t/Exonerate.t

   1 # -*-Perl-*-
   2 ## Bioperl Test Harness Script for Modules
   3
   4
   5 use strict;
   6 BEGIN {
   7     use Bio::Root::Test;
   8     test_begin(-tests => 89);
   9         use_ok('Bio::Tools::Run::Alignment::Exonerate');
  10 }
  11
  12 my $verbose = test_debug() || -1;
  13
  14 my $query= test_input_file("exonerate_cdna.fa");
  15 my $target= test_input_file("exonerate_genomic.fa");
  16 my $targetrev= test_input_file("exonerate_genomic_rev.fa");
  17
  18 my $run = Bio::Tools::Run::Alignment::Exonerate->new(-verbose  => $verbose,
  19                                                      arguments=>'--model est2genome --bestn 1');
  20 SKIP: {
  21         test_skip(-requires_executable => $run, -tests => 88);
  22
  23         isa_ok $run, 'Bio::Tools::Run::Alignment::Exonerate';
  24         ok $run->version;
  25
  26         my $searchio= $run->run($query,$target);
  27         isa_ok $searchio, "Bio::SearchIO";
  28         my @expect = ( [qw(29   268     4 242)],# target-start t-end query-start q-end
  29                            [qw(526  646   243 363)],
  30                            [qw(964 1056   364 456)],
  31                            [qw(1770 1923  457 610)],
  32                            [qw(2250 2479  611 840 )],
  33                            [qw(2565 2687  841 963)],
  34                            [qw(2769 3074  964 1279)] );
  35         RESULT: while(my $result = $searchio->next_result){
  36           while( my $hit = $result->next_hit ) {
  37         #      ok($hit->start('hit'), 29);
  38         #      ok($hit->end('hit'), 3074);
  39                   my $i = 0;
  40                 while( my $hsp = $hit->next_hsp ) {
  41                 is ($hsp->hit->strand, 1);
  42                 is ($hsp->query->strand, 1);
  43                 is ($hsp->hit->start,$expect[$i]->[0]);
  44                 is ($hsp->hit->end,$expect[$i]->[1]);
  45                 is ($hsp->query->start,$expect[$i]->[2]);
  46                 is ($hsp->query->end,$expect[$i]->[3]);
  47                 $i++;
  48                 if( $verbose > 0 ) {
  49                         warn("TARGET:", $hsp->hit->location->to_FTstring, "\n");
  50                         warn("QUERY: ",$hsp->query->location->to_FTstring, "\n");
  51                 }
  52                 }
  53                   last; # only show a single HIT
  54           }
  55           last;
  56         }
  57
  58
  59         $searchio= $run->run($query,$targetrev);
  60         isa_ok $searchio,"Bio::SearchIO";
  61         my @expectrev;
  62         if ($run->version >= 2 ) { # latest 2.0.0 version
  63                 @expectrev = ( # target-start t-end query-start q-end
  64                            [qw(2834 3073  4 242)],
  65                            [qw(2456 2576  243 363)],
  66                            [qw(2046 2138  364 456)],
  67                            [qw(1179 1332  457 610)],
  68                            [qw(623 852    611 840)],
  69                            [qw(415  537   841 963)],
  70                            [qw(28   333   964 1279)]
  71                 );
  72         } else { # version 1.4.0 presumably
  73                 @expectrev = ( # target-start t-end query-start q-end
  74                            [qw(28   333   964 1279)],
  75                            [qw(415  537   841 963)],
  76                            [qw(623 852    611 840)],
  77                            [qw(1179 1332  457 610)],
  78                            [qw(2046 2138  364  456)],
  79                            [qw(2456 2576  243 363)],
  80                            [qw(2834 3073  4 242)]
  81                 );
  82
  83         }
  84         RESULT: while(my $result = $searchio->next_result){
  85                 while( my $hit = $result->next_hit ) {
  86                   my $i = 0;
  87                 while( my $hsp = $hit->next_hsp ) {
  88                 is ($hsp->hit->strand, -1);
  89                 is ($hsp->query->strand, 1);
  90                 is ($hsp->hit->start,$expectrev[$i]->[0]);
  91                 is ($hsp->hit->end,$expectrev[$i]->[1]);
  92                 is ($hsp->query->start,$expectrev[$i]->[2]);
  93                 is ($hsp->query->end,$expectrev[$i]->[3]);
  94                 $i++;
  95                 if( $verbose > 0 ) {
  96                         warn("TARGET:", $hsp->hit->location->to_FTstring, "\n");
  97                         warn("QUERY: ",$hsp->query->location->to_FTstring, "\n");
  98                 }
  99                 }
 100                   last; # only show a single HIT
 101           }
 102           last;
 103         }
 104 }