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 = 13;
  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 = -1;
  28 my @params = ('-verbose' => $verbose, 'silent' => 1, 'quiet' => 1);
  29 my  $factory = Bio::Tools::Run::Genewise->new(@params);
  30 ok $factory->isa('Bio::Tools::Run::Genewise');
  31 unless ($factory->executable) {
  32    warn("Genewise program not found. Skipping tests $Test::ntest to $NTESTS.\n");
  33    exit 0;
  34 }
  35
  36 my $bequiet = 1;
  37 $factory->quiet($bequiet);  # Suppress pseudowise messages to terminal
  38
  39 #test with one file with 2 sequences
  40 my $inputfilename = Bio::Root::IO->catfile(qw(t data new_pep.fa));
  41 my $seqstream1 = Bio::SeqIO->new(-file => $inputfilename,
  42                                  -format => 'fasta');
  43 my $seq1 = Bio::Seq->new();
  44 $seq1 = $seqstream1->next_seq();
  45
  46 $inputfilename = Bio::Root::IO->catfile(qw(t data new_dna.fa));
  47 my $seqstream2 = Bio::SeqIO->new(-file => $inputfilename,
  48                                  -format => 'fasta');
  49 my $seq2 = Bio::Seq->new();
  50 $seq2 = $seqstream2->next_seq();
  51
  52 my ($genes) = $factory->predict_genes($seq1, $seq2);
  53
  54 my @transcripts = $genes->transcripts;
  55 my @feat = $transcripts[0]->exons;
  56 my $seqid = $feat[0]->seq_id;
  57 my $start = $feat[0]->start;
  58 ok($start, 865);#ok3
  59 my $end = $feat[0]->end;
  60 ok($end, 897);#ok4
  61 my $strand = $feat[0]->strand;
  62 ok($strand, 1);#ok5
  63
  64 my ($featpair)= $feat[0]->each_tag_value('supporting_feature');
  65 ok($featpair->feature1->start,865);
  66 ok($featpair->feature1->end,897);
  67 ok($featpair->feature1->strand,1);
  68 ok($featpair->feature1->score,17.01);
  69 ok($featpair->feature2->start,120);
  70 ok($featpair->feature2->end,130);
  71 ok($featpair->feature2->strand,1);
  72 ok($featpair->feature2->score,17.01);
  73
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