t/Prints.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 = 5;
  14    plan tests => $NTESTS;
  15 }
  16
  17 END {
  18    foreach ( $Test::ntest..$NTESTS ) {
  19        skip('Unable to run Prints tests, exe may not be installed',1);
  20    }
  21 }
  22 ok(1);
  23 use Bio::Tools::Run::Prints;
  24 use Bio::Root::IO;
  25 use Bio::SeqIO;
  26 use Bio::Seq;
  27
  28 my $db =  Bio::Root::IO->catfile("t","data","prints.dat");
  29 my @params = ('DB',$db);
  30
  31 my  $factory = Bio::Tools::Run::Prints->new(@params);
  32 ok $factory->isa('Bio::Tools::Run::Prints');
  33 my $prot_file=  Bio::Root::IO->catfile("t","data","Prints_prot.FastA");
  34
  35 my $seq1 = Bio::Seq->new();
  36 my $seqstream = Bio::SeqIO->new(-file => $prot_file, -fmt => 'Fasta');
  37 $seq1 = $seqstream->next_seq();
  38
  39 my $prints_present = $factory->executable();
  40
  41 unless ($prints_present) {
  42     warn("prints program not found. Skipping tests $Test::ntest to $NTESTS.\n");
  43     exit 0;
  44 }
  45
  46 my @feat = $factory->predict_protein_features($seq1);
  47
  48 ok $feat[0]->isa('Bio::SeqFeatureI');
  49 ok ($feat[0]->start,29);
  50 ok ($feat[0]->end,53);
  51
  52 1;
  53