Permalink
Fetching contributors…
Cannot retrieve contributors at this time
74 lines (64 sloc) 1.9 KB
# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id$
#
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 15);
use_ok('Bio::Tools::Run::Alignment::StandAloneFasta');
use_ok('Bio::SeqIO');
}
my $verbose = -1;
my $version = '35';
my @params = ( 'b' =>'15',
'd' => 0,
'O' => test_output_file(),
'm'=>'9',
"program"=>"fasta$version");
my $factory = Bio::Tools::Run::Alignment::StandAloneFasta->new
('-verbose' => $verbose,
@params);
ok $factory;
my $inputfilename = test_input_file("fasta.fa");
SKIP: {
test_skip(-requires_executable => $factory,
-tests => 12);
my $lib = test_input_file("fastalib.fa");
$factory->library($lib);
my ($fastareport) = $factory->run($inputfilename);
my $result = $fastareport->next_result;
my $hit = $result->next_hit();
my $hsp = $hit->next_hsp();
is $hsp->algorithm, 'FASTN';
is $hsp->num_identical, 2982;
is $hsp->length, 2982;
$factory->program_name('ssearch'.$version);
($fastareport) = $factory->run($inputfilename);
$result = $fastareport->next_result;
$hit = $result->next_hit();
$hsp = $hit->next_hsp();
like $hsp->algorithm, qr/SMITH-WATERMAN|SSEARCH/;
is $hsp->num_identical, 2982;
is $hsp->length, 2982;
$factory->program_name('fastx'.$version);
$factory->library(test_input_file("fastaprot.fa"));
($fastareport) = $factory->run($inputfilename);
$result = $fastareport->next_result;
$hit = $result->next_hit();
$hsp = $hit->next_hsp();
is $hsp->algorithm, 'FASTX';
is $hsp->num_identical, 994;
is $hsp->length, 994;
my $sio = Bio::SeqIO->new(-file=>$inputfilename,
-format=>"fasta");
my $seq = $sio->next_seq;
#test with objects
($fastareport) = $factory->run($seq);
$result = $fastareport->next_result;
$hit = $result->next_hit();
$hsp = $hit->next_hsp();
is $hsp->algorithm, 'FASTX';
is $hsp->num_identical, 994;
is $hsp->length, 994;
}