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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: AlignStats.t,v 1.6 2003/10/16 14:15:44 heikki Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
my $error = 0;
use strict;
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; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 21;
}
if( $error == 1 ) {
exit(0);
}
my $debug = -1;
use Bio::Align::DNAStatistics;
use Bio::AlignIO;
use Bio::Root::IO;
# NOTE NOTE NOTE
# A lot more work needs to be done on this DNAStatistics object
# it currently doesn't actually calculate everything correctly
# The currently implemented tests show what DOES work.
# Volunteers welcomed
my $in = new Bio::AlignIO(-format => 'emboss',
-file => Bio::Root::IO->catfile('t', 'data',
'insulin.water'));
my $aln = $in->next_aln();
ok($aln);
my $stats = new Bio::Align::DNAStatistics(-verbose => $debug);
ok( $stats->transversions($aln),4);
ok( $stats->transitions($aln),9);
ok( $stats->pairwise_stats->number_of_gaps($aln),21);
ok( $stats->pairwise_stats->number_of_comparable_bases($aln),173);
ok( $stats->pairwise_stats->number_of_differences($aln),13);
my $d = $stats->distance(-align=> $aln,
-method => 'JC');
ok( sprintf("%.5f",$d->[1]->[2]), 0.07918);
$d = $stats->distance(-align=> $aln,
-method => 'Kimura');
ok( sprintf("%.5f",$d->[1]->[2]), 0.07984);
#$d = $stats->distance(-align=> $aln,
# -method => 'TajimaNei');
#ok( sprintf("%.5f",$d->[1]->[2]), 0.0780);
$aln = $in->next_aln();
ok(! defined $aln);
$in = new Bio::AlignIO(-format => 'fasta',
-file => Bio::Root::IO->catfile('t','data',
'hs_owlmonkey.fasta'));
$aln = $in->next_aln();
ok($aln);
ok( $stats->transversions($aln),4);
ok( $stats->transitions($aln),14);
ok( $stats->pairwise_stats->number_of_gaps($aln),33);
ok( $stats->pairwise_stats->number_of_comparable_bases($aln),163);
ok( $stats->pairwise_stats->number_of_differences($aln),18);
# now test the distance calculations
if( 0 ) {
$d = $stats->distance(-align => $aln, -method => 'jc');
ok( sprintf("%.4f", $d->[1]->[2]), 0.1195);
$d = $stats->distance(-align => $aln,
-method => 'Kimura');
ok( sprintf("%.4f", $d->[1]->[2]), 0.1219);
# $d = $stats->distance(-align => $aln,
# -method => 'TajimaNei');
# ok( sprintf("%.4f", $d->[1]->[2]), 0.1246);
}
#ok( sprintf("%.4f", Bio::Align::DNAStatistics->D_JukesCantorInCor($aln)), 0.1104);
#ok( sprintf("%.4f", Bio::Align::DNAStatistics->D_Tamura($aln)), 0.1233);
#ok( sprintf("%.4f", Bio::Align::DNAStatistics->D_Tamura($aln)), 0.1246);
#ok( sprintf("%.4f", Bio::Align::DNAStatistics->D_JinNeiGamma($aln)), 0.1350);
### now test Nei_gojobori methods ##
$in = Bio::AlignIO->new(-format => 'fasta',
-file => Bio::Root::IO->catfile('t','data', 'nei_gojobori_test.aln'));
my $alnobj = $in->next_aln();
ok($alnobj);
my $result = $stats->calc_KaKs_pair($alnobj, 'seq1', 'seq2');
ok (sprintf ("%.1f", $result->[0]{'S'}), 40.5);
ok (sprintf ("%.1f", $result->[0]{'z_score'}), '4.5');
$result = $stats->calc_all_KaKs_pairs($alnobj);
ok (int( $result->[1]{'S'}), 41);
ok (int( $result->[1]{'z_score'}), 4);
$result = $stats->calc_average_KaKs($alnobj, 100);
ok (sprintf ("%.4f", $result->{'D_n'}), 0.1628);
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