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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
use strict;
BEGIN
{
eval { require Test; };
if ($@)
{
use lib 't';
}
use Test;
use vars qw($NTESTS);
$NTESTS = 26;
plan tests => $NTESTS;
}
use Bio::Tools::Geneid;
use Bio::SeqIO;
ok(1);
my $inputfilename = Bio::Root::IO->catfile("t", "data", "geneid_1.0.out");
my $parser = Bio::Tools::Geneid->new(-file => $inputfilename);
my @genes;
while (my $gene= $parser->next_prediction)
{
push(@genes, $gene);
}
my @transcripts = $genes[0]->transcripts;
my @exons = $transcripts[0]->exons;
ok($transcripts[0]->seq_id, '10');
ok($exons[0]->seq_id, '10');
ok($transcripts[0]->source_tag, 'geneid');
ok($exons[0]->source_tag, 'geneid');
ok($transcripts[0]->primary_tag, 'transcript');
ok($exons[0]->primary_tag, 'Initial');
ok(scalar($transcripts[0]->exons), 2);
ok($transcripts[0]->start, 6090);
ok($transcripts[0]->end, 7276);
ok($transcripts[0]->score, 36.87);
ok($transcripts[0]->strand, 1);
ok($exons[0]->start, 6090);
ok($exons[0]->end, 6155);
ok($exons[0]->score, '1.40');
ok($exons[0]->strand, 1);
my ($type) = $exons[0]->get_tag_values('Type');
ok($type, 'Initial');
my ($phase) = $exons[0]->get_tag_values('phase');
ok($phase, 0);
my ($end_phase) = $exons[0]->get_tag_values('end_phase');
ok($end_phase, 0);
my ($start_signal_score) = $exons[0]->get_tag_values('start_signal_score');
ok($start_signal_score, 2.15);
my ($end_signal_score) = $exons[0]->get_tag_values('end_signal_score');
ok($end_signal_score, 3.63);
my ($coding_potential_score) = $exons[0]->get_tag_values('coding_potential_score');
ok($coding_potential_score, 12.34);
my ($homology_score) = $exons[0]->get_tag_values('homology_score');
ok($homology_score, '0.00');
ok(scalar(@genes), 3);
@transcripts = $genes[1]->transcripts;
ok(scalar($transcripts[0]->exons), 5);
@transcripts = $genes[2]->transcripts;
ok(scalar($transcripts[0]->exons), 1);
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