t/Hmmpfam.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 = 8;
  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::Hmmpfam;
  24 use Bio::Root::IO;
  25 use Bio::SeqIO;
  26 use Bio::Seq;
  27
  28 my $db =  Bio::Root::IO->catfile("t","data","pfam_sample_R11");
  29 my @params = ('DB'=>$db,'E'=>5);
  30
  31
  32 my  $factory = Bio::Tools::Run::Hmmpfam->new(@params);
  33 ok $factory->isa('Bio::Tools::Run::Hmmpfam');
  34 ok $factory->E, 5;
  35 my $prot_file=  Bio::Root::IO->catfile("t","data","hmmpfam_protein_input");
  36
  37 my $seq1 = Bio::Seq->new();
  38 my $seqstream = Bio::SeqIO->new(-file => $prot_file, -fmt => 'Fasta');
  39 $seq1 = $seqstream->next_seq();
  40
  41 my $hmmpfam_present = $factory->executable();
  42
  43 unless ($hmmpfam_present) {
  44        warn("hmmpfam  program not found. Skipping tests $Test::ntest to $NTESTS.\n");
  45        exit 0;
  46 }
  47
  48 my $searchio = $factory->predict_protein_features($seq1);
  49
  50 my @feat;
  51 while (my $result = $searchio->next_result){
  52   while(my $hit = $result->next_hit){
  53     while (my $hsp = $hit->next_hsp){
  54       push @feat, $hsp;
  55     }
  56   }
  57 }
  58
  59 ok $feat[0]->isa('Bio::SeqFeatureI');
  60 ok ($feat[0]->feature1->start,25);
  61 ok ($feat[0]->feature1->end,92);
  62 ok ($feat[0]->feature2->start,1);
  63 ok ($feat[0]->feature2->end,124);
  64
  65 1;
  66