t/Genscan.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 => 6);
   9         use_ok('Bio::Tools::Run::Genscan');
  10         use_ok('Bio::Root::IO');
  11 }
  12
  13 SKIP: {
  14         test_skip(-requires_env => 'GENSCANDIR', -tests => 4);
  15
  16         my $paramfile = Bio::Root::IO->catfile($ENV{'GENSCANDIR'},"HumanIso.smat");
  17         my @params = ('MATRIX',$paramfile);
  18         my  $factory = Bio::Tools::Run::Genscan->new(@params);
  19         isa_ok $factory, 'Bio::Tools::Run::Genscan';
  20         ok $factory->matrix;
  21
  22         my $inputfilename = test_input_file("Genscan.FastA");
  23         my $seq1 = Bio::Seq->new();
  24         my $seqstream = Bio::SeqIO->new(-file => $inputfilename, -format => 'Fasta');
  25         $seq1 = $seqstream->next_seq();
  26
  27         test_skip(-requires_executable => $factory,
  28                           -tests => 2);
  29
  30         $factory->quiet(1);
  31         my @feat = $factory->predict_genes($seq1);
  32
  33         my $protein = $feat[0]->predicted_protein();
  34
  35         isa_ok $feat[0], "Bio::SeqFeatureI";
  36         isa_ok $protein, "Bio::PrimarySeqI";
  37 }