#
# BioPerl module for Bio::TreeIO::pag
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-at-bioperl-dot-org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::TreeIO::pag - Bio::TreeIO driver for Pagel format
=head1 SYNOPSIS
use Bio::TreeIO;
my $in = Bio::TreeIO->new(-format => 'nexus',
-file => 't/data/adh.mb_tree.nexus');
my $out = Bio::TreeIO->new(-format => 'pag');
while( my $tree = $in->next_tree ) {
$out->write_tree($tree);
}
=head1 DESCRIPTION
Convert a Bio::TreeIO to Pagel format.
More information here http://www.evolution.reading.ac.uk/index.html
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::TreeIO::pag;
use strict;
our $TaxonNameLen = 10;
use base qw(Bio::TreeIO);
=head2 new
Title : new
Usage : my $obj = Bio::TreeIO::pag->new();
Function: Builds a new Bio::TreeIO::pag object
Returns : an instance of Bio::TreeIO::pag
Args : -file/-fh for filename or filehandles
-name_length for minimum name length (default = 10)
=cut
sub _initialize {
my $self = shift;
$self->SUPER::_initialize(@_);
my ( $name_length ) = $self->_rearrange(
[
qw(NAME_LENGTH)
],
@_
);
$self->name_length( defined $name_length ? $name_length : $TaxonNameLen );
}
=head2 write_tree
Title : write_tree
Usage :
Function: Write a tree out in Pagel format
Some options are only appropriate for bayesianmultistate and
the simpler output is only proper for discrete
Returns : none
Args : -no_outgroups => (number)
-print_header => 0/1 (leave 0 for discrete, 1 for bayesianms)
-special_node => special node - not sure what they wanted to do here
-keep_outgroup => 0/1 (keep the outgroup node in the output)
-outgroup_ancestor => Bio::Tree::Node (if we want to exclude or include the outgroup this is what we operate on)
-tree_no => a tree number label - only useful for BayesianMultistate
=cut
sub write_tree {
my ($self,$tree,@args) = @_;
my ($keep_outgroup,
$print_header,
$no_outgroups,
$special_node,
$outgroup_ancestor,
$tree_no) = (0,0,1);
my $name_len = $self->name_length;
if( @args ) {
($no_outgroups,
$print_header,
$special_node,
$outgroup_ancestor,
$tree_no,
$keep_outgroup) = $self->_rearrange([qw(
NO_OUTGROUPS
PRINT_HEADER
SPECIAL_NODE
OUTGROUP_ANCESTOR
TREE_NO
KEEP_OUTGROUP
NAME_LENGTH)],@args);
}
my $newname_base = 1;
my $root = $tree->get_root_node;
my $eps = 0.0001;
my (%chars,%names);
my @nodes = $tree->get_nodes;
my $species_ct;
my $traitct;
for my $node ( @nodes ) {
if ((defined $special_node) && ($node eq $special_node)) {
my $no_of_tree_nodes = scalar(@nodes);
my $node_name = sprintf("N%d",$no_of_tree_nodes+1);
$names{$node->internal_id} = $node_name;
} elsif ($node->is_Leaf) {
$species_ct++;
my $node_name = $node->id;
if( length($node_name)> $name_len ) {
$self->warn( "Found a taxon name longer than $name_len letters, \n",
"name will be abbreviated.\n");
$node_name = substr($node_name, 0,$name_len);
} else {
# $node_name = sprintf("%-".$TaxonNameLen."s",$node_name);
}
$names{$node->internal_id} = $node_name;
my @tags = sort $node->get_all_tags;
my @charstates = map { ($node->get_tag_values($_))[0] } @tags;
$traitct = scalar @charstates unless defined $traitct;
$chars{$node->internal_id} = [@charstates];
} else {
$names{$node->internal_id} = sprintf("N%d", $newname_base++);
}
}
# generate PAG representation
if( $print_header ) {
if ($keep_outgroup) {
$self->_print(sprintf("%d %d\n",$species_ct,$traitct));
} else {
$self->_print( sprintf("%d %d\n",$species_ct-$no_outgroups,$traitct));
}
}
my @ancestors = ();
if ($keep_outgroup) {
push @ancestors, $root;
} else {
push @ancestors, ( $root, $outgroup_ancestor);
}
my @rest;
foreach my $node (@nodes) {
my $i = 0;
foreach my $anc (@ancestors) {
if ($anc && $node eq $anc) { $i = 1; last }
}
unless ($i > 0) { # root not given in PAG
my $current_name = $names{$node->internal_id};
my $branch_length_to_output;
if ($node->branch_length < $eps) {
my $msg_nodename = $current_name;
$msg_nodename =~ s/\s+$//;
warn( "TREE $tree_no, node \"$msg_nodename\": branch too ",
"short (", $node->branch_length, "): increasing length to ",
"$eps\n");
$branch_length_to_output = $eps;
} else {
$branch_length_to_output = $node->branch_length;
}
my @line = ( $current_name,
$names{$node->ancestor->internal_id},
$branch_length_to_output);
if ($node->is_Leaf) {
push @line, @{$chars{$node->internal_id}};
$self->_print(join(',', @line),"\n");
} else {
push @rest, \@line;
}
}
}
for ( @rest ) {
$self->_print(join(',', @$_),"\n");
}
}
=head2 next_tree
Title : next_tree
Usage :
Function:
Example :
Returns :
Args :
=cut
sub next_tree{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 name_length
Title : name_length
Usage : $self->name_length(20);
Function: set mininum taxon name length
Returns : integer (length of name)
Args : integer
=cut
sub name_length {
my ($self, $val) = @_;
return $self->{'name_len'} = $val if $val;
return $self->{'name_len'};
}
1;