Comment: Reliable";
 109 my @keys = $coll->get_all_annotation_keys;
 110 ok $keys[0],'comment';
 111 $coll->remove_Annotations('comment');
 112 @anns = $coll->get_Annotations('comment');
 113 ok scalar @anns, 0;
 114
 115 my $term = Bio::Annotation::OntologyTerm->new
 116 (-term => "",
 117  -name => "N-acetylgalactosaminyltransferase",
 118  -label => "test",
 119  -identifier => "000045",
 120  -definition => "Catalysis of galactossaminylation",
 121  -ontology => "GO",
 122  -tagname => "cellular component");
 123 $coll->add_Annotation($term);
 124 ok $interx->annotation($coll);
 125
 126
 127 __END__