t/SeqFeature/Amplicon.t

   1 use strict;
   2
   3 BEGIN {
   4     use Bio::Root::Test;
   5
   6     test_begin(-tests => 21);
   7
   8     use_ok 'Bio::PrimarySeq';
   9     use_ok 'Bio::SeqFeature::Primer';
  10     use_ok 'Bio::SeqFeature::Amplicon';
  11 }
  12
  13 my ($amplicon, $amplicon_seq, $fwd_primer, $rev_primer, $template);
  14
  15
  16 # Basic amplicon object
  17
  18 $amplicon = Bio::SeqFeature::Amplicon->new();
  19 isa_ok $amplicon, 'Bio::SeqFeature::Amplicon';
  20 isa_ok $amplicon, 'Bio::SeqFeature::SubSeq';
  21
  22
  23 # Amplicon with explicit sequence (sequence string)
  24
  25 ok $amplicon = Bio::SeqFeature::Amplicon->new(
  26     -seq => 'CCCCCAAAAAGGGGGTTTTT',
  27 );
  28 ok $amplicon_seq = $amplicon->seq;
  29 isa_ok $amplicon_seq, 'Bio::PrimarySeq';
  30 is $amplicon_seq->seq, 'CCCCCAAAAAGGGGGTTTTT';
  31
  32
  33 # Amplicon with explicit sequence (sequence object)
  34
  35 $fwd_primer = Bio::SeqFeature::Primer->new(
  36     -start  => 1,
  37     -end    => 4,
  38     -strand => 1
  39 );
  40
  41 $rev_primer = Bio::SeqFeature::Primer->new(
  42     -seq    => 'GATTA',
  43     -start  => 16,
  44     -end    => 20,
  45     -strand => -1
  46 );
  47
  48 ok $amplicon = Bio::SeqFeature::Amplicon->new(
  49     -start      => 1,
  50     -end        => 20,
  51     -seq        => Bio::PrimarySeq->new( -seq => 'CCCCCAAAAAGGGGGTTTTT' ),
  52     -fwd_primer => $fwd_primer,
  53 );
  54
  55 ok $amplicon->rev_primer($rev_primer);
  56
  57 is_deeply $amplicon->fwd_primer(), $fwd_primer;
  58 is_deeply $amplicon->rev_primer(), $rev_primer;
  59
  60 ok $amplicon_seq = $amplicon->seq;
  61 isa_ok $amplicon_seq, 'Bio::PrimarySeq';
  62 is $amplicon_seq->seq, 'CCCCCAAAAAGGGGGTTTTT';
  63
  64
  65 # Amplicon with implicit sequence
  66
  67 $template = Bio::Seq->new( -seq => 'ATCGATCGATCCCCCAAAAAGGGGGTTTTTAGCTAGCTAT');
  68
  69 ok $amplicon = Bio::SeqFeature::Amplicon->new(
  70     -start  => 11,
  71     -end    => 30,
  72     -strand => -1
  73 );
  74
  75 ok $template->add_SeqFeature($amplicon);
  76
  77 ok $amplicon_seq = $amplicon->seq;
  78 isa_ok $amplicon_seq, 'Bio::PrimarySeq';
  79 is $amplicon_seq->seq, 'AAAAACCCCCTTTTTGGGGG';