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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 19);
use_ok('Bio::Tools::Run::Phylo::Semphy');
}
# setup input files
my $alignfilename = test_input_file('semphy.seq');
my $treefilename = test_input_file('semphy.tree');
# object setup and testing
my $factory = Bio::Tools::Run::Phylo::Semphy->new(-quiet => 1, -z => '2.0', -H => 1, -jtt => 1, -S => 1);
isa_ok($factory, 'Bio::Tools::Run::Phylo::Semphy');
ok $factory->can('alphabet'), 'has a created method not in args';
is $factory->ratio, '2.0', 'ratio param was set via -z';
ok $factory->jtt, 'jtt switch was set';
is ($factory->program_dir, $ENV{'SEMPHYDIR'}, 'program_dir returned correct default');
is ($factory->program_name(), 'semphy', 'Correct exe default name');
# test the program itself
SKIP: {
test_skip(-requires_executable => $factory,
-tests => 12);
use_ok('Bio::TreeIO');
my $tree_out_file = test_output_file();
my $to = Bio::TreeIO->new(-format => 'newick',
-file => ">$tree_out_file");
# run Semphy with an alignment
ok my $tree1 = $factory->run($alignfilename);
$to->write_tree($tree1);
# or with alignment object
use_ok('Bio::AlignIO');
my $ai = Bio::AlignIO->new(-file => $alignfilename);
my $bio_simplalign = $ai->next_aln;
ok my $tree2 = $factory->run($bio_simplalign);
$to->write_tree($tree2);
# you can supply an initial tree as well, which can be a newick tree file,
# Bio::Tree::Tree object...
my $ti = Bio::TreeIO->new(-file => $treefilename);
my $tree_obj = $ti->next_tree;
ok my $tree3 = $factory->run($bio_simplalign, $tree_obj);
$to->write_tree($tree3);
# ... or Bio::DB::Taxonomy object
my $expected_count = 3;
SKIP: {
test_skip(-tests => 2, -requires_networking => 1);
use_ok('Bio::DB::Taxonomy');
my $bio_db_taxonomy = Bio::DB::Taxonomy->new(-source => 'entrez');
ok my $tree4 = $factory->run($bio_simplalign, $bio_db_taxonomy);
$to->write_tree($tree4);
$expected_count++;
}
$to->close;
my $expected_result = '(Cow:0.280119,((Baboon:0.035422,Human:0.080635):0.000213,(Rat:0.198658,Horse:0.642019):0.120910):0.074791,Semnopithecus_entellus:0.016396);';
open(my $res_fh, $tree_out_file);
my $count = 0;
while (<$res_fh>) {
chomp;
/\S/ || last;
$count++;
is $_, $expected_result;
}
close($res_fh);
is $count, $expected_count;
if ($expected_count == 3) {
ok 1;
}
}