t/SeqAnalysisParser.t

   1 # -*-Perl-*-
   2
   3 use strict;
   4 BEGIN {
   5     eval { require Test; };
   6     if( $@ ) {
   7         use lib 't';
   8     }
   9     use Test;
  10     plan tests => 11;
  11 }
  12
  13 use Bio::Factory::SeqAnalysisParserFactory;
  14 use Bio::SeqIO;
  15 use Bio::Root::IO;
  16
  17 my ($seqio,$seq,$factory,$parser, $gene_seen, $exon_seen);
  18
  19 $seqio = new Bio::SeqIO('-format'=>'fasta', '-file' => Bio::Root::IO->catfile("t","data","genomic-seq.fasta"));
  20 ok $seqio->isa('Bio::SeqIO');# 'seqio was not created';
  21 $seq = $seqio->next_seq;
  22 ok $seq->isa('Bio::PrimarySeqI');#'could not read sequence';
  23
  24 $factory = new Bio::Factory::SeqAnalysisParserFactory();
  25
  26 # let's test the genscan factory
  27 $parser = $factory->get_parser(-input => Bio::Root::IO->catfile("t","data","genomic-seq.genscan"),
  28                                   -method => 'genscan');
  29 ok $parser->isa('Bio::SeqAnalysisParserI');#'noSeqAnalysisParserI created';
  30 while( my $feat = $parser->next_feature() ){
  31     $seq->add_SeqFeature($feat);
  32 }
  33 ($gene_seen, $exon_seen)  = (0,0);
  34 foreach my $feat (  $seq->top_SeqFeatures() ) {
  35     if( $feat->isa("Bio::Tools::Prediction::Gene") ) {
  36         foreach my $exon ( $feat->exons ) {
  37             $exon_seen++;
  38         }
  39         $gene_seen++;
  40     }
  41 }
  42 ok $exon_seen, 37;
  43 ok $gene_seen, 3;
  44
  45 # let's test the mzef factory
  46 $parser = $factory->get_parser(-input => Bio::Root::IO->catfile("t","data","genomic-seq.mzef"),
  47                                -method=> 'mzef');
  48 $seqio = new Bio::SeqIO('-format'=>'fasta', '-file' => Bio::Root::IO->catfile("t","data","genomic-seq.fasta"));
  49 $seq = $seqio->next_seq();
  50 ok(defined $seq && $seq->isa('Bio::PrimarySeqI'));
  51
  52 ok $parser->isa('Bio::SeqAnalysisParserI');#'noSeqAnalysisParserI created';
  53 while( my $feat = $parser->next_feature() ){
  54     $seq->add_SeqFeature($feat);
  55 }
  56 ($gene_seen, $exon_seen)  = (0,0);
  57 foreach my $feat (  $seq->top_SeqFeatures() ) {
  58     if( $feat->isa("Bio::Tools::Prediction::Gene") ) {
  59         foreach my $exon ( $feat->exons ) {
  60             $exon_seen++;
  61         }
  62         $gene_seen++;
  63     }
  64 }
  65 ok $exon_seen, 23;
  66 ok $gene_seen, 1;
  67
  68 # let's test the ePCR factory
  69
  70 $parser = $factory->get_parser(-input => Bio::Root::IO->catfile("t","data", "genomic-seq.epcr"),
  71                                -method => 'epcr');
  72
  73 $seq->flush_SeqFeatures;
  74
  75 ok $parser->isa('Bio::SeqAnalysisParserI');#'noSeqAnalysisParserI created';
  76 while( my $feat = $parser->next_feature() ){
  77     $seq->add_SeqFeature($feat);
  78 }
  79
  80 ok $seq->top_SeqFeatures(), 7;