Bio-Tools-Phylo-PAML

 view release on metacpan or  search on metacpan

bin/bp_pairwise_kaks  view on Meta::CPAN

print OUT join("\t", qw(SEQ1 SEQ2 Ka Ks Ka/Ks PROT_PERCENTID CDNA_PERCENTID)), "\n";
for( my $i = 0; $i < (scalar @otus -1) ; $i++) {
    for( my $j = $i+1; $j < (scalar @otus); $j++ ) {
        my $sub_aa_aln = $aa_aln->select_noncont($pos[$i],$pos[$j]);
        my $sub_dna_aln = $dna_aln->select_noncont($pos[$i],$pos[$j]);
        print OUT join("\t",
                       $otus[$i]->display_id,
                       $otus[$j]->display_id,$MLmatrix->[$i]->[$j]->{'dN'},
                       $MLmatrix->[$i]->[$j]->{'dS'},
                       $MLmatrix->[$i]->[$j]->{'omega'},
                       sprintf("%.2f",$sub_aa_aln->percentage_identity),
                       sprintf("%.2f",$sub_dna_aln->percentage_identity),
                       ), "\n";
    }
}

__END__

=pod

=encoding UTF-8

lib/Bio/Tools/Phylo/PAML.pm  view on Meta::CPAN

            $self->{'_summary'}->{'aafreqs'} = {};    # reset/clear values
            next;
        }
        elsif (
            /^\#\s+constant\s+sites\:\s+
         (\d+)\s+ # constant sites
         \(\s*([\d\.]+)\s*\%\s*\)/x
          )
        {
            $self->{'_summary'}->{'stats'}->{'constant_sites'}            = $1;
            $self->{'_summary'}->{'stats'}->{'constant_sites_percentage'} = $2;
        }
        elsif (/^ln\s+Lmax\s+\(unconstrained\)\s+\=\s+(\S+)/x) {
            $self->{'_summary'}->{'stats'}->{'loglikelihood'} = $1;
            $done = 1;    # done for sure
        }
        else {
            my ( $seqname, @freqs ) = split;
            my $basect = 0;
            foreach my $f (@freqs) {

lib/Bio/Tools/Phylo/PAML.pm  view on Meta::CPAN

            $self->{'_summary'}->{'ntfreqs'} = {};    # reset/clear values
            next;
        }
        elsif (
            /^\#\s+constant\s+sites\:\s+
         (\d+)\s+    # constant sites
         \(\s*([\d\.]+)\s*\%\s*\)/ox
          )
        {
            $self->{'_summary'}->{'stats'}->{'constant_sites'}            = $1;
            $self->{'_summary'}->{'stats'}->{'constant_sites_percentage'} = $2;
        }
        elsif (/^ln\s+Lmax\s+\(unconstrained\)\s+\=\s+(\S+)/ox) {
            $self->{'_summary'}->{'stats'}->{'loglikelihood'} = $1;
            $done = 1;    # done for sure
        }
        else {
            my ( $seqname, @freqs ) = split;
            my $basect = 0;
            foreach my $f (@freqs) {

t/PAML-parser.t  view on Meta::CPAN

is($result->get_AAFreqs('Average')->{'I'},0.0424);

my $patterns = $result->patterns;
my @pat = @{$patterns->{'-patterns'}};
is(scalar @pat, 98);
is($patterns->{'-ns'}, 6);
is($patterns->{'-ls'}, 130);

is((sort $result->get_stat_names)[0], 'constant_sites');
is($result->get_stat('constant_sites'), 46);
is($result->get_stat('constant_sites_percentage'), 35.38);

# AAML parsing - pairwise model
$inpaml = Bio::Tools::Phylo::PAML->new(-file => test_input_file('aaml_pairwise.mlc'));

ok($inpaml);
$result = $inpaml->next_result;
ok($result);
is($result->model, 'Empirical_F (wag.dat)');
is($result->get_stat('loglikelihood'),-1189.106658);
is($result->get_stat('constant_sites'), 170);
is($result->get_stat('constant_sites_percentage'), 59.65);

is($result->get_AAFreqs('Average')->{'R'},0.0211);
is($result->get_AAFreqs('rabbit')->{'L'},0.1228);

$aadistmat = $result->get_AADistMatrix();
ok($aadistmat);
is($aadistmat->get_entry('rabbit', 'marsupial'), 0.2877);
is($aadistmat->get_entry('human', 'goat-cow'), 0.1439);

$aadistmat = $result->get_AAMLDistMatrix();

t/PAML-parser.t  view on Meta::CPAN

    (-file => test_input_file('singleNSsite.mlc'));
ok($codeml_single);
my $result_single = $codeml_single->next_result;
my ($nssite_single) = $result_single->get_NSSite_results;
is($nssite_single->num_site_classes,q/3/);
is($nssite_single->kappa, q/5.28487/);
is($nssite_single->likelihood,q/-30.819156/);

is($baseml->get_stat('loglikelihood'),-110.532715);
is($baseml->get_stat('constant_sites'),46);
is($baseml->get_stat('constant_sites_percentage'),'80.70');
is($baseml->model,'HKY85 dGamma (ncatG=5)');

# user trees
$baseml_p = Bio::Tools::Phylo::PAML->new
    (-file => test_input_file('baseml.usertree'));
$baseml = $baseml_p->next_result;

@trees = $baseml->get_trees;
is(@trees, 1);
is($trees[0]->score, -129.328757);