Bio::TreeIO pag
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Summary
Bio::TreeIO::pag - Bio::TreeIO driver for Pagel format
Package variables
No package variables defined.
Inherit
Bio::TreeIO
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); }
Description
Convert a Bio::TreeIO to Pagel format.
More information here http://www.evolution.reading.ac.uk/index.html
Methods
_initialize
No description
Code
write_treeDescriptionCode
next_treeDescriptionCode
name_lengthDescriptionCode
Methods description
write_treecode    nextTop
 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
next_treecodeprevnextTop
 Title   : next_tree
Usage :
Function:
Example :
Returns :
Args :
name_lengthcodeprevnextTop
 Title   : name_length
Usage : $self->name_length(20);
Function: set mininum taxon name length
Returns : integer (length of name)
Args : integer
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my $self = shift;
    $self->SUPER::_initialize(@_);
    my ( $name_length ) = $self->_rearrange(
        [
            qw(NAME_LENGTH)
        ],
        @_
    );
    $self->name_length( defined $name_length ? $name_length : $TaxonNameLen );
}
write_treedescriptionprevnextTop
sub write_tree {
    my ($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"); }
}
next_treedescriptionprevnextTop
sub next_tree {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
name_lengthdescriptionprevnextTop
sub name_length {
    my ($self, $val) = @_;
    return $self->{'name_len'} = $val if $val;
    return $self->{'name_len'};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
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/
AUTHOR - Jason StajichTop
Email jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 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)