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
Bio::Event::EventGeneratorI
IO::String
Inherit
Bio::TreeIO
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
_initialize
No description
Code
next_treeDescriptionCode
rewind
No description
Code
_parse
No description
Code
write_treeDescriptionCode
_write_tree_Helper
No description
Code
headerDescriptionCode
translate_nodeDescriptionCode
Methods description
next_treecode    nextTop
 Title   : next_tree
Usage : my $tree = $treeio->next_tree
Function: Gets the next tree in the stream
Returns : Bio::Tree::TreeI
Args : none
write_treecodeprevnextTop
 Title   : write_tree
Usage : $treeio->write_tree($tree);
Function: Writes a tree onto the stream
Returns : none
Args : Bio::Tree::TreeI
headercodeprevnextTop
 Title   : header
Usage : $obj->header($newval)
Function:
Example :
Returns : value of header (a scalar)
Args : on set, new value (a scalar or undef, optional)
translate_nodecodeprevnextTop
 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
_initializedescriptionprevnextTop
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 ? $trans : 1 );
}
next_treedescriptionprevnextTop
sub next_tree {
    my ($self) = @_;
    unless ( $self->{'_parsed'} ) {
        $self->_parse;
    }
    return $self->{'_trees'}->[ $self->{'_treeiter'}++ ];
}
rewinddescriptionprevnextTop
sub rewind {
    shift->{'_treeiter'} = 0;
}
_parsedescriptionprevnextTop
sub _parse {
    my ($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"); }
}
write_treedescriptionprevnextTop
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;
}
_write_tree_HelperdescriptionprevnextTop
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;
}
headerdescriptionprevnextTop
sub header {
    my $self = shift;

    return $self->{'header'} = shift if @_;
    return $self->{'header'};
}
translate_nodedescriptionprevnextTop
sub translate_node {
    my $self = shift;

    return $self->{'translate_node'} = shift if @_;
    return $self->{'translate_node'};
}

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-open-bio-dot-org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 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