t/Node.t

   1 # This is -*-Perl-*- code#
   2 # Bioperl Test Harness Script for Modules
   3 # $Id$
   4
   5 use strict;
   6
   7 BEGIN {
   8         use Bio::Root::Test;
   9         test_begin(-tests => 32,
  10                            -requires_module => 'Graph');
  11
  12         use_ok('Bio::Network::ProteinNet');
  13         use_ok('Bio::Network::Node');
  14         use_ok('Bio::Seq');
  15 }
  16
  17 my $verbose = test_debug();
  18
  19 my $seq1 = Bio::Seq->new(-seq => "aaaaaaa",-display_id => 1);
  20 my $seq2 = Bio::Seq->new(-seq => "ttttttt",-display_id => 2);
  21 my $seq3 = Bio::Seq->new(-seq => "ggggggg",-display_id => 3);
  22
  23 #
  24 # 1 protein
  25 #
  26 my $node = Bio::Network::Node->new(-protein => $seq1);
  27 ok $node->is_complex == 0;
  28 my $count = $node->proteins;
  29 ok $count == 1;
  30
  31 my @proteins = $node->proteins;
  32 ok $proteins[0]->seq eq "aaaaaaa";
  33 ok $proteins[0]->display_id == 1;
  34 is $node->subunit_number($proteins[0]), undef;
  35 $node->subunit_number($proteins[0],52);
  36 ok $node->subunit_number($proteins[0]) == 52;
  37
  38 #
  39 # 1 or more proteins, but no subunit composition
  40 #
  41 $node = Bio::Network::Node->new(-protein => [($seq1,$seq2,$seq3)]);
  42 ok $node->is_complex == 1;
  43 @proteins = $node->proteins;
  44 my $x = 0;
  45 my @seqs = qw(aaaaaaa ggggggg ttttttt);
  46 for my $protein (@proteins) {
  47         ok $protein->seq eq $seqs[$x++];
  48         is $node->subunit_number($protein), undef;
  49 }
  50 $count = $node->proteins;
  51 ok $count == 3;
  52
  53 $node = Bio::Network::Node->new(-protein => [($seq1)]);
  54 ok $node->is_complex == 0;
  55
  56 #
  57 # 1 or more proteins, specifying subunit composition
  58 #
  59 $node = Bio::Network::Node->new(-protein => [ [($seq1, 2) ],
  60                                                                                                                   [ ($seq2, 3) ],
  61                                                                                                                   [ ($seq3, 1)] ]);
  62 ok $node->is_complex == 1;
  63 @proteins = $node->proteins;
  64 $x = 0;
  65 @seqs = qw(aaaaaaa ggggggg ttttttt);
  66 my @nums = (2,1,3);
  67 for my $protein (@proteins) {
  68         ok $protein->seq eq $seqs[$x];
  69         ok $node->subunit_number($protein) == $nums[$x++];
  70 }
  71 $count = $node->proteins;
  72 ok $count == 3;
  73
  74 $node = Bio::Network::Node->new(-protein => [ [($seq3, 1)] ]);
  75 ok $node->is_complex == 0;
  76 ok $node->proteins == 1;
  77
  78 $node = Bio::Network::Node->new(-protein => [ [($seq3, 1)],
  79                                                                                                                   [($seq2, 1)] ] );
  80 ok $node->is_complex == 1;
  81 ok $node->proteins == 2;
  82 $node->is_complex(0);
  83 ok $node->is_complex == 0;
  84
  85 $node->subunit_number($seq2,2);
  86 ok $node->subunit_number($seq2) == 2;
  87
  88 __END__
  89