Bio::TreeIO::nexus - A TreeIO driver module for parsing Nexus tree output from PAUP
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Code Index:
NAME
Bio::TreeIO::nexus - A TreeIO driver module for parsing Nexus tree output from PAUP
SYNOPSIS
use Bio::TreeIO;
my $in = Bio::TreeIO->new(-file => 't/data/cat_tre.tre');
while( my $tree = $in->next_tree ) {
}
DESCRIPTION
This is a driver module for parsing PAUP Nexus tree format which
basically is just a remapping of trees.
FEEDBACK
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
Support
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 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/
AUTHOR - Jason Stajich
Email jason-at-open-bio-dot-org
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
new
Title : new
Args : -header => boolean default is true
print/do not print #NEXUS header
-translate => boolean default is true
print/do not print Node Id translation to a number
next_tree
Title : next_tree
Usage : my $tree = $treeio->next_tree
Function: Gets the next tree in the stream
Returns : Bio::Tree::TreeI
Args : none
write_tree
Title : write_tree
Usage : $treeio->write_tree($tree);
Function: Writes a tree onto the stream
Returns : none
Args : Bio::Tree::TreeI
translate_node
Title : translate_node
Usage : $obj->translate_node($newval)
Function:
Example :
Returns : value of translate_node (a scalar)
Args : on set, new value (a scalar or undef, optional)
#
# BioPerl module for Bio::TreeIO::nexus
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-at-open-bio-dot-org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
# Let the code begin...
package Bio::TreeIO::nexus;
use strict;
use Bio::Event::EventGeneratorI;
use IO::String;
use base qw(Bio::TreeIO);
sub _initialize {
my $self = shift;
$self->SUPER::_initialize(@_);
my ( $hdr, $trans ) = $self->_rearrange(
[
qw(HEADER
TRANSLATE)
],
@_
);
$self->header( defined $hdr ? $hdr : 1 );
$self->translate_node( defined $trans ? $trans : 1 );
}
sub next_tree {
my ($self) = @_;
unless ( $self->{'_parsed'} ) {
$self->_parse;
}
return $self->{'_trees'}->[ $self->{'_treeiter'}++ ];
}
sub rewind {
shift->{'_treeiter'} = 0;
}
sub _parse {
my ($self) = @_;
$self->{'_parsed'} = 1;
$self->{'_treeiter'} = 0;
while ( defined( $_ = $self->_readline ) ) {
next if /^\s+$/;
last;
}
return unless ( defined $_ );
unless (/^\#NEXUS/i) {
$self->warn("File does not start with #NEXUS"); #'
return;
}
my $line;
while ( defined( $_ = $self->_readline ) ) {
$line .= $_;
}
my @sections = split( /#NEXUS/i, $line );
for my $s (@sections) {
my %translate;
if ( $self->verbose > 0 ) {
while ( $s =~ s/(\[[^\]]+\])// ) {
$self->debug("removing comment $1\n");
}
}
else {
$s =~ s/(\[[^\]]+\])//g;
}
if ( $s =~ /begin trees;(.+)(end;)?/si ) {
my $trees = $1;
if ( $trees =~ s/\s+translate\s+([^;]+);//i ) {
my @trans;
my $tr = $1;
while ($tr =~ m{\s*([^,\s]+?\s+(?:'[^']+'|[^'\s]+)),?}gc) {
push @trans, $1;
}
for my $n ( @trans ) {
if ($n =~ /^\s*(\S+)\s+(.+)$/) {
my ($id,$tag) = ($1,$2);
$tag =~ s/[\s,]+$//; # remove the extra spaces of the last taxon
$translate{$id} = $tag;
}
}
}
else {
$self->debug("no translate in: $trees\n");
}
while ($trees =~ /\s+tree\s+\*?\s*(\S+)\s*\=
\s*(?:\[\S+\])?\s*([^\;]+;)/igx)
{
my ( $tree_name, $tree_str ) = ( $1, $2 );
# MrBayes does not print colons for node label
# $tree_str =~ s/\)(\d*\.\d+)\)/:$1/g;
my $buf = IO::String->new($tree_str);
my $treeio = Bio::TreeIO->new(
-format => 'newick',
-fh => $buf
);
my $tree = $treeio->next_tree;
foreach my $node ( grep { $_->is_Leaf } $tree->get_nodes ) {
my $id = $node->id;
my $lookup = $translate{$id};
$node->id( $lookup || $id );
}
$tree->id($tree_name) if defined $tree_name;
push @{ $self->{'_trees'} }, $tree;
}
}
else {
$self->debug("begin_trees failed: $s\n");
}
}
if ( !@sections ) {
$self->debug("warn no sections: $line\n");
}
}
sub write_tree {
my ( $self, @trees ) = @_;
if ( $self->header ) {
$self->_print("#NEXUS\n\n");
}
my $translate = $self->translate_node;
my $time = localtime();
$self->_print( sprintf( "Begin trees; [Treefile created %s]\n", $time ) );
my ( $first, $nodecter, %node2num ) = ( 0, 1 );
foreach my $tree (@trees) {
if ( $first == 0
&& $translate )
{
$self->_print("\tTranslate\n");
$self->_print(
join(
",\n",
map {
$node2num{ $_->id } = $nodecter;
sprintf( "\t\t%d %s", $nodecter++, $_->id )
}
grep { $_->is_Leaf } $tree->get_nodes
),
"\n;\n"
);
}
my @data = _write_tree_Helper( $tree->get_root_node, \%node2num );
if ( $data[-1] !~ /\)$/ ) {
$data[0] = "(" . $data[0];
$data[-1] .= ")";
}
# by default all trees in bioperl are currently rooted
# something we'll try and fix one day....
$self->_print(
sprintf(
"\t tree %s = [&%s] %s;\n",
( $tree->id || sprintf( "Bioperl_%d", $first + 1 ) ),
( $tree->get_root_node ) ? 'R' : 'U',
join( ',', @data )
)
);
$first++;
}
$self->_print("End;\n");
$self->flush if $self->_flush_on_write && defined $self->_fh;
return;
}
sub _write_tree_Helper {
my ( $node, $node2num ) = @_;
return () if ( !defined $node );
my @data;
foreach my $n ( $node->each_Descendent() ) {
push @data, _write_tree_Helper( $n, $node2num );
}
if ( @data > 1 ) { # internal node
$data[0] = "(" . $data[0];
$data[-1] .= ")";
# FigTree comments start
my $comment_flag;
$comment_flag = 0
if ( $node->has_tag('color') or $node->has_tag('label') );
$data[-1] .= '[&!' if defined $comment_flag;
if ( $node->has_tag('color')) {
my $color = $node->get_tag_values('color');
$data[-1] .= "color=$color";
$comment_flag++;
}
if ( $node->has_tag('label')) {
my $label = $node->get_tag_values('label');
$data[-1] .= ',' if $comment_flag;
$data[-1] .= 'label="'. $label. '"';
}
$data[-1] .= ']' if defined $comment_flag;
# FigTree comments end
# let's explicitly write out the bootstrap if we've got it
my $b;
my $bl = $node->branch_length;
if ( !defined $bl ) {
}
elsif ( $bl =~ /\#/ ) {
$data[-1] .= $bl;
}
else {
$data[-1] .= ":$bl";
}
if ( defined( $b = $node->bootstrap ) ) {
$data[-1] .= sprintf( "[%s]", $b );
}
elsif ( defined( $b = $node->id ) ) {
$b = $node2num->{$b} if ( $node2num->{$b} ); # translate node2num
$data[-1] .= sprintf( "[%s]", $b ) if defined $b;
}
}
else { # leaf node
if ( defined $node->id || defined $node->branch_length ) {
my $id = defined $node->id ? $node->id : '';
if ( length($id) && $node2num->{$id} ) {
$id = $node2num->{$id};
}
if ( $node->has_tag('color')) {
my ($color) = $node->get_tag_values('color');
$id .= "[&!color=$color\]";
}
push @data,
sprintf( "%s%s",
$id,
defined $node->branch_length
? ":" . $node->branch_length
: '' );
}
}
return @data;
}
sub header {
my $self = shift;
return $self->{'header'} = shift if @_;
return $self->{'header'};
}
sub translate_node {
my $self = shift;
return $self->{'translate_node'} = shift if @_;
return $self->{'translate_node'};
}
1;