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# -*-Perl-*- Test Harness script for Bioperl
# $Id: Molphy.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 18,
-requires_module => 'IO::String');
use_ok('Bio::Tools::Phylo::Molphy');
}
my $verbose = test_debug();
my $inmolphy = Bio::Tools::Phylo::Molphy->new(-file => test_input_file('lysozyme6.simple.protml'));
ok($inmolphy);
my $r = $inmolphy->next_result;
ok($r);
is($r->model, 'JTT');
is($r->search_space,50);
my @trees;
while( my $t = $r->next_tree ) {
push @trees, $t;
}
is(@trees,5);
$inmolphy = Bio::Tools::Phylo::Molphy->new(-file => test_input_file('lysozyme6.protml'));
ok($inmolphy);
$r = $inmolphy->next_result;
is($r->model, 'JTT');
is($r->search_space,50);
@trees = ();
while( my $t = $r->next_tree ) {
push @trees, $t;
}
is(@trees,5);
is($trees[0]->score, -1047.8);
is($trees[-1]->id, 9);
my $tpm = $r->transition_probability_matrix;
is($tpm->{'Val'}->{'Val'}, -122884);
is($tpm->{'Ala'}->{'Arg'}, 2710);
my $sub_mat = $r->substitution_matrix;
is($sub_mat->{'Val'}->{'Tyr'}, 50);
is($sub_mat->{'Arg'}->{'Ile'}, 72);
is($sub_mat->{'Met'}->{'Met'}, '');
my %fmat = $r->residue_frequencies();
is($fmat{'D'}->[0], 0.052);
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