| Bio::Tools::Phylo::Molphy(3pm) | User Contributed Perl Documentation | Bio::Tools::Phylo::Molphy(3pm) |
Bio::Tools::Phylo::Molphy - parser for Molphy output
use Bio::Tools::Phylo::Molphy;
my $parser = Bio::Tools::Phylo::Molphy->new(-file => 'output.protml');
while( my $r = $parser->next_result ) {
# r is a Bio::Tools::Phylo::Molphy::Result object
# print the model name
print $r->model, "\n";
# get the substitution matrix
# this is a hash of 3letter aa codes -> 3letter aa codes representing
# substitution rate
my $smat = $r->substitution_matrix;
print "Arg -> Gln substitution rate is %d\n",
$smat->{'Arg'}->{'Gln'}, "\n";
# get the transition probablity matrix
# this is a hash of 3letter aa codes -> 3letter aa codes representing
# transition probabilty
my $tmat = $r->transition_probability_matrix;
print "Arg -> Gln transition probablity is %.2f\n",
$tmat->{'Arg'}->{'Gln'}, "\n";
# get the frequency for each of the residues
my $rfreqs = $r->residue_frequencies;
foreach my $residue ( keys %{$rfreqs} ) {
printf "residue %s expected freq: %.2f observed freq: %.2f\n",
$residue,$rfreqs->{$residue}->[0], $rfreqs->{$residue}->[1];
}
my @trees;
while( my $t = $r->next_tree ) {
push @trees, $t;
}
print "search space is ", $r->search_space, "\n",
"1st tree score is ", $trees[0]->score, "\n";
# writing to STDOUT, use -file => '>filename' to specify a file
my $out = Bio::TreeIO->new(-format => "newick");
$out->write_tree($trees[0]); # writing only the 1st tree
}
A parser for Molphy output (protml,dnaml)
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = Bio::Tools::Phylo::Molphy->new(); Function: Builds a new Bio::Tools::Phylo::Molphy object Returns : Bio::Tools::Phylo::Molphy Args : -fh/-file => $val, # for initing input, see Bio::Root::IO
Title : next_result Usage : my $r = $molphy->next_result Function: Get the next result set from parser data Returns : Bio::Tools::Phylo::Molphy::Result object Args : none
| 2020-10-28 | perl v5.30.3 |