# $Id: lintree.pm 16123 2009-09-17 12:57:27Z cjfields $
#
# BioPerl module for Bio::TreeIO::lintree
#
# 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::lintree - Parser for lintree output trees
=head1 SYNOPSIS
# do not use directly, use through Bio::TreeIO
use Bio::TreeIO;
my $treeio = Bio::TreeIO->new(-format => 'lintree',
-file => 't/data/crab.nj');
my $tree = $treeio->next_tree;
=head1 DESCRIPTION
Parser for the lintree output which looks like this
13 sequences 1000 bootstraping
1 A-salina
2 C-vittat
3 C-sp.
4 L-aequit
5 P-camtsc
6 E-tenuim
7 L-splend
8 P-bernha
9 P-acadia
10 P-p(NE)
11 P-p(GU)
12 P-l(NE)
13 P-l(GU)
14 and 2 0.098857 1000
14 and 3 0.127932 1000
15 and 1 0.197471 1000
15 and 14 0.029273 874
16 and 10 0.011732 1000
16 and 11 0.004529 1000
17 and 12 0.002258 1000
17 and 13 0.000428 1000
18 and 16 0.017512 1000
18 and 17 0.010824 998
19 and 4 0.006534 1000
19 and 5 0.006992 1000
20 and 15 0.070461 1000
20 and 18 0.030579 998
21 and 8 0.003339 1000
21 and 9 0.002042 1000
22 and 6 0.011142 1000
22 and 21 0.010693 983
23 and 20 0.020714 996
23 and 19 0.020350 1000
24 and 23 0.008665 826
24 and 22 0.013457 972
24 and 7 0.025598 1000
See http://www.bio.psu.edu/People/Faculty/Nei/Lab/software.htm for access
to the program and N Takezaki, A Rzhetsky, and M Nei, "Phylogenetic test
of the molecular clock and linearized trees." Mol Biol Evol 12(5):823-33.
=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:
http://bugzilla.open-bio.org/
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
=head1 CONTRIBUTORS
Ideas and discussion from:
Alan Christoffels
Avril Coghlan
=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::lintree;
use vars qw(%Defaults);
use strict;
use base qw(Bio::TreeIO);
$Defaults{'NodeType'} = "Bio::Tree::Node";
=head2 new
Title : new
Usage : my $obj = Bio::TreeIO::lintree->new();
Function: Builds a new Bio::TreeIO::lintree object
Returns : an instance of Bio::TreeIO::lintree
Args : -nodetype => Node type to create [default Bio::Tree::Node]
=cut
sub _initialize {
my ($self,@args) = @_;
$self->SUPER::_initialize(@args);
my ($nodetype) = $self->_rearrange([qw(NODETYPE)],@args);
$nodetype ||= $Defaults{'NodeType'};
$self->nodetype($nodetype);
}
=head2 next_tree
Title : next_tree
Usage : my $tree = $treeio->next_tree
Function: Gets the next tree in the stream
Returns : Bio::Tree::TreeI
Args : none
=cut
sub next_tree {
my ($self) = @_;
my $seentop = 0;
my ($tipcount,%data,@nodes) = (0);
my $nodetype = $self->nodetype;
while( defined( $_ = $self->_readline) ) {
if( /^\s*(\d+)\s+sequences/ox ) {
if( $seentop ) {
$self->_pushback($_);
last;
}
$tipcount = $1;
$seentop = 1;
} elsif( /^(\d+)\s+(\S+)\s*$/ox ) {
# deal with setting an outgroup
unless( defined $data{'outgroup'} ) {
$data{'outgroup'} = [$1,$2];
}
$nodes[$1 - 1] = { '-id' => $2 };
} elsif( m/^\s*(\d+)\s+and\s+(\d+)\s+(\-?\d+\.\d+)(?:\s+(\d+))?/ox ) {
my ($node,$descend,$blength,$bootstrap) = ( $1, $2, $3, $4 );
# need to -- descend and node because
# array is 0 based
$node--;$descend--;
$nodes[$descend]->{'-branch_length'} = $blength;
$nodes[$descend]->{'-bootstrap'} = $bootstrap; #? here
$nodes[$node]->{'-id'} = $node+1;
push @{$nodes[$node]->{'-d'}}, $descend;
} elsif( /\s+(\S+)\-distance was used\./ox ) {
$data{'method'} = $1;
} elsif( /\s*seed=(\d+)/ox ) {
$data{'seed'} = $1;
} elsif( m/^outgroup:\s+(\d+)\s+(\S+)/ox ) {
$data{'outgroup'} = [$1,$2];
}
}
if( @nodes ) {
my @treenodes;
foreach my $n ( @nodes ) {
push @treenodes, $nodetype->new(%{$n});
}
foreach my $tn ( @treenodes ) {
my $n = shift @nodes;
for my $ptr ( @{ $n->{'-d'} || [] } ) {
$tn->add_Descendent($treenodes[$ptr]);
}
}
my $T = Bio::Tree::Tree->new(-root => (pop @treenodes) );
if( $data{'outgroup'} ) {
my ($outgroup) = $treenodes[$data{'outgroup'}->[0]];
if( ! defined $outgroup) {
$self->warn("cannot find '". $data{'outgroup'}->[1]. "'\n");
} else {
$T->reroot($outgroup->ancestor);
}
}
return $T;
}
return; # if there are no more trees, return undef
}
=head2 nodetype
Title : nodetype
Usage : $obj->nodetype($newval)
Function:
Example :
Returns : value of nodetype (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub nodetype{
my ($self,$value) = @_;
if( defined $value) {
eval "require $value";
if( $@ ) { $self->throw("$@: Unrecognized Node type for ".ref($self).
"'$value'");}
my $a = bless {},$value;
unless( $a->isa('Bio::Tree::NodeI') ) {
$self->throw("Must provide a valid Bio::Tree::NodeI or child class to SeqFactory Not $value");
}
$self->{'nodetype'} = $value;
}
return $self->{'nodetype'};
}
1;