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# BioPerl module for Bio::Tools::Run::Phylo::Njtree::Best
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Albert Vilella <avilella-at-gmail-dot-com>
#
# Copyright Albert Vilella
#
# 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::Njtree::Best - Wrapper around the Njtree (Njtree/phyml) best program.
=head1 SYNOPSIS
use Bio::Tools::Run::Phylo::Njtree::Best;
use Bio::AlignIO;
use Bio::TreeIO;
my $alignio = Bio::AlignIO->new(-format => 'fasta',
-file => 't/data/njtree_aln2.nucl.mfa');
my $aln = $alignio->next_aln;
my $treeio = Bio::TreeIO->new(
-format => 'nhx', -file => 't/data/species_tree_njtree.nh');
my $tree = $treeio->next_tree;
my $njtree_best = Bio::Tools::Run::Phylo::Njtree::Best->new();
$njtree_best->alignment($aln);
$njtree_best->tree($tree);
my $nhx_tree = $njtree_best->run();
=head1 DESCRIPTION
This is a wrapper around the best program of Njtree by Li Heng. See
http://treesoft.sourceforge.net/njtree.shtml for more information.
Wrapper for the calculation of a reconciled phylogenetic tree with
inferred duplication tags from amultiple sequence alignment and a
species tree using NJTREE.
=head2 Helping the module find your executable
You will need to enable NJTREEDIR to find the njtree program. This can be
done in (at least) three ways:
1. Make sure the njtree executable is in your path (i.e.
'which njtree' returns a valid program
2. define an environmental variable NJTREEDIR which points to a
directory containing the 'njtree' app:
In bash
export NJTREEDIR=/home/progs/treesoft/njtree or
In csh/tcsh
setenv NJTREEDIR /home/progs/treesoft/njtree
3. include a definition of an environmental variable NJTREEDIR
in every script that will
BEGIN {$ENV{NJTREEDIR} = '/home/progs/treesoft/njtree'; }
use Bio::Tools::Run::Phylo::Njtree::Best;
=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 - Albert Vilella
Email avilella-at-gmail-dot-com
=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::Njtree::Best;
use vars qw($AUTOLOAD @ISA $PROGRAMNAME $PROGRAM
@NJTREE_BEST_PARAMS @NJTREE_BEST_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::WrapperBase;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
BEGIN {
@NJTREE_BEST_PARAMS = qw(C p F c k a d l L b);
@NJTREE_BEST_SWITCHES = qw(P S A r D s g N);
# Authorize attribute fields
foreach my $attr ( @NJTREE_BEST_PARAMS, @NJTREE_BEST_SWITCHES ) {
$OK_FIELD{$attr}++; }
}
=head2 program_name
Title : program_name
Usage : $factory->program_name()
Function: holds the program name
Returns: string
Args : None
=cut
sub program_name {
return 'njtree';
}
=head2 program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
=cut
sub program_dir {
return Bio::Root::IO->catfile($ENV{NJTREEDIR}) if $ENV{NJTREEDIR};
}
=head2 new
Title : new
Usage : my $njtree_best = Bio::Tools::Run::Phylo::Njtree::Best->new();
Function: Builds a new Bio::Tools::Run::Phylo::Njtree::Best
Returns : Bio::Tools::Run::Phylo::Njtree::Best
Args : -alignment => the Bio::Align::AlignI object
-tree => the Bio::Tree::TreeI object
-save_tempfiles => boolean to save the generated tempfiles and
NOT cleanup after onesself (default FALSE)
-executable => where the njtree executable resides
See also: L<Bio::Tree::TreeI>, L<Bio::Align::AlignI>
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($aln, $tree, $st, $exe,
$ubl) = $self->_rearrange([qw(ALIGNMENT TREE SAVE_TEMPFILES
EXECUTABLE)],
@args);
defined $aln && $self->alignment($aln);
defined $tree && $self->tree($tree);
defined $st && $self->save_tempfiles($st);
defined $exe && $self->executable($exe);
return $self;
}
=head2 prepare
Title : prepare
Usage : my $rundir = $njtree_best->prepare();
Function: prepare the njtree_best analysis using the default or updated parameters
the alignment parameter and species tree must have been set
Returns : value of rundir
Args : L<Bio::Align::AlignI> object,
L<Bio::Tree::TreeI> object [optional]
=cut
sub prepare {
my ($self,$aln,$tree) = @_;
unless ( $self->save_tempfiles ) {
# brush so we don't get plaque buildup ;)
$self->cleanup();
}
$tree = $self->tree unless $tree;
$aln = $self->alignment unless $aln;
if( ! $aln ) {
$self->warn("Must have supplied a valid alignment file in order to run njtree_best");
return 0;
}
if( ! $tree ) {
$self->warn("Must have supplied a valid species tree file in order to run njtree_best");
return 0;
}
my ($tempdir) = $self->tempdir();
my $tempalnFH;
if( ! ref($aln) && -e $aln ) {
$self->{_tempalnfile} = $aln;
} else {
($tempalnFH,$self->{_tempalnfile}) = $self->io->tempfile
('-dir' => $tempdir,
UNLINK => ($self->save_tempfiles ? 0 : 1));
my $alnout = Bio::AlignIO->new('-format' => 'fasta',
'-fh' => $tempalnFH);
$aln->set_displayname_flat(1);
$alnout->write_aln($aln);
$alnout->close();
undef $alnout;
close($tempalnFH);
}
my ($temptreeFH);
if( ! ref($tree) && -e $tree ) {
$self->{_temptreefile} = $tree;
} else {
($temptreeFH,$self->{_temptreefile}) = $self->io->tempfile
('-dir' => $tempdir,
UNLINK => ($self->save_tempfiles ? 0 : 1));
my $treeout = Bio::TreeIO->new('-format' => 'newick',
'-fh' => $temptreeFH);
$treeout->write_tree($tree);
$treeout->close();
close($temptreeFH);
}
$self->{_prepared} = 1;
$self->{_njtree_best_params} = $self->_setparams();
return $tempdir;
}
=head2 run
Title : run
Usage : my $nhx_tree = $njtree_best->run();
Function: run the njtree_best analysis using the default or updated parameters
the alignment parameter must have been set
Returns : L<Bio::Tree::TreeI> object [optional]
Args : L<Bio::Align::AlignI> object
L<Bio::Tree::TreeI> object
=cut
sub run {
my ($self,$aln,$tree) = @_;
$self->prepare($aln,$tree) unless (defined($self->{_prepared}));
my ($rc,$nhx_tree) = (1);
my ($tmpdir) = $self->tempdir();
my $outfile = $self->outfile_name;
{
my $commandstring;
my $exit_status;
#./njtree best [other_params] -f species_file.nh -p tree -o inputfile.best.nhx inputfile.nucl.mfa
my $njtree_executable = $self->executable;
$commandstring = $njtree_executable." best ";
$commandstring .= $self->{_njtree_best_params};
$commandstring .= " -f $self->{_temptreefile} -p tree -o ";
unless ($self->outfile_name ) {
my ($tfh, $outfile) = $self->io->tempfile(-dir=>$self->tempdir());
close($tfh);
undef $tfh;
$self->outfile_name($outfile);
}
$commandstring .= $self->outfile_name;
$commandstring .= " $self->{_tempalnfile} ";
$self->throw("unable to find or run executable for 'njtree'")
unless $njtree_executable && -e $njtree_executable && -x _;
open(RUN, "$commandstring |")
or $self->throw("Cannot run $commandstring");
my @output = <RUN>;
$exit_status = close(RUN);
$self->error_string(join('',@output));
if( (grep { /^\[ /io } @output) || !$exit_status) {
$self->warn("There was an error - see error_string for the program output");
$rc = 0;
}
eval {
$nhx_tree = Bio::TreeIO->new(-file => "$tmpdir/$outfile",
-format => 'nhx');
};
if( $@ ) {
$self->warn($self->error_string);
}
}
unless ( $self->save_tempfiles ) {
$self->cleanup();
}
return ($rc,$nhx_tree);
}
sub AUTOLOAD {
my $self = shift;
my $attr = $AUTOLOAD;
$attr =~ s/.*:://;
$attr = $attr;
# aliasing
$self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
$self->{$attr} = shift if @_;
return $self->{$attr};
}
=head2 error_string
Title : error_string
Usage : $obj->error_string($newval)
Function: Where the output from the last analysus run is stored.
Returns : value of error_string
Args : newvalue (optional)
=cut
sub error_string {
my ($self,$value) = @_;
if( defined $value) {
$self->{'error_string'} = $value;
}
return $self->{'error_string'};
}
=head2 version
Title : version
Usage : exit if $prog->version() < 1.8
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
=cut
sub version {
my ($self) = @_;
my $exe;
return undef unless $exe = $self->executable;
my $string = `$exe 2>&1` ;
$string =~ /Version\:\s+(\d+.\d+.\d+)/m;
return $1 || undef;
}
=head2 alignment
Title : alignment
Usage : $njtree_best->align($aln);
Function: Get/Set the L<Bio::Align::AlignI> object
Returns : L<Bio::Align::AlignI> object
Args : [optional] L<Bio::Align::AlignI>
Comment : We could potentially add support for running directly on a file
but we shall keep it simple
See also: L<Bio::SimpleAlign>
=cut
sub alignment {
my ($self,$aln) = @_;
if( defined $aln ) {
if( -e $aln ) {
$self->{'_alignment'} = $aln;
} elsif( !ref($aln) || ! $aln->isa('Bio::Align::AlignI') ) {
$self->warn("Must specify a valid Bio::Align::AlignI object to the alignment function not $aln");
return undef;
} else {
$self->{'_alignment'} = $aln;
}
}
return $self->{'_alignment'};
}
=head2 tree
Title : tree
Usage : $njtree_best->tree($tree, %params);
Function: Get/Set the L<Bio::Tree::TreeI> object
Returns : L<Bio::Tree::TreeI>
Args : [optional] $tree => L<Bio::Tree::TreeI>,
[optional] %parameters => hash of tree-specific parameters
Comment : We could potentially add support for running directly on a file
but we shall keep it simple
See also: L<Bio::Tree::Tree>
=cut
sub tree {
my ($self, $tree, %params) = @_;
if( defined $tree ) {
if( ! ref($tree) || ! $tree->isa('Bio::Tree::TreeI') ) {
$self->warn("Must specify a valid Bio::Tree::TreeI object to the alignment function");
}
$self->{'_tree'} = $tree;
}
return $self->{'_tree'};
}
=head2 check_names
Title : check_names
Usage :
Function:
Example :
Returns :
Args :
=cut
sub check_names {
my $self = shift;
my $tree = $self->tree;
my $aln = $self->alignment;
if( ! $aln ) {
$self->warn("must have supplied a valid alignment file in order to run njtree_best");
return 0;
}
if( ! $tree ) {
$self->warn("must have supplied a valid species tree file in order to run njtree_best");
return 0;
}
foreach my $leaf ($tree->get_leaf_nodes) {
my $id = $leaf->id;
$id =~ s/\-\*.+//; # njtree does not consider anything after a \-\*
$self->{_treeids}{$id} = 1;
}
foreach my $seq ($aln->each_seq) {
my $id = $seq->id;
$id =~ s/.+\_//; # njtree only looks at the right side of the \_
$self->{_alnids}{$id} = 1;
}
foreach my $alnid (keys %{$self->{_alnids}}) {
$self->{_unmappedids}{$alnid} = 1 unless (defined($self->{_treeids}{$alnid}));
}
if (defined($self->{_unmappedids})) {
my $count = scalar(keys%{$self->{_unmappedids}});
my $unmapped = join(",",keys %{$self->{_unmappedids}});
$self->warn("$count unmapped ids between the aln and the tree $unmapped");
}
}
=head2 _setparams
Title : _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for njtree_best program
Example :
Returns : parameter string to be passed to njtree_best
during align or profile_align
Args : name of calling object
=cut
sub _setparams {
my ($self) = @_;
my ($attr, $value,$param_string);
$param_string = '';
my $laststr;
for $attr ( @NJTREE_BEST_PARAMS ) {
$value = $self->$attr();
next unless (defined $value);
my $attr_key = $attr;
$attr_key = ' -'.$attr_key;
$param_string .= $attr_key .' '.$value;
}
for $attr ( @NJTREE_BEST_SWITCHES) {
$value = $self->$attr();
next unless ($value);
my $attr_key = $attr;
$attr_key = ' -'.$attr_key;
$param_string .= $attr_key ;
}
return $param_string;
}
=head1 Bio::Tools::Run::BaseWrapper methods
=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 = $njtree_best->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 : $njtree_best->cleanup();
Function: Will cleanup the tempdir directory
Returns : none
Args : none
=cut
=head2 io
Title : io
Usage : $obj->io($newval)
Function: Gets a L<Bio::Root::IO> object
Returns : L<Bio::Root::IO>
Args : none
=cut
sub DESTROY {
my $self= shift;
unless ( $self->save_tempfiles ) {
$self->cleanup();
}
$self->SUPER::DESTROY();
}
1; # Needed to keep compiler happy
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