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# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id: Molphy.t,v 1.1 2002/07/25 04:34:52 jason Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use vars qw($NUMTESTS $error);
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
eval { require Test; };
$error = 0;
if( $@ ) {
use lib 't';
}
use Test;
$NUMTESTS = 17;
plan tests => $NUMTESTS;
eval { require IO::String;
require Bio::Tools::Phylo::Molphy;};
if( $@ ) { print STDERR "no IO string installed\n";
$error = 1;
}
}
END {
foreach ( $Test::ntest .. $NUMTESTS ) {
skip("unable to run all of the Molphy tests",1);
}
}
exit(0) if( $error );
my $testnum;
my $verbose = 0;
## End of black magic.
##
## Insert additional test code below but remember to change
## the print "1..x\n" in the BEGIN block to reflect the
## total number of tests that will be run.
my $inmolphy = new Bio::Tools::Phylo::Molphy(-file => 't/data/lysozyme6.simple.protml');
ok($inmolphy);
my $r = $inmolphy->next_result;
ok($r);
ok($r->model, 'JTT');
ok($r->search_space,50);
my @trees;
while( my $t = $r->next_tree ) {
push @trees, $t;
}
ok(@trees,5);
$inmolphy = new Bio::Tools::Phylo::Molphy(-file => 't/data/lysozyme6.protml');
ok($inmolphy);
$r = $inmolphy->next_result;
ok($r->model, 'JTT');
ok($r->search_space,50);
@trees = ();
while( my $t = $r->next_tree ) {
push @trees, $t;
}
ok(@trees,5);
ok($trees[0]->score, -1047.8);
ok($trees[-1]->id, 9);
my $tpm = $r->transition_probability_matrix;
ok($tpm->{'Val'}->{'Val'}, -122884);
ok($tpm->{'Ala'}->{'Arg'}, 2710);
my $sub_mat = $r->substitution_matrix;
ok($sub_mat->{'Val'}->{'Tyr'}, 50);
ok($sub_mat->{'Arg'}->{'Ile'}, 72);
ok($sub_mat->{'Met'}->{'Met'}, '');
my %fmat = $r->residue_frequencies();
ok($fmat{'D'}->[0], 0.052);
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