# $Id$
#
# BioPerl module for Bio::Tools::Run::Phylo::Phylip::DrawTree
#
# 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::Tools::Run::Phylo::Phylip::DrawTree - use Phylip DrawTree
program to draw trees
=head1 SYNOPSIS
use Bio::Tools::Run::Phylo::Phylip::DrawTree;
my $treedraw = Bio::Tools::Run::Phylo::Phylip::DrawTree->new();
my $treeimagefile = $drawfact->run($tree);
=head1 DESCRIPTION
This is a module for automating drawing of trees through Joe
Felsenstein's Phylip suite.
To set parameters with option you need to pass in an array reference or
a string, depending on the parameter. For example:
$treedraw->HORIZMARGINS(['2.00','2.5']);
$treedraw->ANCESTRALNODES('C');
$treedraw->TREESTYLE('PHEN');
$treedraw->USEBRANCHLENS('N');
This can be a brittle module as the menus change in PHYLIP. It should
support phylip 3.6 but no guarantees.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::Run::Phylo::Phylip::DrawTree;
use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR $PROGRAMNAME
$FONTFILE @DRAW_PARAMS @OTHER_SWITCHES
%OK_FIELD %DEFAULT);
use strict;
# inherit from Phylip::Base which has some methods for dealing with
# Phylip specifics
use Bio::Tools::Run::Phylo::Phylip::Base;
use Cwd;
@ISA = qw( Bio::Tools::Run::Phylo::Phylip::Base );
use Bio::Tools::Run::Phylo::Phylip::PhylipConf qw(%Menu);
# 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 DrawTree.pm.
# $ENV{PHYLIPDIR} = '/home/shawnh/PHYLIP/bin';
#
# 3. You can set the path to the program through doing:
# my @params('program'=>'/usr/local/bin/drawgram');
# my $neighbor_factory = Bio::Tools::Run::Phylo::Phylip::DrawTree->new(@params)
BEGIN {
%DEFAULT = ('PLOTTER' => 'P',
'SCREEN' => 'N');
$DEFAULT{'FONTFILE'} = Bio::Root::IO->catfile($ENV{'PHYLIPDIR'},"font1") if $ENV{'PHYLIPDIR'};
$PROGRAMNAME="drawtree";
if (defined $ENV{'PHYLIPDIR'}) {
$PROGRAMDIR = $ENV{'PHYLIPDIR'} || '';
$PROGRAM = Bio::Root::IO->catfile($PROGRAMDIR,
$PROGRAMNAME.($^O =~ /mswin/i ?'.exe':''));
$DEFAULT{'FONTFILE'} = Bio::Root::IO->catfile($ENV{'PHYLIPDIR'},"font1");
}
else {
$PROGRAM = $PROGRAMNAME;
}
@DRAW_PARAMS = qw(PLOTTER SCREEN LABEL_ANGLE ROTATION TREEARC
ITERATE SCALE HORIZMARGINS VERTICALMARGINS FONT
);
@OTHER_SWITCHES = qw(QUIET);
foreach my $attr(@DRAW_PARAMS,@OTHER_SWITCHES) {
$OK_FIELD{$attr}++;
}
}
=head2 program_name
Title : program_name
Usage : $obj->program_name()
Function: holds the program name
Returns: string
Args : None
=cut
sub program_name {
return $PROGRAMNAME;
}
=head2 program_dir
Title : program_dir
Usage : $drawfact->program_dir()
Function: returns the program directory, obtained from ENV variable.
Returns : string
Args :
=cut
sub program_dir {
return Bio::Root::IO->catfile($ENV{PHYLIPDIR}) if $ENV{PHYLIPDIR};
}
=head2 new
Title : new
Usage : my $obj = Bio::Tools::Run::Phylo::Phylip::DrawTree->new();
Function: Builds a new Bio::Tools::Run::Phylo::Phylip::DrawTree object
Returns : an instance of Bio::Tools::Run::Phylo::Phylip::DrawTree
Args : The available DrawGram parameters
=cut
sub new {
my($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 =~/PROGRAM/i) {
$self->executable($value);
next;
}
$self->$attr($value);
}
$self->plotter($DEFAULT{'PLOTTER'}) unless $self->plotter;
$self->screen($DEFAULT{'SCREEN'}) unless $self->screen;
$self->fontfile($DEFAULT{'FONTFILE'}) unless $self->fontfile;
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 run
Title : run
Usage : my $file = $app->run($treefile);
Function: Draw a tree
Returns : File containing the rendered tree
Args : either a Bio::Tree::TreeI
OR
filename of a tree in newick format
=cut
sub run{
my ($self,$input) = @_;
# Create input file pointer
my ($infilename) = $self->_setinput($input);
if (!$infilename) {
$self->throw("Problems setting up for drawgram. Probably bad input data in $input !");
}
# Create parameter string to pass to neighbor program
my $param_string = $self->_setparams();
# run drawgram
my $plotfile = $self->_run($infilename,$param_string);
return $plotfile;
}
=head2 draw_tree
Title : draw_tree
Usage : my $file = $app->draw_tree($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 draw_tree{
return shift->run(@_);
}
=head2 _run
Title : _run
Usage : Internal function, not to be called directly
Function: makes actual system call to drawgram program
Example :
Returns : Bio::Tree object
Args : Name of a file the tree to draw in newick format
and a parameter string to be passed to drawgram
=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";
if( ! defined $self->fontfile ) {
$self->throw("You must have defined a fontfile");
}
if( -e $self->io->catfile($curpath,'fontfile') ) {
$instring .= $self->io->catfile($curpath,'fontfile')."\n";
} elsif( File::Spec->file_name_is_absolute($self->fontfile) ) {
#$instring .= $self->io->catfile($self->tempdir,$self->fontfile)."\n";
$instring .= $self->io->catfile($self->fontfile)."\n";
} else {
$instring .= $self->io->catfile($curpath,$self->fontfile)."\n";
}
chdir($self->tempdir);
$instring .= $param_string;
$self->debug( "Program ".$self->executable." $param_string\n");
# open a pipe to run drawgram to bypass interactive menus
if ($self->quiet() || $self->verbose() < 0) {
open(DRAW,"|".$self->executable.">/dev/null");
}
else {
open(DRAW,"|".$self->executable);
}
print DRAW $instring;
close(DRAW);
chdir($curpath);
#get the results
my $plotfile = $self->io->catfile($self->tempdir,$self->plotfile);
$self->throw("drawgram did not create plotfile correctly ($plotfile)")
unless (-e $plotfile);
return $plotfile;
}
=head2 _setinput()
Title : _setinput
Usage : Internal function, not to be called directly
Function: Create input file for drawing program
Example :
Returns : filename containing tree in newick format
Args : Bio::Tree::TreeI object
=cut
sub _setinput {
my ($self, $input) = @_;
my $treefile;
unless (ref $input) {
# check that file exists or throw
$treefile = $input;
unless (-e $input) {return 0;}
} elsif ($input->isa("Bio::Tree::TreeI")) {
# Open temporary file for both reading & writing of BioSeq array
my $tfh;
($tfh,$treefile) = $self->io->tempfile(-dir=>$self->tempdir);
my $treeIO = Bio::TreeIO->new(-fh => $tfh,
-format=>'newick');
$treeIO->write_tree($input);
$treeIO->close();
close($tfh);
undef $tfh;
}
return $treefile;
}
=head2 _setparams()
Title : _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for drawgram program
Example :
Returns : parameter string to be passed to drawgram
Args : name of calling object
=cut
sub _setparams {
my ($attr, $value, $self);
#do nothing for now
$self = shift;
my $param_string = "";
my $cat = 0;
my ($hmargin,$vmargin);
my %menu = %{$Menu{$self->version}->{'DRAWTREE'}};
foreach my $attr ( @DRAW_PARAMS) {
$value = $self->$attr();
next unless defined $value;
my @vals;
if( ref($value) ) {
($value,@vals) = @$value;
}
$attr = uc($attr);
if( ! exists $menu{$attr} ) {
$self->warn("unknown parameter $attr, known params are ".
join(",",keys %menu). "\n");
}
if( ref ($menu{$attr}) !~ /HASH/i ) {
unless( @vals ) {
$param_string .= $menu{$attr};
} else {
$param_string .= sprintf($menu{$attr},$value,@vals);
}
next;
}
my $seen = 0;
for my $stype ( keys %{$menu{$attr}} ) {
if( $value =~ /$stype/i ) {
$param_string .= sprintf($menu{$attr}->{$stype},@vals);
$seen = 1;
last;
}
}
unless( $seen ) {
$self->warn("Unknown requested attribute $attr, $value is not known\n");
}
}
$param_string .="Y\n";
return $param_string;
}
=head1 Bio::Tools::Run::Wrapper methods
=cut
=head2 no_param_checks
Title : no_param_checks
Usage : $obj->no_param_checks($newval)
Function: Boolean flag as to whether or not we should
trust the sanity checks for parameter values
Returns : value of no_param_checks
Args : newvalue (optional)
=cut
=head2 save_tempfiles
Title : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)
=cut
=head2 outfile_name
Title : outfile_name
Usage : my $outfile = $dragram->outfile_name();
Function: Get/Set the name of the output file for this run
(if you wanted to do something special)
Returns : string
Args : [optional] string to set value to
=cut
=head2 tempdir
Title : tempdir
Usage : my $tmpdir = $self->tempdir();
Function: Retrieve a temporary directory name (which is created)
Returns : string which is the name of the temporary directory
Args : none
=cut
=head2 cleanup
Title : cleanup
Usage : $codeml->cleanup();
Function: Will cleanup the tempdir directory after a DrawTree run
Returns : none
Args : none
=cut
=head2 io
Title : io
Usage : $obj->io($newval)
Function: Gets a Bio::Root::IO object
Returns : Bio::Root::IO object
Args : none
See L<Bio::Root::IO>
=cut
1; # Needed to keep compiler happy