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# -*-Perl-*-
use strict;
BEGIN {
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 11;
}
use Bio::Factory::SeqAnalysisParserFactory;
use Bio::SeqIO;
use Bio::Root::IO;
my ($seqio,$seq,$factory,$parser, $gene_seen, $exon_seen);
$seqio = new Bio::SeqIO('-format'=>'fasta', '-file' => Bio::Root::IO->catfile("t","data","genomic-seq.fasta"));
ok $seqio->isa('Bio::SeqIO');# 'seqio was not created';
$seq = $seqio->next_seq;
ok $seq->isa('Bio::PrimarySeqI');#'could not read sequence';
$factory = new Bio::Factory::SeqAnalysisParserFactory();
# let's test the genscan factory
$parser = $factory->get_parser(-input => Bio::Root::IO->catfile("t","data","genomic-seq.genscan"),
-method => 'genscan');
ok $parser->isa('Bio::SeqAnalysisParserI');#'noSeqAnalysisParserI created';
while( my $feat = $parser->next_feature() ){
$seq->add_SeqFeature($feat);
}
($gene_seen, $exon_seen) = (0,0);
foreach my $feat ( $seq->top_SeqFeatures() ) {
if( $feat->isa("Bio::Tools::Prediction::Gene") ) {
foreach my $exon ( $feat->exons ) {
$exon_seen++;
}
$gene_seen++;
}
}
ok $exon_seen, 37;
ok $gene_seen, 3;
# let's test the mzef factory
$parser = $factory->get_parser(-input => Bio::Root::IO->catfile("t","data","genomic-seq.mzef"),
-method=> 'mzef');
$seqio = new Bio::SeqIO('-format'=>'fasta', '-file' => Bio::Root::IO->catfile("t","data","genomic-seq.fasta"));
$seq = $seqio->next_seq();
ok(defined $seq && $seq->isa('Bio::PrimarySeqI'));
ok $parser->isa('Bio::SeqAnalysisParserI');#'noSeqAnalysisParserI created';
while( my $feat = $parser->next_feature() ){
$seq->add_SeqFeature($feat);
}
($gene_seen, $exon_seen) = (0,0);
foreach my $feat ( $seq->top_SeqFeatures() ) {
if( $feat->isa("Bio::Tools::Prediction::Gene") ) {
foreach my $exon ( $feat->exons ) {
$exon_seen++;
}
$gene_seen++;
}
}
ok $exon_seen, 23;
ok $gene_seen, 1;
# let's test the ePCR factory
$parser = $factory->get_parser(-input => Bio::Root::IO->catfile("t","data", "genomic-seq.epcr"),
-method => 'epcr');
$seq->flush_SeqFeatures;
ok $parser->isa('Bio::SeqAnalysisParserI');#'noSeqAnalysisParserI created';
while( my $feat = $parser->next_feature() ){
$seq->add_SeqFeature($feat);
}
ok $seq->top_SeqFeatures(), 7;
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