t/Seq/PrimedSeq.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4
   5 use strict;
   6
   7 BEGIN {
   8     use lib '.';
   9     use Bio::Root::Test;
  10
  11     test_begin(-tests => 10);
  12
  13     use_ok('Bio::SeqIO');
  14     use_ok('Bio::Seq::PrimedSeq');
  15 }
  16
  17 my ($seqio, $seq, $left, $right, $primed_seq, $left_test, $annseq, $amplicon, $returnedseq);
  18
  19 $seqio=Bio::SeqIO->new(-file=>test_input_file('primedseq.fa'));
  20 $seq=$seqio->next_seq;
  21 $left=Bio::SeqFeature::Primer->new(-seq=>'CTTTTCATTCTGACTGCAACG');
  22 $right=Bio::SeqFeature::Primer->new(-seq=>'GGTGGTGCTAATGCGT');
  23
  24
  25 ok $primed_seq = Bio::Seq::PrimedSeq->new(-seq=>$seq, -left_primer=>$left, -right_primer=>$right);
  26 ok $left_test = $primed_seq->get_primer('left');
  27 is $left_test,$left;
  28 ok $annseq = $primed_seq->annotated_sequence; # should I check that this is what I think it is, or just be happy?
  29 ok $amplicon=$primed_seq->amplicon->seq;
  30 is uc($amplicon), uc('cttttcattctgactgcaacgGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAacgcattagcaccacc');
  31 ok $returnedseq=$primed_seq->seq;
  32 is $returnedseq->seq, $seq->seq;