t/Variation/AAChange.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7     use lib '.';
   8     use Bio::Root::Test;
   9
  10     test_begin(-tests => 27);
  11
  12         use_ok('Bio::Variation::Allele');
  13         use_ok('Bio::Variation::AAChange');
  14         use_ok('Bio::Variation::RNAChange');
  15 }
  16
  17
  18 ok my $obj = Bio::Variation::AAChange->new();
  19 isa_ok $obj, 'Bio::Variation::AAChange';
  20
  21 $obj->start(3);
  22 is $obj->start, 3;
  23
  24 $obj->end(3);
  25 is $obj->end, 3;
  26
  27 $obj->length(3);
  28
  29 is $obj->length, 3;
  30
  31 $obj->strand('1');
  32 is $obj->strand, '1';
  33
  34 is $obj->primary_tag, 'Variation';
  35
  36 $obj->source_tag('source');
  37 is $obj->source_tag, 'source';
  38
  39 $obj->frame(2);
  40 is $obj->frame,2;
  41
  42 $obj->score(2);
  43 is $obj->score, 2;
  44
  45 $obj->isMutation(1);
  46 ok $obj->isMutation;
  47
  48 my $a1 = Bio::Variation::Allele->new(-seq => 'V');
  49 $obj->allele_ori($a1);
  50
  51 is $obj->allele_ori->seq, 'V';
  52
  53 my $a2 = Bio::Variation::Allele->new('-seq' => 'A');
  54 $obj->add_Allele($a2);
  55
  56 is $obj->allele_mut->seq, 'A';
  57
  58 is $obj->similarity_score, 0;
  59
  60 $obj->upStreamSeq('upStreamSeq');
  61 is $obj->upStreamSeq, 'upStreamSeq';
  62
  63 $obj->dnStreamSeq('dnStreamSeq');
  64 is $obj->dnStreamSeq, 'dnStreamSeq' ;
  65
  66 is $obj->label, 'substitution, conservative';
  67
  68 $obj->status('proven');
  69 is $obj->status, 'proven';
  70
  71 $obj->proof('experimental');
  72 is $obj->proof, 'experimental';
  73
  74 $obj->region('region');
  75 is $obj->region, 'region';
  76
  77 $obj->region_value('region_value');
  78 is $obj->region_value, 'region_value';
  79
  80 $obj->numbering('coding');
  81 is $obj->numbering, 'coding';
  82
  83 my $obj2 = Bio::Variation::RNAChange->new(-start => 7,
  84                                           -end => 7,
  85                                           -cds_end => 100,
  86                                           -codon_pos => 1,
  87                                           -upStreamSeq => 'acgcgcgcgc',
  88                                           -dnStreamSeq => 'acgcgcgcgc'
  89                                           );
  90 $obj2->label('missense');
  91 $obj->RNAChange($obj2);
  92
  93 is $obj->trivname, 'V3A', "Trivial name is [". $obj->trivname. "]";
  94
  95 $obj->mut_number(2);
  96 is $obj->mut_number, 2;