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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 27);
use_ok('Bio::Tools::Run::Hmmer');
use_ok('Bio::SeqIO');
use_ok('Bio::AlignIO');
}
my $verbose = test_debug();
my $quiet = $verbose > 0 ? 0 : 1;
my $db = test_input_file('pfam_sample_R11');
my @params = ('DB'=>$db,'E'=>5,'program'=>'hmmpfam','A'=>2,'-verbose' => $verbose, -quiet => $quiet);
#test HMMPFAM
my $factory = Bio::Tools::Run::Hmmer->new(@params);
isa_ok($factory, 'Bio::Tools::Run::Hmmer');
is $factory->E, 5;
is $factory->DB, $db;
is $factory->hmm, $db;
my $prot_file = test_input_file('hmmpfam_protein_input');
my $seqstream = Bio::SeqIO->new(-file => $prot_file,
-format => 'fasta');
my $seq1 = $seqstream->next_seq();
SKIP: {
# here we assume if hmmpfam isn't present, nothing is present
test_skip(-requires_executable => $factory,
-tests => 20);
my $searchio = $factory->run($seq1);
my @feat;
while (my $result = $searchio->next_result){
while(my $hit = $result->next_hit){
while (my $hsp = $hit->next_hsp){
push @feat, $hsp;
}
}
}
isa_ok $feat[0], 'Bio::SeqFeatureI';
is ($feat[0]->feature1->start,25);
is ($feat[0]->feature1->end,92);
is ($feat[0]->feature2->start,1);
is ($feat[0]->feature2->end,124);
#test HMMSEARCH
@params = ('HMM'=>$db,'E'=>5,'program'=>'hmmsearch','-verbose' => $verbose, -quiet => $quiet);
$factory = Bio::Tools::Run::Hmmer->new(@params);
isa_ok $factory, 'Bio::Tools::Run::Hmmer';
is $factory->E, 5;
SKIP: {
test_skip(-requires_executable => $factory,
-tests => 5);
my $searchio = $factory->run($seq1);
my @feat;
while (my $result = $searchio->next_result){
while(my $hit = $result->next_hit){
while (my $hsp = $hit->next_hsp){
push @feat, $hsp;
}
}
}
isa_ok $feat[0], 'Bio::SeqFeatureI';#Bio::Search::HSP::HMMERHSP
is ($feat[0]->feature1->start,1);
is ($feat[0]->feature1->end,124);
is ($feat[0]->feature2->start,25);
is ($feat[0]->feature2->end,92);
}
#test HMMBUILD
my $hmmout = test_output_file();
unlink($hmmout);
@params = ('HMM'=>$hmmout,'program'=>'hmmbuild', -verbose => $verbose, -quiet => $quiet);
$factory = Bio::Tools::Run::Hmmer->new(@params);
isa_ok $factory, 'Bio::Tools::Run::Hmmer';
is $factory->quiet, $quiet;
my $aln_file = test_input_file('cysprot.msf');
my $aio = Bio::AlignIO->new(-file=>$aln_file,-format=>'msf');
my $aln = $aio->next_aln;
SKIP: {
test_skip(-requires_executable => $factory,
-tests => 2);
ok $factory->run($aln);
ok -s $hmmout;
}
#test HMMCALIBRATE, and from now on, alternate (preferred) run method calling,
#though we need to check the executables are present in the normal way first
$factory->program_name('hmmcalibrate');
SKIP: {
test_skip(-requires_executable => $factory,
-tests => 1);
ok $factory->hmmcalibrate();
}
$factory->program_name('hmmalign');
#test HMMALIGN
my $seqfile = test_input_file('cysprot1a.fa');
my $seqio = Bio::SeqIO->new(-file => $seqfile,
-format=> 'fasta');
my @seqs;
while( my $seq = $seqio->next_seq ) {
push @seqs, $seq;
}
SKIP: {
test_skip(-requires_executable => $factory,
-tests => 2);
$aio = $factory->hmmalign(@seqs);
ok $aln = $aio->next_aln;
is($aln->each_seq, 3);
}
$factory->program_name('hmmemit');
#test HMMEMIT
SKIP: {
test_skip(-requires_executable => $factory,
-tests => 1);
my $seqio = $factory->hmmemit();
my @seqs;
while (my $seq = $seqio->next_seq) {
push(@seqs, $seq);
}
is @seqs, 10; # emits 10 seqs by default
}
# Delete temporary file
unlink($hmmout);
}