# BioPerl module for Bio::Tools::Run::Phylo::Phylip::Neighbor
#
# Created by
#
# Shawn Hoon
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::Phylo::Phylip::Neighbor - Wrapper for the phylip
program neighbor by Joseph Felsenstein for creating a phylogenetic
tree(either through Neighbor or UPGMA) based on protein distances
based on amino substitution rate.
14 Nov 2002 Shawn
Works with Phylip version 3.6
=head1 SYNOPSIS
#Create a SimpleAlign object
@params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
$factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
$inputfilename = 't/data/cysprot.fa';
$aln = $factory->run($inputfilename); # $aln is a SimpleAlign object.
# Create the Distance Matrix
# using a default PAM matrix and id name lengths limit of 30 note to
# use id name length greater than the standard 10 in neighbor, you
# will need to modify the neighbor source code
$protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
my $matrix = $protdist_factory->run($aln);
#Create the tree passing in the distance matrix
@params = ('type'=>'NJ','outgroup'=>2,'lowtri'=>1,
'upptri'=>1,'subrep'=>1);
my $neighbor_factory =
Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params);
#you can set your outgroup using either a number specifying
#the rank in the matrix or you can just use the name of the
#species
$neighbor_factory->outgroup('ENSP00001');
#or
$neighbor_factory->outgroup(1);
my ($tree) = $neighbor_factory->run($matrix);
# Alternatively, one can create the tree by passing in a file name
# containing a phylip formatted distance matrix(using protdist)
my $neighbor_factory =
Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params);
my ($tree) = $neighbor_factory->run('/home/shawnh/prot.dist');
# To prevent PHYLIP from truncating sequence names:
# Step 1. Shelf the original names:
my ($aln_safe, $ref_name)= # $aln_safe has serial names
$aln->set_displayname_safe(); # $ref_name holds original names
# Step 2. Run ProtDist and Neighbor:
$matrix = $protdist_factory->
creat_distance_matrix($aln_safe); # Use $aln_safe instead of $aln
$tree = $neighbor_factory->run($matrix);
# Step 3. Retrieve orgininal OTU names:
use Bio::Tree::Tree;
my @nodes=$tree->get_nodes();
foreach my $nd (@nodes){
$nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf;
}
=head1 PARAMTERS FOR NEIGHBOR COMPUTATION
=cut
=head2 TYPE
Title : TYPE
Description : (optional)
This sets the type of tree to construct, using
neighbor joining or UPGMA.
NJ Neighbor Joining
UPGMA UPGMA
Usage : @params = ('type'=>'X');#where X is one of the values above
Defaults to NJ
For more information on the usage of the different
models, please refer to the documentation found in
the phylip package.
=head2 OUTGROUP (*ONLY AVAILABLE FOR NEIGHBOR JOINING)
Title : OUTGROUP
Description : (optional)
This option selects the species to be used as the outgroup
Acceptable Values: integer
Usage : @params = ('outgroup'=>'X');
where X is an positive integer not more than the
number of sequences
Defaults to 1
=head2 LOWTRI
Title : LOWTRI
Description : (optional)
This indicates that the distance matrix is
input in Lower-triangular form (the lower-left
half of the distance matrix only, without the zero
diagonal elements)
Usage : @params = ('lowtri'=>'X'); where X is either 1 or 0
Defaults to 0
=head2 UPPTRI
Title : UPPTRI
Description : (optional)
This indicates that the distance matrix is input in
upper-triangular form (the upper-right half of the
distance matrix only, without the zero diagonal elements.)
Usage : @params = ('upptri'=>'X'); where X is either 1 or 0
Defaults to 0
=head2 SUBREP
Title : SUBREP
Description : (optional)
This is the Subreplication option.
It informs the program that after each distance will
be provided an integer indicating that the distance
is a mean of that many replicates.
Usage : @params = ('subrep'=>'X'); where X is either 1 or 0
Defaults to 0
=head2 JUMBLE
Title : JUMBLE
Description : (optional)
This enables you to tell the program to use a random
number generator to choose the input order of
species. seed: an integer between 1 and 32767 and of
the form 4n+1 which means that it must give a
remainder of 1 when divided by 4. Each different
seed leads to a different sequence of addition of
species. By simply changing the random number seed
and re-running programs one can look for other, and
better trees. iterations:
Usage : @params = ('jumble'=>'17); where 17 is the random seed
Defaults to no jumble
=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 one
of the Bioperl mailing lists. 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
the bugs and their resolution. Bug reports can be submitted via the
web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Shawn Hoon
Email shawnh@fugu-sg.org
=head1 CONTRIBUTORS
Email:jason-at-bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
#'
package Bio::Tools::Run::Phylo::Phylip::Neighbor;
use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR $PROGRAMNAME
@NEIGHBOR_PARAMS @OTHER_SWITCHES
%OK_FIELD);
use strict;
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::TreeIO;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Tools::Run::Phylo::Phylip::Base;
use Bio::Tools::Run::Phylo::Phylip::PhylipConf qw(%Menu);
use Cwd;
# inherit from Phylip::Base which has some methods for dealing with
# Phylip specifics
@ISA = qw(Bio::Tools::Run::Phylo::Phylip::Base);
# You will need to enable the neighbor program. This
# can be done in (at least) 3 ways:
#
# 1. define an environmental variable PHYLIPDIR:
# export PHYLIPDIR=/home/shawnh/PHYLIP/bin
#
# 2. include a definition of an environmental variable PHYLIPDIR in
# every script that will use Neighbor.pm.
# $ENV{PHYLIPDIR} = '/home/shawnh/PHYLIP/bin';
#
# 3. You can set the path to the program through doing:
# my @params('program'=>'/usr/local/bin/neighbor');
# my $neighbor_factory = Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params);
#
BEGIN {
$PROGRAMNAME="neighbor";
if (defined $ENV{PHYLIPDIR}) {
$PROGRAMDIR = $ENV{PHYLIPDIR} || '';
$PROGRAM = Bio::Root::IO->catfile($PROGRAMDIR,
$PROGRAMNAME.($^O =~ /mswin/i ?'.exe':''));
}
else {
$PROGRAM = $PROGRAMNAME;
}
@NEIGHBOR_PARAMS = qw(TYPE OUTGROUP LOWTRI UPPTRI SUBREP JUMBLE MULTIPLE);
@OTHER_SWITCHES = qw(QUIET);
foreach my $attr(@NEIGHBOR_PARAMS,@OTHER_SWITCHES) {
$OK_FIELD{$attr}++;
}
}
=head2 program_name
Title : program_name
Usage : >program_name()
Function: holds the program name
Returns: string
Args : None
=cut
sub program_name {
return 'neighbor';
}
=head2 program_dir
Title : program_dir
Usage : ->program_dir()
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
=cut
sub program_dir {
return Bio::Root::IO->catfile($ENV{PHYLIPDIR}) if $ENV{PHYLIPDIR};
}
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($attr, $value);
while (@args) {
$attr = shift @args;
$value = shift @args;
next if( $attr =~ /^-/ ); # don't want named parameters
if ($attr =~ /IDLENGTH/i){
$self->idlength($value);
next;
}
$self->$attr($value);
}
if (! defined $self->idlength){
$self->idlength(10);
}
return $self;
}
sub AUTOLOAD {
my $self = shift;
my $attr = $AUTOLOAD;
$attr =~ s/.*:://;
$attr = uc $attr;
$self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
$self->{$attr} = shift if @_;
return $self->{$attr};
}
=head2 idlength
Title : idlength
Usage : $obj->idlength ($newval)
Function:
Returns : value of idlength
Args : newvalue (optional)
=cut
sub idlength{
my $self = shift;
if( @_ ) {
my $value = shift;
$self->{'idlength'} = $value;
}
return $self->{'idlength'};
}
=head2 run
Title : run
Usage :
$inputfilename = 't/data/prot.dist';
$tree = $neighborfactory->run($inputfilename);
or
$protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
$matrix = $protdist_factory->create_distance_matrix($aln);
$tree= $neighborfactory->run($matrix);
Function: a Bio:Tree from a protein distance matrix created by protidst
Example :
Returns : Bio::Tree
Args : Name of a file containing a protein distance matrix in Phylip format
or a hash ref to a matrix
Throws an exception if argument is not either a string (eg a
filename) or a Hash. If argument is string, throws exception
if file corresponding to string name can not be found.
=cut
sub run{
my ($self,$input) = @_;
my ($temp,$infilename, $seq);
my ($attr, $value, $switch);
# Create input file pointer
$infilename = $self->_setinput($input);
if (!$infilename) {$self->throw("Problems setting up for neighbor. Probably bad input data in $input !");}
# Create parameter string to pass to neighbor program
my $param_string = $self->_setparams();
# run neighbor
my @tree = $self->_run($infilename,$param_string);
return wantarray ? @tree: \@tree;
}
=head2 create_tree
Title : create_tree
Usage : my $file = $app->create_tree($treefile);
Function: This method is deprecated. Please use run method.
Returns : File containing the rendered tree
Args : either a Bio::Tree::TreeI
OR
filename of a tree in newick format
=cut
sub create_tree{
return shift->run(@_);
}
#################################################
=head2 _run
Title : _run
Usage : Internal function, not to be called directly
Function: makes actual system call to neighbor program
Example :
Returns : Bio::Tree object
Args : Name of a file containing protein distances in Phylip format
and a parameter string to be passed to neighbor
=cut
sub _run {
my ($self,$infile,$param_string) = @_;
my $instring;
my $curpath = cwd;
unless( File::Spec->file_name_is_absolute($infile) ) {
$infile = $self->io->catfile($curpath,$infile);
}
$instring = $infile."\n$param_string";
$self->debug( "Program ".$self->executable."\n");
chdir($self->tempdir);
#open a pipe to run neighbor to bypass interactive menus
if ($self->quiet() || $self->verbose() < 0) {
my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';
open(NEIGHBOR,"|".$self->executable.">$null");
}
else {
open(NEIGHBOR,"|".$self->executable);
}
print NEIGHBOR $instring;
close(NEIGHBOR);
chdir($curpath);
#get the results
my $outfile = $self->io->catfile($self->tempdir,$self->outfile);
my $treefile = $self->io->catfile($self->tempdir,$self->treefile);
$self->throw("neighbor did not create tree correctly (expected $treefile) ") unless (-e $treefile);
my $in = Bio::TreeIO->new(-file => $treefile, '-format' => 'newick');
my @tree;
while (my $tree = $in->next_tree){
push @tree, $tree;
}
# Clean up the temporary files created along the way...
unless ( $self->save_tempfiles ) {
unlink $outfile;
unlink $treefile;
}
return @tree;
}
=head2 _setinput()
Title : _setinput
Usage : Internal function, not to be called directly
Function: Create input file for neighbor program
Example :
Returns : name of file containing the protein distance matrix in Phylip format
Args : name of file created by protdist or ref to hash created by
Bio::Tools:Run::Phylo::Phylip::ProtDist
=cut
sub _setinput {
my ($self, $input) = @_;
my ($alnfilename,$infilename, $temp, $tfh,$input_tmp,$input_fh);
#If $input is not a filename it better be a HASF reference
# a phy formatted alignment file created by protdist
unless (ref $input) {
# check that file exists or throw
$alnfilename= $input;
unless (-e $input) {return 0;}
return $alnfilename;
}
my @input = ref($input) eq "ARRAY" ? @{$input} : ($input);
($tfh,$alnfilename) = $self->io->tempfile(-dir=>$self->tempdir);
my $input_count = 0;
foreach my $input(@input){
if ($input->isa("Bio::Matrix::PhylipDist")){
# Open temporary file for both reading & writing of distance matrix
print $tfh $input->print_matrix;
$input_count++;
}
}
$self->_input_nbr($input_count);
close($tfh);
#get names from the first matrix, to be used in outgroup ordering
my %names;
$input = shift @input;
#set the species names
my @names = @{$input->names};
for(my $i=0; $i<= $#names; $i++){
$names{$names[$i]} = $i+1;
}
$self->names(\%names);
return $alnfilename;
}
sub _input_nbr {
my ($self,$val) = @_;
if($val){
$self->{'_input_nbr'} = $val;
} return $self->{'_input_nbr'};
}
=head2 names()
Title : names
Usage : $tree->names(\%names)
Function: get/set for a hash ref for storing names in matrix
with rank as values.
Example :
Returns : hash reference
Args : hash reference
=cut
sub names {
my ($self,$name) = @_;
if($name){
$self->{'_names'} = $name;
}
return $self->{'_names'};
}
=head2 _setparams()
Title : _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for neighbor program
Example :
Returns : parameter string to be passed to neighbor
Args : name of calling object
=cut
sub _setparams {
my ($attr, $value, $self);
#do nothing for now
$self = shift;
my $param_string = "";
my $type ="";
my $version = $self->version;
my %menu = %{$Menu{$version}->{'NEIGHBOR'}};
foreach my $attr ( @NEIGHBOR_PARAMS) {
$value = $self->$attr();
next unless (defined $value && $value);
if ($attr =~/TYPE/i){
if ($value=~/UPGMA/i){
$type = "UPGMA";
$param_string .= $menu{'TYPE'}{'UPGMA'};
}
}
elsif($attr =~ /OUTGROUP/i){
if ($type ne "UPGMA"){
if($value !~/^\d+$/){ # is a name so find the rank
my %names = %{$self->names};
$names{$value} || $self->throw("Outgroup $value not found");
$value = $names{$value};
}
$param_string .= $menu{'OUTGROUP'}."$value\n";
}
else {
$self->throw("Can't set outgroup using UPGMA. Use Neighbor-Joining instead");
}
}
elsif ($attr =~ /JUMBLE/i){
$self->throw("Unallowed value for random seed, need odd number") unless ($value =~ /\d+/ && ($value % 2 == 1));
$param_string .=$menu{'JUMBLE'}."$value\n";
}
elsif($attr=~/MULTIPLE/i){
$param_string.=$menu{'MULTIPLE'}."$value\n";
#version 3.6 needs a random seed
if($version eq "3.6"){
$param_string .= (2 * int(rand(10000)) + 1)."\n";
}
}
else{
$param_string .= $menu{uc $attr};
}
}
if (($param_string !~ $menu{'MULTIPLE'}) && (defined ($self->_input_nbr) &&($self->_input_nbr > 1))){
$param_string.=$menu{'MULTIPLE'}.$self->_input_nbr."\n";
}
$param_string .=$menu{'SUBMIT'};
return $param_string;
}
=head2 outfile
Title : outfile
Usage : $obj->outfile($newval)
Function: Get/Set default PHYLIP outfile name ('outfile' usually)
Returns : value of outfile
Args : newvalue (optional)
=cut
=head2 treefile
Title : treefile
Usage : $obj->treefile($newval)
Function: Get/Set the default PHYLIP treefile name ('treefile' usually)
Returns : value of treefile
Args : newvalue (optional)
=cut
1; # Needed to keep compiler happy