t/Profile.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 => 7);
   9    use_ok('Bio::Tools::Run::Profile');
  10    use_ok('Bio::SeqIO');
  11    use_ok('Bio::Seq');
  12 }
  13
  14 my @params;
  15 my $db =  test_input_file('prosite.dat');
  16 push @params, ('DB',$db);
  17 my  $factory = Bio::Tools::Run::Profile->new(@params);
  18 isa_ok $factory,'Bio::Tools::Run::Profile';
  19 my $prot_file=  test_input_file('profile_prot.FastA');
  20
  21 my $seq1 = Bio::Seq->new();
  22 my $seqstream = Bio::SeqIO->new(-file =>$prot_file, -fmt =>'Fasta');
  23 $seq1 = $seqstream->next_seq();
  24
  25 SKIP: {
  26    test_skip(-requires_executable => $factory,
  27           -tests => 3);
  28
  29    my @feat = $factory->predict_protein_features($seq1);
  30
  31    isa_ok $feat[0],'Bio::SeqFeatureI';
  32    ok ($feat[0]->start, 15);
  33    ok ($feat[0]->end, 340);
  34
  35 }