t/Genewise.t

   1 #!/usr/local/bin/perl
   2 # -*-Perl-*-
   3 ## Bioperl Test Harness Script for Modules
   4
   5 use strict;
   6 BEGIN {
   7     eval { require Test; };
   8     if( $@ ) {
   9         use lib 't';
  10     }
  11     use Test;
  12     use vars qw($NTESTS);
  13     $NTESTS = 18;
  14     plan tests => $NTESTS;
  15 }
  16 use Bio::Tools::Run::Genewise;
  17 use Bio::Root::IO;
  18 use Bio::Seq;
  19
  20 END {
  21     for ( $Test::ntest..$NTESTS ) {
  22         skip("genewise program not found. Skipping. (Be sure you have the wise package > 2.2.0)",1);
  23     }
  24 }
  25
  26 ok(1);
  27 my $verbose = $ENV{BIOPERLDEBUG} ? 1 : -1;
  28 my @params = ('-verbose' => $verbose,
  29               'silent' => 1,
  30               'quiet' => 1);
  31
  32 my  $factory = Bio::Tools::Run::Genewise->new(@params);
  33 my $version = $factory->version;
  34 warn("version is $version\n") if $verbose > 0;
  35 ok $factory->isa('Bio::Tools::Run::Genewise');
  36 unless ($factory->executable) {
  37    warn("Genewise program not found. Skipping tests $Test::ntest to $NTESTS.\n");
  38    exit 0;
  39 }
  40
  41 my $bequiet = 1;
  42 $factory->quiet($bequiet);  # Suppress pseudowise messages to terminal
  43
  44 #test with one file with 2 sequences
  45 my $inputfilename = Bio::Root::IO->catfile(qw(t data road.pep));
  46 my $seqstream1 = Bio::SeqIO->new(-file => $inputfilename,
  47                                  -format => 'fasta');
  48 my $seq1 = Bio::Seq->new();
  49 $seq1 = $seqstream1->next_seq();
  50
  51 $inputfilename = Bio::Root::IO->catfile(qw(t data human.genomic));
  52 my $seqstream2 = Bio::SeqIO->new(-file => $inputfilename,
  53                                  -format => 'fasta');
  54 my $seq2 = Bio::Seq->new();
  55 $seq2 = $seqstream2->next_seq();
  56
  57 my ($genes) = $factory->predict_genes($seq1, $seq2);
  58
  59 my @transcripts = $genes->transcripts;
  60 my @feat = $transcripts[0]->exons;
  61 my $seqid = $feat[0]->seq_id;
  62 ok($seqid, 'HSHNRNPA');
  63 my ($featpair)= $feat[0]->each_tag_value('supporting_feature');
  64 ok($featpair->feature2->seq_id,'roa1_drome');
  65 ok($featpair->feature1->seq_id,'HSHNRNPA');
  66 if( defined $version && $version eq 'wise2-2-0' ) {
  67     ok($transcripts[0]->start, 1386);
  68     ok($transcripts[0]->end, 3963);
  69     ok($feat[0]->start, 1386);
  70     ok($feat[0]->end, 1493);
  71     ok($feat[0]->strand,1);
  72     ok($featpair->feature2->start,26);
  73     ok($featpair->feature2->end,61);
  74     ok($featpair->feature2->strand,1);
  75     ok($featpair->feature2->score,'253.10');
  76     ok($featpair->feature1->start,1386);
  77     ok($featpair->feature1->end,1493);
  78     ok($featpair->feature1->strand,1);
  79     ok($featpair->feature1->score,'253.10');
  80 } else {
  81     warn("These tests may fail because I'm not sure about your genewise version -- using wise 2.2.3-rc7 values\n");
  82     ok($transcripts[0]->start, 1386);
  83     ok($transcripts[0]->end, 4304);
  84
  85     ok($feat[0]->start, 1386);
  86     ok($feat[0]->end, 1493);
  87     ok($feat[0]->strand,1);
  88     ok($featpair->feature2->start,26);
  89     ok($featpair->feature2->end,61);
  90     ok($featpair->feature2->strand,1);
  91     ok($featpair->feature2->score,'319.10');
  92     ok($featpair->feature1->start,1386);
  93     ok($featpair->feature1->end,1493);
  94     ok($featpair->feature1->strand,1);
  95     ok($featpair->feature1->score,'319.10');
  96
  97 }
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