t/Signalp.t

   1 #!/usr/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 = 5;
  14    plan tests => $NTESTS;
  15 }
  16
  17 END {
  18    foreach ( $Test::ntest..$NTESTS ) {
  19        skip('Unable to run SignalP tests, exe may not be installed',1);
  20    }
  21 }
  22 ok(1);
  23 use Bio::Tools::Run::Signalp;
  24 use Bio::Root::IO;
  25 use Bio::SeqIO;
  26 use Bio::Seq;
  27
  28 my  $factory = Bio::Tools::Run::Signalp->new();
  29 ok $factory->isa('Bio::Tools::Run::Signalp');
  30
  31
  32 my $prot_file = Bio::Root::IO->catfile("t","data","signalp_input_protein");
  33
  34 my $seq1 = Bio::Seq->new();
  35 my $seqstream = Bio::SeqIO->new(-file =>$prot_file, -fmt =>'Fasta');
  36 $seq1 = $seqstream->next_seq();
  37
  38 my $signalp_present = $factory->executable();
  39
  40 unless ($signalp_present) {
  41        warn("signalp program not found. Skipping tests $Test::ntest to $NTESTS.\n");
  42        exit 0;
  43 }
  44
  45 my @feat = $factory->predict_protein_features($seq1);
  46
  47 ok $feat[0]->isa('Bio::SeqFeatureI');
  48 ok ($feat[0]->start,1);
  49 ok ($feat[0]->end,29);
  50
  51