t/StandAloneFasta.t

   1 # -*-Perl-*-
   2 ## Bioperl Test Harness Script for Modules
   3 ## $Id$
   4 #
   5
   6 use strict;
   7 use constant NUMTESTS => 15;
   8 BEGIN {
   9     eval { require Test; };
  10     if( $@ ) {
  11         use lib 't';
  12     }
  13     use Test;
  14     plan tests => NUMTESTS;
  15 }
  16
  17 END {
  18     foreach( $Test::ntest..NUMTESTS) {
  19         skip('Fasta or env variables not installed correctly',1);
  20     }
  21     unlink('blastreport.out');
  22 }
  23
  24 use Bio::Tools::Run::Alignment::StandAloneFasta;
  25 use Bio::SeqIO;
  26
  27 ok(1);
  28 my $verbose = -1;
  29
  30 my $version = '34';
  31 my @params = ( 'b' =>'15',
  32                'd' => 0,
  33                'O' =>'resultfile',
  34                'm'=>'9',
  35                "program"=>"fasta$version");
  36 my $factory = Bio::Tools::Run::Alignment::StandAloneFasta->new
  37     ('-verbose' => $verbose,
  38      @params);
  39 ok $factory;
  40 my $inputfilename = Bio::Root::IO->catfile("t","data","fasta.fa");
  41
  42 my $fasta_present = $factory->executable();
  43 if( ! $fasta_present ) {
  44     skip('Fasta  not installed',1);
  45     exit;
  46 } else {
  47     ok($fasta_present);
  48 }
  49 my $lib = Bio::Root::IO->catfile("t","data","fastalib.fa");
  50 $factory->library($lib);
  51 my ($fastareport) = $factory->run($inputfilename);
  52 my $result = $fastareport->next_result;
  53 my $hit    = $result->next_hit();
  54 my $hsp    = $hit->next_hsp();
  55 ok $hsp->algorithm, 'FASTN';
  56 ok $hsp->num_identical, 2982;
  57 ok $hsp->length, 2982;
  58
  59 $factory->program_name('ssearch'.$version);
  60 ($fastareport) = $factory->run($inputfilename);
  61 $result = $fastareport->next_result;
  62 $hit    = $result->next_hit();
  63 $hsp    = $hit->next_hsp();
  64 ok $hsp->algorithm, 'SMITH-WATERMAN';
  65 ok $hsp->num_identical, 2982;
  66 ok $hsp->length, 2982;
  67
  68 $factory->program_name('fastx'.$version);
  69 $factory->library(Bio::Root::IO->catfile("t","data","fastaprot.fa"));
  70 ($fastareport) = $factory->run($inputfilename);
  71 $result = $fastareport->next_result;
  72 $hit    = $result->next_hit();
  73 $hsp    = $hit->next_hsp();
  74 ok $hsp->algorithm, 'FASTX';
  75 ok $hsp->num_identical, 994;
  76 ok $hsp->length, 994;
  77
  78 my $sio = Bio::SeqIO->new(-file=>$inputfilename,
  79                           -format=>"fasta");
  80 my $seq = $sio->next_seq;
  81
  82 #test with objects
  83 ($fastareport) = $factory->run($seq);
  84 $result = $fastareport->next_result;
  85 $hit    = $result->next_hit();
  86 $hsp    = $hit->next_hsp();
  87 ok $hsp->algorithm, 'FASTX';
  88 ok $hsp->num_identical, 994;
  89 ok $hsp->length, 994;