t/Genewise.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 => 20);
   9         use_ok('Bio::Tools::Run::Genewise');
  10         use_ok('Bio::Root::IO');
  11         use_ok('Bio::Seq');
  12 }
  13
  14 my $verbose = test_debug() || -1;
  15 my @params = ('-verbose' => $verbose,
  16               'silent' => 1,
  17               'quiet' => 1);
  18
  19 my $factory = Bio::Tools::Run::Genewise->new(@params);
  20
  21 SKIP:{
  22         test_skip(-requires_executable => $factory, -tests => 17);
  23
  24         my $version = $factory->version;
  25         warn("version is $version\n") if $verbose > 0;
  26         isa_ok $factory,'Bio::Tools::Run::Genewise';
  27
  28         my $bequiet = 1;
  29         $factory->quiet($bequiet);  # Suppress pseudowise messages to terminal
  30
  31         #test with one file with 2 sequences
  32         my $inputfilename = test_input_file('road.pep');
  33         my $seqstream1 = Bio::SeqIO->new(-file => $inputfilename,
  34                                          -format => 'fasta');
  35         my $seq1 = Bio::Seq->new();
  36         $seq1 = $seqstream1->next_seq();
  37
  38         $inputfilename = test_input_file('human.genomic');
  39         my $seqstream2 = Bio::SeqIO->new(-file => $inputfilename,
  40                                          -format => 'fasta');
  41         my $seq2 = Bio::Seq->new();
  42         $seq2 = $seqstream2->next_seq();
  43
  44         my ($genes) = $factory->predict_genes($seq1, $seq2);
  45
  46         my @transcripts = $genes->transcripts;
  47         my @feat = $transcripts[0]->exons;
  48         my $seqid = $feat[0]->seq_id;
  49         is($seqid, 'HSHNRNPA');
  50         my ($featpair)= $feat[0]->each_tag_value('supporting_feature');
  51         is($featpair->feature2->seq_id,'roa1_drome');
  52         is($featpair->feature1->seq_id,'HSHNRNPA');
  53         if( defined $version && $version eq 'wise2-2-0' ) {
  54                 is($transcripts[0]->start, 1386);
  55                 is($transcripts[0]->end, 3963);
  56                 is($feat[0]->start, 1386);
  57                 is($feat[0]->end, 1493);
  58                 is($feat[0]->strand,1);
  59                 is($featpair->feature2->start,26);
  60                 is($featpair->feature2->end,61);
  61                 is($featpair->feature2->strand,1);
  62                 is($featpair->feature2->score,'253.10');
  63                 is($featpair->feature1->start,1386);
  64                 is($featpair->feature1->end,1493);
  65                 is($featpair->feature1->strand,1);
  66                 is($featpair->feature1->score,'253.10');
  67         } else {
  68                 warn("These tests may fail because I'm not sure about your genewise version -- using wise 2.2.3-rc7 values\n");
  69                 is($transcripts[0]->start, 1386);
  70                 is($transcripts[0]->end, 4304);
  71
  72                 is($feat[0]->start, 1386);
  73                 is($feat[0]->end, 1493);
  74                 is($feat[0]->strand,1);
  75                 is($featpair->feature2->start,26);
  76                 is($featpair->feature2->end,61);
  77                 is($featpair->feature2->strand,1);
  78                 is($featpair->feature2->score,'319.10');
  79                 is($featpair->feature1->start,1386);
  80                 is($featpair->feature1->end,1493);
  81                 is($featpair->feature1->strand,1);
  82                 is($featpair->feature1->score,'319.10');
  83
  84         }
  85
  86 }