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#-*-Perl-*-
# ## Bioperl Test Harness Script for Modules
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 40);
use_ok 'Bio::Tools::Run::Alignment::Blat';
use_ok 'Bio::SeqIO';
use_ok 'Bio::Seq';
}
my $db = test_input_file('blat_dna.fa');
my $query = test_input_file('blat_dna.fa');
my $factory = Bio::Tools::Run::Alignment::Blat->new(-db => $db);
ok $factory->isa('Bio::Tools::Run::Alignment::Blat');
my $blat_present = $factory->executable();
SKIP: {
test_skip(-requires_executable => $factory,
-tests => 24);
my $searchio = $factory->align($query);
isa_ok $searchio, 'Bio::SearchIO';
my $result = $searchio->next_result;
my $hit = $result->next_hit;
my $hsp = $hit->next_hsp;
isa_ok($hsp, "Bio::Search::HSP::HSPI");
is $hsp->query->start, 1;
is $hsp->query->end, 1775;
is $hsp->hit->start, 1;
is $hsp->hit->end, 1775;
is $hsp->hsp_length, 1775;
my $sio = Bio::SeqIO->new(-file => $query, -format => 'fasta');
my $seq = $sio->next_seq ;
$searchio = $factory->align($seq);
like $searchio, qr/psl/, 'PSL parser (default)';
$result = $searchio->next_result;
$hit = $result->next_hit;
$hsp = $hit->next_hsp;
isa_ok $hsp, 'Bio::Search::HSP::HSPI';
is $hsp->query->start, 1;
is $hsp->query->end, 1775;
is $hsp->hit->start, 1;
is $hsp->hit->end, 1775;
# test alternate formats (not all of these work!)
$factory->reset_parameters(#-quiet => 1,
-db => $db,
-out => 'blast');
$searchio = $factory->align($query);
like $searchio, qr/blast/, 'BLAST parser';
$result = $searchio->next_result;
$hit = $result->next_hit;
$hsp = $hit->next_hsp;
isa_ok $hsp, 'Bio::Search::HSP::HSPI';
is $hsp->query->start, 1;
is $hsp->query->end, 1775;
is $hsp->hit->start, 1;
is $hsp->hit->end, 1775;
$factory->reset_parameters(#-quiet => 1,
-db => $db,
-out => 'blast9');
$searchio = $factory->align($query);
like $searchio, qr/blasttable/, 'Tabular BLAST parser';
$result = $searchio->next_result;
$hit = $result->next_hit;
$hsp = $hit->next_hsp;
isa_ok $hsp, 'Bio::Search::HSP::HSPI';
is $hsp->query->start, 1;
is $hsp->query->end, 1775;
is $hsp->hit->start, 1;
is $hsp->hit->end, 1775;
}
# new wrapper; regions
$db = test_input_file('blat_dna.2bit');
$factory = Bio::Tools::Run::Alignment::Blat->new(
-db => $db,
#-quiet => 1,
-qsegment => 'sequence_10:0-100',
-tsegment => 'sequence_10:0-100',
# 0-based, Blat-compatible coordinates (start, end]
);
ok $factory->isa('Bio::Tools::Run::Alignment::Blat');
SKIP: {
skip("tests that require file named blat_dna.2bit and executable", 10) if ! -e $db;
test_skip(-requires_executable => $factory,
-tests => 10);
my $searchio = $factory->align($db);
my $result = $searchio->next_result;
my $hit = $result->next_hit;
my $hsp = $hit->next_hsp;
isa_ok $hsp, 'Bio::Search::HSP::HSPI';
is $hsp->query->start, 1;
is $hsp->query->end, 100;
is $hsp->hit->start, 1;
is $hsp->hit->end, 100;
# No on-the-fly conversion of Bio::Seq yet
my $sio = Bio::SeqIO->new(-file=>$query,-format=>'fasta');
my $seq = $sio->next_seq ;
$searchio = $factory->align($seq);
$result = $searchio->next_result;
$hit = $result->next_hit;
$hsp = $hit->next_hsp;
isa_ok $hsp, 'Bio::Search::HSP::HSPI';
is $hsp->query->start, 1;
is $hsp->query->end, 1775;
is $hsp->hit->start, 1;
is $hsp->hit->end, 1775;
}
1;
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