t/SeqFeature/SeqAnalysisParser.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 => 14);
  11
  12         use_ok('Bio::Factory::SeqAnalysisParserFactory');
  13         use_ok('Bio::SeqIO');
  14 }
  15
  16 my ($seqio,$seq,$factory,$parser, $gene_seen, $exon_seen);
  17
  18 $seqio = Bio::SeqIO->new('-format'=>'fasta', '-file' => test_input_file('genomic-seq.fasta'));
  19 isa_ok $seqio, 'Bio::SeqIO';
  20 $seq = $seqio->next_seq;
  21 isa_ok $seq, 'Bio::PrimarySeqI';
  22
  23 $factory = Bio::Factory::SeqAnalysisParserFactory->new();
  24
  25 # let's test the genscan factory
  26 $parser = $factory->get_parser(-input => test_input_file('genomic-seq.genscan'),
  27                                   -method => 'genscan');
  28 isa_ok $parser, 'Bio::SeqAnalysisParserI';
  29 while( my $feat = $parser->next_feature() ){
  30     $seq->add_SeqFeature($feat);
  31 }
  32 ($gene_seen, $exon_seen)  = (0,0);
  33 foreach my $feat (  $seq->top_SeqFeatures() ) {
  34     if( $feat->isa("Bio::Tools::Prediction::Gene") ) {
  35         foreach my $exon ( $feat->exons ) {
  36             $exon_seen++;
  37         }
  38         $gene_seen++;
  39     }
  40 }
  41 is $exon_seen, 37;
  42 is $gene_seen, 3;
  43
  44 # let's test the mzef factory
  45 $parser = $factory->get_parser(-input => test_input_file('genomic-seq.mzef'),
  46                                -method=> 'mzef');
  47 $seqio = Bio::SeqIO->new('-format'=>'fasta', '-file' => test_input_file('genomic-seq.fasta'));
  48 ok $seq = $seqio->next_seq();
  49 isa_ok $seq, 'Bio::PrimarySeqI';
  50
  51 isa_ok $parser, 'Bio::SeqAnalysisParserI';
  52 while( my $feat = $parser->next_feature() ){
  53     $seq->add_SeqFeature($feat);
  54 }
  55 ($gene_seen, $exon_seen)  = (0,0);
  56 foreach my $feat (  $seq->top_SeqFeatures() ) {
  57     if( $feat->isa("Bio::Tools::Prediction::Gene") ) {
  58         foreach my $exon ( $feat->exons ) {
  59             $exon_seen++;
  60         }
  61         $gene_seen++;
  62     }
  63 }
  64 is $exon_seen, 23;
  65 is $gene_seen, 1;
  66
  67 # let's test the ePCR factory
  68
  69 $parser = $factory->get_parser(-input => test_input_file('genomic-seq.epcr'),
  70                                -method => 'epcr');
  71
  72 $seq->flush_SeqFeatures;
  73
  74 isa_ok $parser, 'Bio::SeqAnalysisParserI';
  75 while( my $feat = $parser->next_feature() ){
  76     $seq->add_SeqFeature($feat);
  77 }
  78
  79 is $seq->top_SeqFeatures(), 7;