use strict;
use Test::More;
use Bio::Phylo::Forest::Tree;
use Bio::Phylo::Util::Logger;
BEGIN {
eval { require Bio::TreeIO };
if ($@) {
plan 'skip_all' => 'Bio::TreeIO not found';
}
if ( not $ENV{'BIOPERL_LIVE_ROOT'} ) {
plan 'skip_all' => 'env var BIOPERL_LIVE_ROOT not set';
}
}
BEGIN {
use lib $ENV{'BIOPERL_LIVE_ROOT'} . '/t/lib';
use Bio::Root::Test;
test_begin( '-tests' => 73 );
use_ok('Bio::TreeIO');
}
no warnings 'redefine';
sub test_input_file {
my $file = shift;
return $ENV{'BIOPERL_LIVE_ROOT'} . '/t/data/' . $file;
}
my $logger = Bio::Phylo::Util::Logger->new;
$logger->VERBOSE( '-level' => 0 );
my $verbose = test_debug();
ok my $treeio = Bio::TreeIO->new(
'-verbose' => $verbose,
'-format' => 'newick',
'-file' => test_input_file('cysprot1b.newick')
);
my $tree = Bio::Phylo::Forest::Tree->new_from_bioperl( $treeio->next_tree );
isa_ok( $tree, 'Bio::Tree::TreeI' );
my @nodes = $tree->get_nodes;
is( @nodes, 6 );
my ($rat) = $tree->find_node('CATL_RAT');
ok($rat);
is( $rat->branch_length, '0.12788' );
# move the id to the bootstap
is( $rat->ancestor->bootstrap( $rat->ancestor->id ), '95' );
$rat->ancestor->id('');
# maybe this can be auto-detected, but then can't distinguish
# between internal node labels and bootstraps...
is( $rat->ancestor->bootstrap, '95' );
is( $rat->ancestor->branch_length, '0.18794' );
is( $rat->ancestor->id, '' );
if ($verbose) {
foreach my $node ( $tree->get_root_node()->each_Descendent() ) {
print "node: ", $node->to_string(), "\n";
my @ch = $node->each_Descendent();
if (@ch) {
print "\tchildren are: \n";
foreach my $node ( $node->each_Descendent() ) {
print "\t\t ", $node->to_string(), "\n";
}
}
}
}
my $FILE1 = test_output_file();
$treeio = Bio::TreeIO->new(
'-verbose' => $verbose,
'-format' => 'newick',
'-file' => ">$FILE1"
);
$treeio->write_tree($tree);
undef $treeio;
ok( -s $FILE1 );
$treeio = Bio::TreeIO->new(
'-verbose' => $verbose,
'-format' => 'newick',
'-file' => test_input_file('LOAD_Ccd1.dnd')
);
ok($treeio);
$tree = Bio::Phylo::Forest::Tree->new_from_bioperl( $treeio->next_tree );
isa_ok( $tree, 'Bio::Tree::TreeI' );
@nodes = $tree->get_nodes;
is( @nodes, 52 );
if ($verbose) {
foreach my $node (@nodes) {
print "node: ", $node->to_string(), "\n";
my @ch = $node->each_Descendent();
if (@ch) {
print "\tchildren are: \n";
foreach my $node ( $node->each_Descendent() ) {
print "\t\t ", $node->to_string(), "\n";
}
}
}
}
is( $tree->total_branch_length, 7.12148 );
my $FILE2 = test_output_file();
$treeio = Bio::TreeIO->new(
'-verbose' => $verbose,
'-format' => 'newick',
'-file' => ">$FILE2"
);
$treeio->write_tree($tree);
undef $treeio;
ok( -s $FILE2 );
$treeio = Bio::TreeIO->new(
'-verbose' => $verbose,
'-format' => 'newick',
'-file' => test_input_file('hs_fugu.newick')
);
$tree = Bio::Phylo::Forest::Tree->new_from_bioperl( $treeio->next_tree() );
@nodes = $tree->get_nodes();
is( @nodes, 5 );
# no relable order for the bottom nodes because they have no branchlen
my @vals = qw(SINFRUP0000006110);
my $saw = 0;
foreach my $node ( $tree->get_root_node()->each_Descendent() ) {
foreach my $v (@vals) {
if ( defined $node->id && $node->id eq $v ) { $saw = 1; last; }
}
last if $saw;
}
is( $saw, 1, "Saw $vals[0] as expected" );
if ($verbose) {
foreach my $node (@nodes) {
print "\t", $node->id, "\n" if $node->id;
}
}
$treeio = Bio::TreeIO->new(
'-format' => 'newick',
'-fh' => \*DATA
);
my $treeout = Bio::TreeIO->new( '-format' => 'tabtree' );
my $treeout2 = Bio::TreeIO->new( '-format' => 'newick' );
$tree = Bio::Phylo::Forest::Tree->new_from_bioperl( $treeio->next_tree );
if ( $verbose > 0 ) {
$treeout->write_tree($tree);
$treeout2->write_tree($tree);
}
$treeio = Bio::TreeIO->new(
'-verbose' => $verbose,
'-file' => test_input_file('test.nhx')
);
SKIP: {
test_skip( '-tests' => 2, '-requires_module' => 'SVG::Graph' );
my $FILE3 = test_output_file();
my $treeout3 = Bio::TreeIO->new(
'-format' => 'svggraph',
'-file' => ">$FILE3"
);
ok($treeout3);
eval { $treeout3->write_tree($tree); };
ok( -s $FILE3 );
}
ok($treeio);
$tree = Bio::Phylo::Forest::Tree->new_from_bioperl( $treeio->next_tree );
isa_ok( $tree, 'Bio::Tree::TreeI' );
@nodes = $tree->get_nodes;
is( @nodes, 13, "Total Nodes" );
my $adhy = $tree->find_node('ADHY');
is( $adhy->branch_length, 0.1 );
is( ( $adhy->get_tag_values('S') )[0], 'nematode' );
is( ( $adhy->get_tag_values('E') )[0], '1.1.1.1' );
# try lintree parsing
$treeio = Bio::TreeIO->new(
'-format' => 'lintree',
'-file' => test_input_file('crab.njb')
);
my ( @leaves, $node );
while ( $tree = $treeio->next_tree ) {
$tree = Bio::Phylo::Forest::Tree->new_from_bioperl($tree);
isa_ok( $tree, 'Bio::Tree::TreeI' );
@nodes = $tree->get_nodes;
@leaves = $tree->get_leaf_nodes;
is( @leaves, 13 );
SKIP: {
skip "for some reason we get 24", 1 unless 0;
is( @nodes, 25 );
}
($node) = $tree->find_node( -id => '18' );
ok($node);
is( $node->id, '18' );
is( $node->branch_length, '0.030579' );
is( $node->bootstrap, 998 );
}
$treeio = Bio::TreeIO->new(
'-format' => 'lintree',
'-file' => test_input_file('crab.nj')
);
$tree = Bio::Phylo::Forest::Tree->new_from_bioperl( $treeio->next_tree );
isa_ok( $tree, 'Bio::Tree::TreeI' );
@nodes = $tree->get_nodes;
@leaves = $tree->get_leaf_nodes;
is( @leaves, 13 );
SKIP: {
skip "for some reason we get 24", 1 unless 0;
is( @nodes, 25 );
}
($node) = $tree->find_node('18');
is( $node->id, '18' );
is( $node->branch_length, '0.028117' );
($node) = $tree->find_node( -id => 'C-vittat' );
is( $node->id, 'C-vittat' );
is( $node->branch_length, '0.087619' );
is( $node->ancestor->id, '14' );
$treeio = Bio::TreeIO->new(
'-format' => 'lintree',
'-file' => test_input_file('crab.dat.cn')
);
$tree = Bio::Phylo::Forest::Tree->new_from_bioperl( $treeio->next_tree );
isa_ok( $tree, 'Bio::Tree::TreeI' );
@nodes = $tree->get_nodes;
@leaves = $tree->get_leaf_nodes;
is( @leaves, 13, "Leaf nodes" );
SKIP: {
skip "for some reason we get 24", 1 unless 0;
is( @nodes, 25, "All nodes" );
}
($node) = $tree->find_node('18');
is( $node->id, '18' );
is( $node->branch_length, '0.029044' );
($node) = $tree->find_node( -id => 'C-vittat' );
is( $node->id, 'C-vittat' );
is( $node->branch_length, '0.097855' );
is( $node->ancestor->id, '14' );
SKIP: {
test_skip( -tests => 8, -requires_module => 'IO::String' );
# test nexus tree parsing
$treeio = Bio::TreeIO->new(
'-format' => 'nexus',
'-verbose' => $verbose,
'-file' => test_input_file('urease.tre.nexus')
);
$tree = Bio::Phylo::Forest::Tree->new_from_bioperl( $treeio->next_tree );
ok($tree);
is( $tree->id, 'PAUP_1' );
is( $tree->get_leaf_nodes, 6 );
($node) = $tree->find_node( '-id' => 'Spombe' );
is( $node->branch_length, 0.221404 );
# test nexus MrBayes tree parsing
$treeio = Bio::TreeIO->new(
'-format' => 'nexus',
'-file' => test_input_file('adh.mb_tree.nexus')
);
$tree = Bio::Phylo::Forest::Tree->new_from_bioperl( $treeio->next_tree );
ok($tree);
is( $tree->id, 'rep.1' );
is( $tree->get_leaf_nodes, 54 );
($node) = $tree->find_node( -id => 'd.madeirensis' );
is( $node->branch_length, 0.039223 );
}
# bug #1854
# process no-newlined tree
$treeio = Bio::TreeIO->new(
'-format' => 'nexus',
'-verbose' => $verbose,
'-file' => test_input_file('tree_nonewline.nexus')
);
$tree = Bio::Phylo::Forest::Tree->new_from_bioperl( $treeio->next_tree );
ok($tree);
ok( $tree->find_node('TRXHomo') );
# parse trees with scores
$treeio = Bio::TreeIO->new(
'-format' => 'newick',
'-file' => test_input_file('puzzle.tre')
);
$tree = Bio::Phylo::Forest::Tree->new_from_bioperl( $treeio->next_tree );
ok($tree);
is( $tree->score, '-2673.059726' );
# bug #2205
# process trees with node IDs containing spaces
$treeio = Bio::TreeIO->new(
'-format' => 'nexus',
'-verbose' => $verbose,
'-file' => test_input_file('spaces.nex')
);
$tree = Bio::Phylo::Forest::Tree->new_from_bioperl( $treeio->next_tree );
my @nodeids = ( "'Allium drummondii'", "'Allium cernuum'", 'A.cyaneum' );
ok($tree);
for my $node ( $tree->get_leaf_nodes ) {
is( $node->id, shift @nodeids );
}
# bug #2221
# process tree with names containing quoted commas
$tree = Bio::Phylo::Forest::Tree->new_from_bioperl( $treeio->next_tree );
@nodeids =
( "'Allium drummondii, USA'", "'Allium drummondii, Russia'", 'A.cyaneum' );
ok($tree);
for my $node ( $tree->get_leaf_nodes ) {
is( $node->id, shift @nodeids );
}
# bug #2221
# process tree with names containing quoted commas on one line
$tree = Bio::Phylo::Forest::Tree->new_from_bioperl( $treeio->next_tree );
@nodeids =
( "'Allium drummondii, Russia'", "'Allium drummondii, USA'", 'A.cyaneum' );
ok($tree);
for my $node ( $tree->get_leaf_nodes ) {
is( $node->id, shift @nodeids );
}
__DATA__
(((A:1,B:1):1,(C:1,D:1):1):1,((E:1,F:1):1,(G:1,H:1):1):1);