t/Genscan.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 = 4;
  14     plan tests => $NTESTS;
  15 }
  16
  17 END {
  18   foreach ( $Test::ntest..$NTESTS ) {
  19         skip('Unable to run Genscan tests, exe may not be installed',1);
  20   }
  21 }
  22
  23 use Bio::Tools::Run::Genscan;
  24 use Bio::Root::IO;
  25
  26
  27 if(! $ENV{'GENSCANDIR'}){
  28     warn("Need to define env variable GENSCANDIR to run test");
  29     exit(0);
  30 }
  31
  32 my $paramfile = Bio::Root::IO->catfile($ENV{'GENSCANDIR'},"HumanIso.smat");
  33 my @params = ('MATRIX',$paramfile);
  34 my  $factory = Bio::Tools::Run::Genscan->new(@params);
  35 ok $factory->isa('Bio::Tools::Run::Genscan');
  36 ok $factory->matrix;
  37
  38 my $inputfilename = Bio::Root::IO->catfile("t","data","Genscan.FastA");
  39 my $seq1 = Bio::Seq->new();
  40 my $seqstream = Bio::SeqIO->new(-file => $inputfilename, -format => 'Fasta');
  41 $seq1 = $seqstream->next_seq();
  42
  43 my $genscan_present = $factory->executable();
  44
  45 unless ($genscan_present) {
  46         warn("Genscan program not found. Skipping tests $Test::ntest to $NTESTS.\n");
  47             exit 0;
  48 }
  49 $factory->quiet(1);
  50 my @feat = $factory->predict_genes($seq1);
  51
  52 my $protein = $feat[0]->predicted_protein();
  53
  54 ok $feat[0]->isa("Bio::SeqFeatureI");
  55 ok $protein->isa("Bio::PrimarySeqI");
  56