t/Blat.t

   1 #!/usr/local/bin/perl
   2 #-*-Perl-*-
   3 # ## Bioperl Test Harness Script for Modules
   4 # #
   5 use strict;
   6 my $verbose = $ENV{'BIOPERLDEBUG'} || 0;
   7 BEGIN {
   8    eval { require Test; };
   9    if( $@ ) {
  10       use lib 't';
  11    }
  12    use Test;
  13    use vars qw($NTESTS);
  14    $NTESTS = 11;
  15    plan tests => $NTESTS;
  16 }
  17
  18 END {
  19     foreach ( $Test::ntest..$NTESTS ) {
  20         skip('Unable to run Blat  tests, exe may not be installed',1);
  21    }
  22 }
  23
  24 use Bio::Tools::Run::Alignment::Blat;
  25 use Bio::Root::IO;
  26 use Bio::SeqIO;
  27 use Bio::Seq;
  28
  29 my $db =  Bio::Root::IO->catfile("t","data","blat_dna.fa");
  30
  31 my $query = Bio::Root::IO->catfile("t","data","blat_dna.fa");
  32
  33 my $factory = Bio::Tools::Run::Alignment::Blat->new('quiet'  => 1,
  34                                                     -verbose => $verbose,
  35                                                     "DB"     => $db);
  36 ok $factory->isa('Bio::Tools::Run::Alignment::Blat');
  37
  38 my $blat_present = $factory->executable();
  39
  40 unless ($blat_present) {
  41        warn("blat  program not found. Skipping tests $Test::ntest to $NTESTS.\n");
  42        exit 0;
  43 }
  44
  45 my $searchio = $factory->align($query);
  46 my $result = $searchio->next_result;
  47 my $hit    = $result->next_hit;
  48 my $hsp    = $hit->next_hsp;
  49 ok $hsp->isa("Bio::Search::HSP::HSPI");
  50 ok ($hsp->query->start,1);
  51 ok ($hsp->query->end,1775);
  52 ok ($hsp->hit->start,1);
  53 ok ($hsp->hit->end,1775);
  54 my $sio = Bio::SeqIO->new(-file=>$query,-format=>'fasta');
  55
  56 my $seq  = $sio->next_seq ;
  57
  58 $searchio = $factory->align($seq);
  59 $result = $searchio->next_result;
  60 $hit    = $result->next_hit;
  61 $hsp    = $hit->next_hsp;
  62 ok $hsp->isa("Bio::Search::HSP::HSPI");
  63 ok ($hsp->query->start,1);
  64 ok ($hsp->query->end,1775);
  65 ok ($hsp->hit->start,1);
  66 ok ($hsp->hit->end,1775);
  67
  68 1;
  69