3 ## Bioperl Test Harness Script for Modules
8 test_begin
(-tests
=> 20);
9 use_ok
('Bio::Tools::Run::Genewise');
10 use_ok
('Bio::Root::IO');
14 my $verbose = test_debug
() || -1;
15 my @params = ('-verbose' => $verbose,
19 my $factory = Bio
::Tools
::Run
::Genewise
->new(@params);
22 test_skip
(-requires_executable
=> $factory, -tests
=> 17);
24 my $version = $factory->version;
25 warn("version is $version\n") if $verbose > 0;
26 isa_ok
$factory,'Bio::Tools::Run::Genewise';
29 $factory->quiet($bequiet); # Suppress pseudowise messages to terminal
31 #test with one file with 2 sequences
32 my $inputfilename = test_input_file
('road.pep');
33 my $seqstream1 = Bio
::SeqIO
->new(-file
=> $inputfilename,
35 my $seq1 = Bio
::Seq
->new();
36 $seq1 = $seqstream1->next_seq();
38 $inputfilename = test_input_file
('human.genomic');
39 my $seqstream2 = Bio
::SeqIO
->new(-file
=> $inputfilename,
41 my $seq2 = Bio
::Seq
->new();
42 $seq2 = $seqstream2->next_seq();
44 my ($genes) = $factory->predict_genes($seq1, $seq2);
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');
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);
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');