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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
##
my $error;
use strict;
use vars qw($DEBUG);
$DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
$error = 0;
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
use vars qw($TESTCOUNT);
$TESTCOUNT = 22;
plan tests => $TESTCOUNT;
}
use Bio::TreeIO;
my $verbose = 0;
my $treeio = new Bio::TreeIO(-verbose => $verbose,
-format => 'nhx',
-file => Bio::Root::IO->catfile('t','data',
'test.nhx'));
my $tree = $treeio->next_tree;
my @nodes = $tree->find_node('ADH2');
ok(@nodes, 2);
if( $verbose ) {
$treeio = new Bio::TreeIO(-verbose => $verbose,
-format => 'nhx',
);
$treeio->write_tree($tree);
print "nodes are: \n",
join(", ", map { $_->id . ":". (defined $_->branch_length ?
$_->branch_length : '' ) } @nodes), "\n";
}
$treeio = new Bio::TreeIO(-format => 'newick',
-file => Bio::Root::IO->catfile('t','data',
'test.nh'));
$tree = $treeio->next_tree;
if( $verbose ) {
my $out = new Bio::TreeIO(-format => 'tabtree');
$out->write_tree($tree);
}
my @hADH = ( $tree->find_node('hADH1'),
$tree->find_node('hADH2') );
my ($n4) = $tree->find_node('yADH4');
ok($tree->is_monophyletic(-nodes => \@hADH,
-outgroup => $n4));
my @mixgroup = ( $tree->find_node('hADH1'),
$tree->find_node('yADH2'),
$tree->find_node('yADH3'),
);
my ($iADHX) = $tree->find_node('iADHX');
ok(! $tree->is_monophyletic(-nodes => \@mixgroup,
-outgroup=> $iADHX));
my $in = new Bio::TreeIO(-format => 'newick',
-fh => \*DATA);
$tree = $in->next_tree;
my ($a,$b,$c,$d) = ( $tree->find_node('A'),
$tree->find_node('B'),
$tree->find_node('C'),
$tree->find_node('D'));
ok($tree->is_monophyletic(-nodes => [$b,$c],
-outgroup => $d));
ok($tree->is_monophyletic(-nodes => [$b,$a],
-outgroup => $d) );
$tree = $in->next_tree;
my ($e,$f,$i);
($a,$b,$c,$d,$e,$f,$i) = ( $tree->find_node('A'),
$tree->find_node('B'),
$tree->find_node('C'),
$tree->find_node('D'),
$tree->find_node('E'),
$tree->find_node('F'),
$tree->find_node('I'),
);
ok(! $tree->is_monophyletic(-nodes => [$b,$f],
-outgroup => $d) );
ok($tree->is_monophyletic(-nodes => [$b,$a],
-outgroup => $f));
# test for paraphyly
ok( $tree->is_paraphyletic(-nodes => [$a,$b,$c],
-outgroup => $d), 0);
ok( $tree->is_paraphyletic(-nodes => [$a,$f,$e],
-outgroup => $i), 1);
# test for rerooting the tree
$tree = $in->next_tree;
$tree->verbose( -1 ) unless $DEBUG;
# reroot on an internal node: should work fine
$a = $tree->find_node('A');
my $node_cnt_orig = scalar($tree->get_nodes);
my $total_length_orig = $tree->total_branch_length;
ok($tree->reroot($a->ancestor) eq '1');
ok($node_cnt_orig, scalar($tree->get_nodes));
my $total_length_new = $tree->total_branch_length;
my $eps = 0.001 * $total_length_new; # tolerance for checking length
ok(($total_length_orig >= $tree->total_branch_length - $eps)
and ($total_length_orig <= $tree->total_branch_length + $eps));
ok($tree->get_root_node, $a->ancestor);
# try to reroot on a leaf: should end up rerooting on its ancestor
$a = $tree->find_node('C');
ok($tree->reroot($a) eq '1');
ok($node_cnt_orig, scalar($tree->get_nodes));
ok(($total_length_orig >= $tree->total_branch_length - $eps)
and ($total_length_orig <= $tree->total_branch_length + $eps));
ok($tree->get_root_node, $a->ancestor);
# try to reroot on existing root: should fail
$a = $tree->get_root_node;
ok($tree->reroot($a) eq '0');
# try a more realistic tree
$tree = $in->next_tree;
$a = $tree->find_node('VV');
$node_cnt_orig = scalar($tree->get_nodes);
$total_length_orig = $tree->total_branch_length;
ok($tree->reroot($a->ancestor) eq '1');
ok($node_cnt_orig, scalar($tree->get_nodes));
$total_length_new = $tree->total_branch_length;
$eps = 0.001 * $total_length_new; # tolerance for checking length
ok(($total_length_orig >= $tree->total_branch_length - $eps)
and ($total_length_orig <= $tree->total_branch_length + $eps));
ok($tree->get_root_node, $a->ancestor);
__DATA__
(D,(C,(A,B)));
(I,((D,(C,(A,B))),(E,(F,G))));
((A:0.3,B:2.1):0.000003,C:1e-2,D:4);
(A:0.031162,((((((B:0.022910,C:0.002796):0.010713,(D:0.015277,E:0.020484):0.005336):0.005588,((F:0.013293,(G:0.018374,H:0.003108):0.005318):0.006047,I:0.014607):0.001677):0.004196,(((((J:0.003307,K:0.001523):0.011884,L:0.006960):0.006514,((M:0.001683,N:0.000100):0.002226,O:0.007085):0.014649):0.008004,P:0.037422):0.005201,(Q:0.000805,R:0.000100):0.015280):0.005736):0.004612,S:0.042283):0.017979,(T:0.006883,U:0.016655):0.040226):0.014239,((((((V:0.000726,W:0.000100):0.028490,((((X:0.011182,Y:0.001407):0.005293,Z:0.011175):0.004701,AA:0.007825):0.016256,BB:0.029618):0.008146):0.004279,CC:0.035012):0.060215,((((((DD:0.014933,(EE:0.008148,FF:0.000100):0.015458):0.003891,GG:0.010996):0.001489,(HH:0.000100,II:0.000100):0.054265):0.003253,JJ:0.019722):0.013796,((KK:0.001960,LL:0.004924):0.013034,MM:0.010071):0.043273):0.011912,(NN:0.031543,OO:0.018307):0.059182):0.026517):0.011087,((PP:0.000100,QQ:0.002916):0.067214,(RR:0.064486,SS:0.013444):0.011613):0.050846):0.015644,((TT:0.000100,UU:0.009287):0.072710,(VV:0.009242,WW:0.009690):0.035346):0.042993):0.060365);
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