t/Coil.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
  10    use_ok('Bio::Tools::Run::Coil');
  11    use_ok('Bio::SeqIO');
  12 }
  13
  14 SKIP: {
  15    my  $factory = Bio::Tools::Run::Coil->new();
  16    test_skip(-requires_executable => $factory,
  17              -requires_env => 'COILSDIR',
  18              -tests => 4);
  19    ok $factory->isa('Bio::Tools::Run::Coil');
  20
  21    my $prot_file=  test_input_file("coil_protein_input");
  22
  23    my $seq1 = Bio::Seq->new();
  24    my $seqstream = Bio::SeqIO->new(-file => $prot_file, -fmt => 'Fasta');
  25    $seq1 = $seqstream->next_seq();
  26
  27    my $coil_present = $factory->executable();
  28    unless ($coil_present) {
  29       skip("coil program not found", 3);
  30    }
  31
  32    $factory->quiet(1);
  33    my @feat = $factory->predict_protein_features($seq1);
  34
  35    ok $feat[0]->isa('Bio::SeqFeatureI');
  36    ok ($feat[0]->start,71);
  37    ok ($feat[0]->end,91);
  38 }