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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 42);
use_ok('Bio::Tools::Run::Phylo::Phyml');
use_ok('Bio::AlignIO');
}
# setup input files etc
my $inputfilename = test_input_file("protpars.phy");
ok (-e $inputfilename, 'Found protein input file');
my $factory = Bio::Tools::Run::Phylo::Phyml->new(-verbose => test_debug());
isa_ok($factory, 'Bio::Tools::Run::Phylo::Phyml');
# test default factory values
is ($factory->program_dir, $ENV{'PHYMLDIR'}, 'program_dir returned correct default');
is ($factory->program_name(), 'phyml', 'Correct exe default name');
is ($factory->data_format, 'i', 'data_format, default');
is ($factory->data_format('s'), 's', 'data_format, sequential');
is ($factory->data_format('i'), 'i', 'data_format, interleaved');
is ($factory->dataset_count, 1, 'dataset_count, default');
is ($factory->dataset_count(2), 2, 'data_count, 2');
is ($factory->kappa, 'e', 'kappa, default');
is ($factory->kappa(4), '4.0', 'kappa');
is ($factory->invar, 'e', 'invar, default');
is ($factory->invar(.5), '0.5', 'invar');
is ($factory->category_number, 1, 'category_number, default');
is ($factory->category_number(4), 4, 'category_number');
is ($factory->alpha, 'e', 'alpha, default');
is ($factory->alpha(1.0), '1.0', 'alpha');
is ($factory->alpha('e'), 'e', 'alpha');
is ($factory->tree, 'BIONJ', 'tree, default');
# not a valid tree for this MSA, just testing
my $mock_treefile = test_input_file("treefile.example");
is ($factory->tree($mock_treefile), $mock_treefile, 'tree');
is ($factory->tree('BIONJ'), 'BIONJ', 'tree');
# test the program itself
SKIP: {
test_skip(-requires_executable => $factory,
-tests => 23);
cmp_ok $factory->version, '>', '2.4','version';
# test version-specific parameters
if ($factory->version >= 3 ) {
is ($factory->data_type, 'aa', 'data_type, default');
is ($factory->data_type('nt'), 'nt', 'data_type, dna');
is ($factory->data_type('aa'), 'aa', 'data_type, aa');
is ($factory->model, 'LG', 'model, default');
is ($factory->opt, 'n', 'opt, default');
is ($factory->opt('tl'), 'tl', 'opt_topology');
is ($factory->freq, undef, 'freq, default');
is ($factory->freq('d'), 'd', 'freq');
is ($factory->search, 'NNI', 'search, default');
is ($factory->search('SPR'), 'SPR', 'search');
is ($factory->rand_start, 0, 'rand_start, default');
is ($factory->rand_start(1), 1, 'rand_start');
is ($factory->rand_starts, 1, 'rand_starts, default');
is ($factory->rand_starts(10), 10, 'rand_starts');
cmp_ok $factory->rand_seed, '>=', 1, 'rand_seed, default';
is ($factory->rand_seed(10), 10, 'rand_seed');
$factory->search('NNI'); #to take the fastest option for running
} else { # version 2.4.4
is ($factory->data_type, '1', 'data_type, default');
is ($factory->data_type('dna'), '0', 'data_type, dna');
is ($factory->data_type('protein'), '1', 'data_type, protein');
is ($factory->model, 'JTT', 'model, default');
is ($factory->opt_topology, '1', 'opt_topology, default'); # got: '1' instead of 'y'
is ($factory->opt_topology('0'), '1', 'opt_topology'); # got: '1' instead of 'y'
is ($factory->opt_topology('1'), '1', 'opt_topology'); # got: '1' instead of 'y'
is ($factory->opt_lengths, '1', 'opt_lengths, default'); # got: '1' instead of 'y'
is ($factory->opt_lengths('0'), '1', 'opt_lengths'); # got: '1' instead of 'n'
is ($factory->opt_lengths('1'), '1', 'opt_lengths'); # got: '1' instead of 'y'
for (1..6) {ok 1;} # to have same number of tests for all versions
}
# $factory->save_tempfiles(1);
# my $workdir = '/tmp/phyml_test';
# $factory->tempdir($workdir);
# using filename input
# my $tree = $factory->run($inputfilename);
# isa_ok($tree, 'Bio::Tree::Tree');
# ------------- EXCEPTION -------------
# MSG: Phyml call (/usr/bin/phyml /tmp/fL3jNAmzKP/protpars.phy 1 i 2 0 WAG 0.5 4 e BIONJ y y) did not give an output [/tmp/fL3jNAmzKP/protpars.phy_phyml_stat.txt]: 256
# STACK Bio::Tools::Run::Phylo::Phyml::_run /build/bioperl-run-1.6.9/blib/lib/Bio/Tools/Run/Phylo/Phyml.pm:851
# STACK Bio::Tools::Run::Phylo::Phyml::run /build/bioperl-run-1.6.9/blib/lib/Bio/Tools/Run/Phylo/Phyml.pm:338
# STACK toplevel t/Phyml.t:109
# -------------------------------------
# delete more tests that need to fail as a consequence
is substr($factory->tree_string, 0, 5), 'BIONJ', 'tree_string()';
# using AlignIO on a DNA MSA
$inputfilename = test_input_file("dna_seqs1.phy");
ok (-e $inputfilename, 'Found DNA input file');
my $alignio = Bio::AlignIO->new(-file => $inputfilename);
my $aln = $alignio->next_aln;
my $alphabet;
if ($factory->version >= 3){
$alphabet = 'nt';
} else {
$alphabet = 'dna';
}
#testing passing attributes to the constructor
my %args = (
-data_type => $alphabet,
-model => 'JC69',
-kappa => 4,
-invar => 'e',
-category_number => 4,
-alpha => 'e',
-tree => 'BIONJ',
-verbose => 0
);
$factory = Bio::Tools::Run::Phylo::Phyml->new(%args);
$factory->save_tempfiles(1);
#$tree = $factory->run($aln);
#@leaves = $tree->get_leaf_nodes;
#is (@leaves, 5, 'Result tree from DNA SimpleAlign input had correct number of leaves');
}
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