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,
  11                -requires_modules => [qw(URI::Escape Graph::Directed)],
  12                -requires_networking => 1
  13         );
  14
  15         use_ok('Bio::SeqFeature::Generic');
  16         use_ok('Bio::SeqFeature::Annotated');
  17 }
  18
  19 my $sfa = Bio::SeqFeature::Annotated->new(-start => 1,
  20                                           -end => 5,
  21                                           -strand => "+",
  22                                           -frame => 2,
  23                                           -type => 'nucleotide_motif',
  24                                           -phase => 2,
  25                                           -score => 12,
  26                                           -source => 'program_b',
  27                                           -display_name => 'test.annot',
  28                                           -seq_id => 'test.displayname' );
  29
  30 ok (defined $sfa);
  31 my $loc = $sfa->location;
  32 ok $loc->isa("Bio::Location::Simple");
  33 ok $sfa->display_name eq 'test.annot';
  34
  35 #test bsfa::from_feature
  36 my $sfg = Bio::SeqFeature::Generic->new ( -start => 400,
  37                                           -end => 440,
  38                                           -strand => 1,
  39                                           -primary => 'nucleotide_motif',
  40                                           -source  => 'program_a',
  41                                           -tag => {
  42                                           silly => 20,
  43                                           new => 1
  44                                           }
  45                                           );
  46 my $sfa2;
  47 $sfa2 = Bio::SeqFeature::Annotated->new(-feature => $sfg);
  48
  49 is $sfa2->type->name,'nucleotide_motif';
  50 is $sfa2->primary_tag, 'nucleotide_motif';
  51 is $sfa2->source->display_text,'program_a';
  52 is $sfa2->source_tag,'program_a';
  53 is $sfa2->strand,1;
  54 is $sfa2->start,400;
  55 is $sfa2->end,440;
  56 is $sfa2->get_Annotations('silly')->value,20;
  57 is $sfa2->get_Annotations('new')->value,1;
  58 my $sfaa = Bio::SeqFeature::Annotated->new(-feature => $sfa);
  59 is $sfaa->type->name,'nucleotide_motif';
  60 is $sfaa->primary_tag, 'nucleotide_motif';
  61 is $sfaa->source->display_text,'program_b';
  62 is $sfaa->source_tag,'program_b';
  63 is $sfaa->strand,1;
  64 is $sfaa->start,1;
  65 is $sfaa->end,5;
  66 is $sfaa->score,12;
  67
  68 my $sfa3 = Bio::SeqFeature::Annotated->new( -start => 1,
  69                                         -end => 5,
  70                                         -strand => "+",
  71                                         -frame => 2,
  72                                         -phase => 2,
  73                                         -score => 12,
  74                                         -display_name => 'test.annot',
  75                                         -seq_id => 'test.displayname' );
  76 $sfa3->from_feature($sfg);
  77
  78 is $sfa3->type->name,'nucleotide_motif', 'type->name';
  79 is $sfa3->primary_tag, 'nucleotide_motif', 'primary_tag';
  80 is $sfa3->source->display_text,'program_a';
  81 is $sfa3->source_tag,'program_a';
  82 is $sfa3->strand,1;
  83 is $sfa3->start,400;
  84 is $sfa3->end,440;
  85 is $sfa3->get_Annotations('silly')->value,20;
  86 is $sfa3->get_Annotations('new')->value,1;
  87
  88 # Note there is an API conflict with SeqFeature::Generic, where score is a
  89 # simple scalar, and here it is a Bio::Annotation::SimpleValue
  90 # By popular vote there is no operator overloading, so this needs to be
  91 # resolved
  92 is $sfa3->score(), 12;
  93 $sfa3->score(11);
  94 is $sfa3->score(), 11;
  95 $sfa3->score(0);
  96 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)
  97