t/Promoterwise.t

   1 #!/usr/local/bin/perl
   2 # -*-Perl-*-
   3 ## Bioperl Test Harness Script for Modules
   4
   5 use strict;
   6 BEGIN {
   7     use Bio::Root::Test;
   8     test_begin(-tests => 9);
   9         use_ok('Bio::Tools::Run::Promoterwise');
  10         use_ok('Bio::Seq');
  11 }
  12
  13 my $verbose = -1;
  14 my @params = ('-verbose' => test_debug(), 'silent' => 1, 'quiet' => 1);
  15 my  $factory = Bio::Tools::Run::Promoterwise->new(@params);
  16 isa_ok $factory,'Bio::Tools::Run::Promoterwise';
  17
  18 SKIP: {
  19         test_skip(-requires_executable => $factory,
  20                   -tests => 6);
  21
  22         my $bequiet = 1;
  23         $factory->quiet($bequiet);  # Suppress pseudowise messages to terminal
  24
  25         #test with one file with 2 sequences
  26         my $inputfilename = test_input_file('sim4_cdna.fa');
  27         my $seqstream1 = Bio::SeqIO->new(-file => $inputfilename,
  28                                          -format => 'fasta');
  29         my $seq1 = Bio::Seq->new();
  30         $seq1 = $seqstream1->next_seq();
  31
  32         $inputfilename = test_input_file('sim4_genomic.fa');
  33         my $seqstream2 = Bio::SeqIO->new(-file => $inputfilename,
  34                                          -format => 'fasta');
  35         my $seq2 = Bio::Seq->new();
  36         $seq2 = $seqstream2->next_seq();
  37
  38         my @fp = $factory->run($seq1, $seq2);
  39         my $first = $fp[0]->feature1;
  40         my $second = $fp[0]->feature2;
  41
  42         my @sub = $first->sub_SeqFeature;
  43         my @sub2 = $second->sub_SeqFeature;
  44
  45         is $sub[0]->start,4;
  46         is $sub2[0]->start,29;
  47         is $sub[0]->end,18;
  48         is $sub2[0]->end,43;
  49         is $sub[0]->seq->seq,'GTTGTGCTGGGGGGG';
  50         is $sub[0]->score,1596.49;
  51 }