t/Tools/GFF.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7     use lib '.';
   8     use Bio::Root::Test;
   9
  10     test_begin(-tests => 34);
  11
  12     use_ok('Bio::Tools::GFF');
  13     use_ok('Bio::SeqFeature::Generic');
  14 }
  15
  16 my $feat = Bio::SeqFeature::Generic->new( -start => 10, -end => 100,
  17                                 -strand => -1, -primary => 'repeat',
  18                                 -source => 'repeatmasker',
  19                                 -score  => 1000,
  20                                 -tag    => {
  21                                     new => 1,
  22                                     author => 'someone',
  23                                     sillytag => 'this is silly!;breakfast' } );
  24 ok($feat);
  25
  26 my ($out1, $out2) = (test_output_file(), test_output_file());
  27 my $gff1out = Bio::Tools::GFF->new(-gff_version => 1, -file => ">$out1");
  28 ok($gff1out);
  29 my $gff2out = Bio::Tools::GFF->new(-gff_version => 2, -file => ">$out2");
  30 ok($gff2out);
  31
  32 $gff1out->write_feature($feat);
  33 $gff2out->write_feature($feat);
  34
  35 $gff1out->close();
  36 $gff2out->close();
  37
  38 my $gff1in = Bio::Tools::GFF->new(-gff_version => 1,  -file => "$out1");
  39 ok($gff1in);
  40 my $gff2in = Bio::Tools::GFF->new(-gff_version => 2, -file => "$out2");
  41 ok($gff2in);
  42
  43 my $feat1 = $gff1in->next_feature();
  44 ok($feat1);
  45 is($feat1->start, $feat->start);
  46 is($feat1->end, $feat->end);
  47 is($feat1->primary_tag, $feat->primary_tag);
  48 is($feat1->score, $feat->score);
  49
  50 my $feat2 = $gff2in->next_feature();
  51 ok($feat2);
  52 is($feat2->start, $feat->start);
  53 is($feat2->end, $feat->end);
  54 is($feat2->primary_tag, $feat->primary_tag);
  55 is($feat2->score, $feat->score);
  56 is(($feat2->get_tag_values('sillytag'))[0], 'this is silly!;breakfast');
  57
  58 #test sequence-region parsing
  59 $gff2in = Bio::Tools::GFF->new(-gff_version => 2, -file => test_input_file('hg16_chroms.gff'));
  60 is($gff2in->next_feature(),undef);
  61 my $seq = $gff2in->next_segment;
  62 is($seq->display_id, 'chr1');
  63 is($seq->end, 246127941);
  64 is($seq->start, 1);
  65
  66
  67 # GFF3
  68 SKIP: {
  69         test_skip(-tests => 12, -requires_module => 'IO::String');
  70     my $str = IO::String->new;
  71     my $gffout = Bio::Tools::GFF->new(-fh => $str, -gff_version => 3);
  72     my $feat_test = Bio::SeqFeature::Generic->new
  73     (-primary_tag => 'tag',
  74      -source_tag  => 'exon',
  75      -seq_id      => 'testseq',
  76      -score       => undef,
  77      -start       => 10,
  78      -end         => 120,
  79      -strand      => 1,
  80      -tag         => {
  81          'bungle' => 'jungle;mumble',
  82          'lion'   => 'snake=tree'
  83          });
  84     $feat_test->add_tag_value('giant_squid', 'lakeshore manor');
  85     $gffout->write_feature($feat_test);
  86     seek($str,0,0);
  87     my $in = Bio::Tools::GFF->new(-fh          => $str,
  88                  -gff_version => 3);
  89     my $f_recon = $in->next_feature;
  90     is($f_recon->primary_tag, $feat_test->primary_tag);
  91     is($f_recon->source_tag,  $feat_test->source_tag);
  92     is($f_recon->score, $feat_test->score);
  93     is($f_recon->start, $feat_test->start);
  94     is($f_recon->end, $feat_test->end);
  95     is($f_recon->strand, $feat_test->strand);
  96     for my $tag ( $feat_test->get_all_tags ) {
  97         ok($f_recon->has_tag($tag));
  98         if( $f_recon->has_tag($tag) ) {
  99             my @v = $feat_test->get_tag_values($tag);
 100             my @g = $f_recon->get_tag_values($tag);
 101             while( @v && @g ) {
 102                is(shift @v, shift @g);
 103             }
 104         }
 105     }
 106 }