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|
#!/usr/bin/env perl
use utf8;
use strict;
use warnings;
use Test::More;
use File::Spec;
use Bio::AlignIO;
use Bio::TreeIO;
use Bio::Tools::Phylo::PAML;
use Bio::Tools::Run::Phylo::PAML::Codeml;
use Bio::Tools::Run::Phylo::PAML::Yn00;
sub test_input_file {
return File::Spec->catfile('t', 'data', @_);
}
my $verbose = 0;
my $inpaml = Bio::Tools::Phylo::PAML->new(-file =>
test_input_file('codeml.mlc'));
ok($inpaml);
my $codeml = Bio::Tools::Run::Phylo::PAML::Codeml->new
(-params => {'runmode' => -2,
'seqtype' => 1,
'model' => 0,
'alpha' => '0',
'omega' => 0.4,
'kappa' => 2,
'CodonFreq'=> 2,
'NSsites' => 0,
'model' => 0,
},
-verbose => $verbose);
my $in = Bio::AlignIO->new(-format => 'phylip',
-file => test_input_file('gf-s85.phylip'));
my $aln = $in->next_aln;
$codeml->alignment($aln);
my ($rc,$results) = $codeml->run();
is($rc,1);
ok(defined $results, "got results");
my $result = $results->next_result;
ok(defined $result, "got a result");
my $MLmatrix = $result->get_MLmatrix;
my ($vnum) = ($result->version =~ /(\d+(\.\d+)?)/);
SKIP: {
if( $vnum == 3.12 ) {
# PAML 2.12 results
is($MLmatrix->[0]->[1]->{'dN'}, 0.0693);
is($MLmatrix->[0]->[1]->{'dS'},1.1459);
is($MLmatrix->[0]->[1]->{'omega'}, 0.0605);
is($MLmatrix->[0]->[1]->{'S'}, 273.5);
is($MLmatrix->[0]->[1]->{'N'}, 728.5);
is($MLmatrix->[0]->[1]->{'t'}, 1.0895);
skip($MLmatrix->[0]->[1]->{'lnL'},
"I don't know what this should be, if you run this part, email the list so we can update the value",
1);
} elsif( $vnum >= 3.13 && $vnum < 4) {
# PAML 2.13 results
is($MLmatrix->[0]->[1]->{'dN'}, 0.0713);
is($MLmatrix->[0]->[1]->{'dS'},1.2462);
is(sprintf("%.4f",$MLmatrix->[0]->[1]->{'omega'}), 0.0572);
is($MLmatrix->[0]->[1]->{'S'}, 278.8);
is($MLmatrix->[0]->[1]->{'N'}, 723.2);
is(sprintf("%.4f",$MLmatrix->[0]->[1]->{'t'}), 1.1946);
skip($MLmatrix->[0]->[1]->{'lnL'},
"I don't know what this should be, if you run this part, email the list so we can update the value",
1);
} elsif( $vnum >= 4 ) {
## PAML 4, 4.8, and 4.9h results
is($MLmatrix->[0]->[1]->{'dN'}, 0.0713);
is($MLmatrix->[0]->[1]->{'dS'},1.2462);
is(sprintf("%.4f",$MLmatrix->[0]->[1]->{'omega'}), 0.0572);
is($MLmatrix->[0]->[1]->{'S'}, 278.8);
is($MLmatrix->[0]->[1]->{'N'}, 723.2);
is(sprintf("%.4f",$MLmatrix->[0]->[1]->{'t'}), 1.1946);
is($MLmatrix->[0]->[1]->{'lnL'}, -1929.935243);
} else {
skip("Can't test the result output, don't know about PAML version ".$result->version,
7);
}
}
unlike($codeml->error_string, qr/Error/); # we don't expect any errors;
my $yn00 = Bio::Tools::Run::Phylo::PAML::Yn00->new();
$yn00->alignment($aln);
($rc,$results) = $yn00->run();
is($rc,1);
ok(defined $results, "got results");
$result = $results->next_result;
ok(defined $result, "got a result");
$MLmatrix = $result->get_MLmatrix;
is($MLmatrix->[0]->[1]->{'dN'}, 0.0846);
is($MLmatrix->[0]->[1]->{'dS'}, 1.0926);
is($MLmatrix->[0]->[1]->{'omega'}, 0.0774);
is($MLmatrix->[0]->[1]->{'S'}, 278.4);
is($MLmatrix->[0]->[1]->{'N'}, 723.6);
is($MLmatrix->[0]->[1]->{'t'}, 1.0941);
unlike($yn00->error_string, qr/Error/); # we don't expect any errors;
$codeml = Bio::Tools::Run::Phylo::PAML::Codeml->new
(-params => { 'alpha' => 1.53 },
-verbose => $verbose);
ok($codeml);
# AAML
my $cysaln = Bio::AlignIO->new(-format => 'msf',
-file => test_input_file('cysprot.msf'))->next_aln;
my $cystre = Bio::TreeIO->new(-format => 'newick',
-file => test_input_file('cysprot.raxml.tre'))->next_tree;
ok($cysaln);
ok($cystre);
$codeml = Bio::Tools::Run::Phylo::PAML::Codeml->new
(
-verbose => 0,
-tree => $cystre,
-params => { 'runmode' => 0, # provide a usertree
'seqtype' => 2, # AMINO ACIDS,
'model' => 0, # one dN/dS rate
'NSsites' => 0, # one -- swap this with 1, 2, 3 etc
'clock' => 0, # 0 = no clock
'getSE' => 1, # get Standard Error
'fix_blength' => 0, # use initial BLengths
'ncatG' => 1, #increase approrpriately for NSsites,
},
-alignment => $cysaln,
-save_tempfiles => 1,
);
ok($codeml);
($rc,$results) = $codeml->run();
is($rc,1);
ok(defined $results, "got results");
$result = $results->next_result;
($vnum) = ($result->version =~ /(\d+(\.\d+)?)/);
for my $tree ( $result->get_trees ) {
my $node = $tree->find_node(-id => 'CATL_HUMAN');
if( $vnum == 4 ) {
is($node->branch_length, '0.216223');
} else {
is($node->branch_length, '0.216223');
}
}
done_testing ();
|
