t/Seg.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 = 6;
  14    plan tests => $NTESTS;
  15 }
  16
  17 END {
  18    foreach ( $Test::ntest..$NTESTS ) {
  19        skip('Unable to run Seg tests, exe may not be installed',1);
  20    }
  21 }
  22 ok(1);
  23 use Bio::Tools::Run::Seg;
  24 use Bio::Root::IO;
  25 use Bio::SeqIO;
  26 use Bio::Seq;
  27
  28 my  $factory = Bio::Tools::Run::Seg->new();
  29 ok $factory->isa('Bio::Tools::Run::Seg');
  30 my $prot_file=  Bio::Root::IO->catfile("t","data","test_prot.FastA");
  31
  32 my $seq1 = Bio::Seq->new();
  33 my $seqstream = Bio::SeqIO->new(-file =>$prot_file, -fmt =>'Fasta');
  34 $seq1 = $seqstream->next_seq();
  35
  36 my $seg_present = $factory->executable();
  37
  38 unless ($seg_present) {
  39     warn("seg  program not found. Skipping tests $Test::ntest to $NTESTS.\n");
  40     exit 0;
  41 }
  42
  43 my @feat = $factory->predict_protein_features($seq1);
  44
  45 ok $feat[0]->isa('Bio::SeqFeatureI');
  46 ok ($feat[0]->start, 214);
  47 ok ($feat[0]->end, 226);
  48 ok ($feat[0]->score, 2.26);
  49
  50