t/SeqFeatAnnotated.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7     use lib 't/lib';
   8     use BioperlTest;
   9
  10     test_begin(-tests => 34, -requires_modules => [qw(URI::Escape Graph::Directed)]);
  11
  12         use_ok('Bio::SeqFeature::Generic');
  13         use_ok('Bio::SeqFeature::Annotated');
  14 }
  15
  16 my $sfa = Bio::SeqFeature::Annotated->new(-start => 1,
  17                                           -end => 5,
  18                                           -strand => "+",
  19                                           -frame => 2,
  20                                           -type => 'nucleotide_motif',
  21                                           -phase => 2,
  22                                           -score => 12,
  23                                           -source => 'program_b',
  24                                           -display_name => 'test.annot',
  25                                           -seq_id => 'test.displayname' );
  26
  27 ok (defined $sfa);
  28 my $loc = $sfa->location;
  29 ok $loc->isa("Bio::Location::Simple");
  30 ok $sfa->display_name eq 'test.annot';
  31
  32 #test bsfa::from_feature
  33 my $sfg = Bio::SeqFeature::Generic->new ( -start => 400,
  34                                           -end => 440,
  35                                           -strand => 1,
  36                                           -primary => 'nucleotide_motif',
  37                                           -source  => 'program_a',
  38                                           -tag => {
  39                                           silly => 20,
  40                                           new => 1
  41                                           }
  42                                           );
  43 my $sfa2;
  44 $sfa2 = Bio::SeqFeature::Annotated->new(-feature => $sfg);
  45
  46 is $sfa2->type->name,'nucleotide_motif';
  47 is $sfa2->primary_tag, 'nucleotide_motif';
  48 is $sfa2->source->display_text,'program_a';
  49 is $sfa2->source_tag,'program_a';
  50 is $sfa2->strand,1;
  51 is $sfa2->start,400;
  52 is $sfa2->end,440;
  53 is $sfa2->get_Annotations('silly')->value,20;
  54 is $sfa2->get_Annotations('new')->value,1;
  55 my $sfaa = Bio::SeqFeature::Annotated->new(-feature => $sfa);
  56 is $sfaa->type->name,'nucleotide_motif';
  57 is $sfaa->primary_tag, 'nucleotide_motif';
  58 is $sfaa->source->display_text,'program_b';
  59 is $sfaa->source_tag,'program_b';
  60 is $sfaa->strand,1;
  61 is $sfaa->start,1;
  62 is $sfaa->end,5;
  63 is $sfaa->score,12;
  64
  65 my $sfa3 = Bio::SeqFeature::Annotated->new( -start => 1,
  66                                         -end => 5,
  67                                         -strand => "+",
  68                                         -frame => 2,
  69                                         -phase => 2,
  70                                         -score => 12,
  71                                         -display_name => 'test.annot',
  72                                         -seq_id => 'test.displayname' );
  73 $sfa3->from_feature($sfg);
  74
  75 is $sfa3->type->name,'nucleotide_motif', 'type->name';
  76 is $sfa3->primary_tag, 'nucleotide_motif', 'primary_tag';
  77 is $sfa3->source->display_text,'program_a';
  78 is $sfa3->source_tag,'program_a';
  79 is $sfa3->strand,1;
  80 is $sfa3->start,400;
  81 is $sfa3->end,440;
  82 is $sfa3->get_Annotations('silly')->value,20;
  83 is $sfa3->get_Annotations('new')->value,1;
  84
  85 # Note there is an API conflict with SeqFeature::Generic, where score is a
  86 # simple scalar, and here it is a Bio::Annotation::SimpleValue
  87 # By popular vote there is no operator overloading, so this needs to be
  88 # resolved
  89 is $sfa3->score(), 12;
  90 $sfa3->score(11);
  91 is $sfa3->score(), 11;
  92 $sfa3->score(0);
  93 is $sfa3->score(), 0;   # test that setting to 0 no longer is overriddent to set score to '.' (fixed in Bio::SeqFeature::Annotated version 1.3.7)
  94