t/SeqFeature/SeqAnalysisParser.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7     use Bio::Root::Test;
   8
   9     test_begin(-tests => 14);
  10
  11         use_ok('Bio::Factory::SeqAnalysisParserFactory');
  12         use_ok('Bio::SeqIO');
  13 }
  14
  15 my ($seqio,$seq,$factory,$parser, $gene_seen, $exon_seen);
  16
  17 $seqio = Bio::SeqIO->new('-format'=>'fasta', '-file' => test_input_file('genomic-seq.fasta'));
  18 isa_ok $seqio, 'Bio::SeqIO';
  19 $seq = $seqio->next_seq;
  20 isa_ok $seq, 'Bio::PrimarySeqI';
  21
  22 $factory = Bio::Factory::SeqAnalysisParserFactory->new();
  23
  24 # let's test the genscan factory
  25 $parser = $factory->get_parser(-input => test_input_file('genomic-seq.genscan'),
  26                                   -method => 'genscan');
  27 isa_ok $parser, 'Bio::SeqAnalysisParserI';
  28 while( my $feat = $parser->next_feature() ){
  29     $seq->add_SeqFeature($feat);
  30 }
  31 ($gene_seen, $exon_seen)  = (0,0);
  32 foreach my $feat (  $seq->top_SeqFeatures() ) {
  33     if( $feat->isa("Bio::Tools::Prediction::Gene") ) {
  34         foreach my $exon ( $feat->exons ) {
  35             $exon_seen++;
  36         }
  37         $gene_seen++;
  38     }
  39 }
  40 is $exon_seen, 37;
  41 is $gene_seen, 3;
  42
  43 # let's test the mzef factory
  44 $parser = $factory->get_parser(-input => test_input_file('genomic-seq.mzef'),
  45                                -method=> 'mzef');
  46 $seqio = Bio::SeqIO->new('-format'=>'fasta', '-file' => test_input_file('genomic-seq.fasta'));
  47 ok $seq = $seqio->next_seq();
  48 isa_ok $seq, 'Bio::PrimarySeqI';
  49
  50 isa_ok $parser, 'Bio::SeqAnalysisParserI';
  51 while( my $feat = $parser->next_feature() ){
  52     $seq->add_SeqFeature($feat);
  53 }
  54 ($gene_seen, $exon_seen)  = (0,0);
  55 foreach my $feat (  $seq->top_SeqFeatures() ) {
  56     if( $feat->isa("Bio::Tools::Prediction::Gene") ) {
  57         foreach my $exon ( $feat->exons ) {
  58             $exon_seen++;
  59         }
  60         $gene_seen++;
  61     }
  62 }
  63 is $exon_seen, 23;
  64 is $gene_seen, 1;
  65
  66 # let's test the ePCR factory
  67
  68 $parser = $factory->get_parser(-input => test_input_file('genomic-seq.epcr'),
  69                                -method => 'epcr');
  70
  71 $seq->flush_SeqFeatures;
  72
  73 isa_ok $parser, 'Bio::SeqAnalysisParserI';
  74 while( my $feat = $parser->next_feature() ){
  75     $seq->add_SeqFeature($feat);
  76 }
  77
  78 is $seq->top_SeqFeatures(), 7;