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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 27);
use_ok('Bio::Tools::Run::Alignment::TCoffee');
use_ok('Bio::SimpleAlign');
use_ok('Bio::AlignIO');
use_ok('Bio::SeqIO');
}
END { unlink qw(cysprot.dnd cysprot1a.dnd) }
END {
unlink("t_coffee.log");
}
my @params;
my $factory = Bio::Tools::Run::Alignment::TCoffee->new(@params);
isa_ok ($factory, 'Bio::Tools::Run::Alignment::TCoffee');
my $ktuple = 3;
$factory->ktuple($ktuple);
my $new_ktuple = $factory->ktuple();
is $new_ktuple, 3, "set factory parameter";
my $what_matrix = $factory->matrix();
like $what_matrix, qr/BLOSUM/i, "get factory parameter";
my $bequiet = 1;
$factory->quiet($bequiet); # Suppress tcoffee messages to terminal
my $inputfilename = test_input_file('cysprot.fa');
my $aln;
SKIP: {
test_skip(-requires_executable => $factory,
-tests => 20);
my $version = $factory->version;
cmp_ok ($version, '>=', 1.22, "Code tested only on t_coffee versions > 1.22" );
$aln = $factory->align($inputfilename);
ok($aln);
is( $aln->num_sequences, 7);
my $str = Bio::SeqIO->new('-file' =>
test_input_file("cysprot.fa"),
'-format' => 'fasta');
my @seq_array =();
while ( my $seq = $str->next_seq() ) {
push (@seq_array, $seq) ;
}
my $seq_array_ref = \@seq_array;
$aln = $factory->align($seq_array_ref);
is $aln->num_sequences, 7;
my $s1_perid = $aln->average_percentage_identity;
my $profile1 = test_input_file("cysprot1a.msf");
my $profile2 = test_input_file("cysprot1b.msf");
# convert any warnings about program to an actual exception
$factory->verbose(2);
lives_ok {$aln = $factory->profile_align($profile1,$profile2)};
skip("T-COFFEE error, skipping tests", 15) if $@;
is $aln->num_sequences, 7;
my $str1 = Bio::AlignIO->new(-file=> test_input_file("cysprot1a.msf"));
my $aln1 = $str1->next_aln();
is $aln1->num_sequences, 3;
my $str2 = Bio::AlignIO->new(-file=> test_input_file("cysprot1b.msf"));
my $aln2 = $str2->next_aln();
is $aln2->num_sequences, 4;
$aln = $factory->profile_align($aln1,$aln2);
is $aln->num_sequences, 7;
$str1 = Bio::AlignIO->new(-file=> test_input_file("cysprot1a.msf"));
$aln1 = $str1->next_aln();
$str2 = Bio::SeqIO->new(-file=> test_input_file("cysprot1b.fa"));
my $seq = $str2->next_seq();
is $aln1->num_sequences, 3;
is( int($aln1->average_percentage_identity), 39);
$aln = $factory->profile_align($aln1,$seq);
is( $aln->num_sequences, 4);
if( $version <= 1.22 ) {
cmp_ok( $aln->overall_percentage_identity, '>', 18);
is( int($aln->average_percentage_identity), 44);
} else {
my $overall = int($aln->overall_percentage_identity);
ok( $overall >=21 && $overall <= 23, 'expect 21 >= val >= 23');
my $avg = int($aln->average_percentage_identity);
ok( $avg == 47 || $avg ==48, 'expect 47 or 48');
}
# test new 'run' generic running of factory
$aln = $factory->run('-type' => 'align',
'-seq' => test_input_file("cysprot.fa"));
is ($aln->num_sequences, 7, 'simple generic run');
is ($aln->percentage_identity,$s1_perid); #calculated before
lives_ok{ $aln = $factory->run('-type' => 'profile',
'-profile' => $aln1,
'-seq' => test_input_file("cysprot1b.fa"))} ;
skip("T-COFFEE error, skipping tests",3) if $@;
is( $aln->num_sequences, 7);
if( $version <= 1.22 ) {
cmp_ok( $aln->overall_percentage_identity, '>', 18);
is( int($aln->average_percentage_identity), 44);
} else {
my $overall = int $aln->overall_percentage_identity;
ok($overall == 14 || $overall == 13, 'expect 13 or 14');
my $avg = int($aln->average_percentage_identity);
ok($avg == 41 || $avg == 42, 'expect 41 or 42');
}
}
END {
# warnings are already given above, no need to keep report
if (-e 'error_report.T-COFFEE') {
unlink('error_report.T-COFFEE');
}
if (my @dnds = glob('*.dnd')) {
for my $file (@dnds) {
unlink($file)
}
}
}