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#-*-Perl-*-
# ## Bioperl Test Harness Script for Modules
# #
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 99,
-requires_modules => [qw(IPC::Run)]);
use_ok('Bio::Tools::Run::Genemark');
use_ok('Bio::Root::IO');
use_ok('Bio::Seq');
}
my $verbose = test_debug();
my $model_dir = $ENV{'GENEMARK_MODELS'} if $ENV{'GENEMARK_MODELS'};
SKIP: {
my $fasta_file = test_input_file('H_pylori_J99.fasta');
test_skip(-tests => 96,
-requires_env => 'GENEMARK_MODELS');
my $model_file = '';
for my $mod (qw(Helicobacter_pylori_26695.mod Helicobacter_pylori.mod)) {
my $modpath = Bio::Root::IO->catfile($model_dir, 'Helicobacter_pylori_26695.mod');
if (-e $modpath) {
$model_file = $modpath;
last;
}
}
ok($model_file, "Found model file: $model_file");
skip('Test model file not found', 95) if !$model_file;
my $factory = Bio::Tools::Run::Genemark->new( -m => $model_file,
-program => 'gmhmmp');
test_skip(-tests => 95,
-requires_executable => $factory);
isa_ok $factory, 'Bio::Tools::Run::Genemark';
my $seqstream = Bio::SeqIO->new(-file => $fasta_file, -format => 'fasta');
my $seq = $seqstream->next_seq();
my $gmhmmp = $factory->run($seq);
isa_ok $gmhmmp,'Bio::Tools::Genemark';
my $first_gene = $gmhmmp->next_prediction();
isa_ok $first_gene, 'Bio::Tools::Prediction::Gene';
is $first_gene->seq_id(), 'gi|15611071|ref|NC_000921.1|';
my $ct = 0;
# may fluctuate based on the model, stop after 91 checks
while (my $gene = $gmhmmp->next_prediction()) {
isa_ok $gene, 'Bio::Tools::Prediction::Gene';
last if $ct++ == 90;
}
}
1;