t/StandAloneFasta.t

   1 # -*-Perl-*-
   2 ## Bioperl Test Harness Script for Modules
   3 ## $Id$
   4 #
   5
   6 use strict;
   7 BEGIN {
   8     use Bio::Root::Test;
   9     test_begin(-tests => 15);
  10         use_ok('Bio::Tools::Run::Alignment::StandAloneFasta');
  11         use_ok('Bio::SeqIO');
  12 }
  13
  14 my $verbose = -1;
  15
  16 my $version = '35';
  17 my @params = ( 'b' =>'15',
  18                'd' => 0,
  19                'O' => test_output_file(),
  20                'm'=>'9',
  21                "program"=>"fasta$version");
  22 my $factory = Bio::Tools::Run::Alignment::StandAloneFasta->new
  23     ('-verbose' => $verbose,
  24      @params);
  25 ok $factory;
  26 my $inputfilename = test_input_file("fasta.fa");
  27
  28 SKIP: {
  29     test_skip(-requires_executable => $factory,
  30               -tests => 12);
  31         my $lib = test_input_file("fastalib.fa");
  32         $factory->library($lib);
  33         my ($fastareport) = $factory->run($inputfilename);
  34         my $result = $fastareport->next_result;
  35         my $hit    = $result->next_hit();
  36         my $hsp    = $hit->next_hsp();
  37         is $hsp->algorithm, 'FASTN';
  38         is $hsp->num_identical, 2982;
  39         is $hsp->length, 2982;
  40
  41         $factory->program_name('ssearch'.$version);
  42         ($fastareport) = $factory->run($inputfilename);
  43         $result = $fastareport->next_result;
  44         $hit    = $result->next_hit();
  45         $hsp    = $hit->next_hsp();
  46         like $hsp->algorithm, qr/SMITH-WATERMAN|SSEARCH/;
  47         is $hsp->num_identical, 2982;
  48         is $hsp->length, 2982;
  49
  50         $factory->program_name('fastx'.$version);
  51         $factory->library(test_input_file("fastaprot.fa"));
  52         ($fastareport) = $factory->run($inputfilename);
  53         $result = $fastareport->next_result;
  54         $hit    = $result->next_hit();
  55         $hsp    = $hit->next_hsp();
  56         is $hsp->algorithm, 'FASTX';
  57         is $hsp->num_identical, 994;
  58         is $hsp->length, 994;
  59
  60         my $sio = Bio::SeqIO->new(-file=>$inputfilename,
  61                                   -format=>"fasta");
  62         my $seq = $sio->next_seq;
  63
  64         #test with objects
  65         ($fastareport) = $factory->run($seq);
  66         $result = $fastareport->next_result;
  67         $hit    = $result->next_hit();
  68         $hsp    = $hit->next_hsp();
  69         is $hsp->algorithm, 'FASTX';
  70         is $hsp->num_identical, 994;
  71         is $hsp->length, 994;
  72 }
  73