Bio::TreeIO
nexus
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Summary
Bio::TreeIO::nexus - A TreeIO driver module for parsing Nexus tree output from PAUP
Package variables
No package variables defined.
Included modules
Inherit
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.
The nexus format allows node comments that are placed inside square
brackets. Usually the comments (implemented as tags for nodes) are
used to give a name for an internal node or record the bootstap value,
but other uses are possible.
The FigTree program by Andrew Rambaut adds various rendering
parameters inside comments and flags these comments by starting them
with '&!'. The parameters implemented here are 'label' and 'color'.
Methods
Methods description
Title : next_tree
Usage : my $tree = $treeio->next_tree
Function: Gets the next tree in the stream
Returns : Bio::Tree::TreeI
Args : none |
Title : write_tree
Usage : $treeio->write_tree($tree);
Function: Writes a tree onto the stream
Returns : none
Args : Bio::Tree::TreeI |
Title : header
Usage : $obj->header($newval)
Function:
Example :
Returns : value of header (a scalar)
Args : on set, new value (a scalar or undef, optional) |
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) |
Methods code
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);
$tag =~ s/[\s,]+$//;
$translate{$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 );
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] .= ")";
}
$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 ) {
$data[0] = "(" . $data[0];
$data[-1] .= ")";
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;
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} );
$data[-1] .= sprintf( "[%s]", $b ) if defined $b;
}
}
else {
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;} | General documentation
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
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.
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 | Top |
Email jason-at-open-bio-dot-org
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
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