#
# BioPerl module for Bio::Tools::Run::Simprot
#
# 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::Simprot - Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree
=head1 SYNOPSIS
use Bio::Tools::Run::Simprot;
use Bio::TreeIO;
my $treeio = Bio::TreeIO->new(
-format => 'nh', -file => 't/data/tree.nh');
my $tree = $treeio->next_tree;
my $simprot = Bio::Tools::Run::Simprot->new();
$simprot->tree($tree);
my ($rc,$aln,$seq) = $simprot->run();
=head1 DESCRIPTION
This is a wrapper around the Simprot program by Andy Pang, Andrew D
Smith, Paulo AS Nuin and Elisabeth RM Tillier.
Simprot allows for several models of amino acid substitution (PAM, JTT
and PMB), allows for gamma distributed sites rates according to Yang's
model, and implements a parameterised Qian and Goldstein distribution
model for insertion and deletion.
See http://www.uhnres.utoronto.ca/labs/tillier/software.htm for more
information.
=head2 Helping the module find your executable
You will need to enable SIMPROTDIR to find the simprot program. This can be
done in (at least) three ways:
1. Make sure the simprot executable is in your path (i.e.
'which simprot' returns a valid program
2. define an environmental variable SIMPROTDIR which points to a
directory containing the 'simprot' app:
In bash
export SIMPROTDIR=/home/progs/simprot or
In csh/tcsh
setenv SIMPROTDIR /home/progs/simprot
3. include a definition of an environmental variable SIMPROTDIR
in every script that will
BEGIN {$ENV{SIMPROTDIR} = '/home/progs/simprot'; }
use Bio::Tools::Run::Simprot;
=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::Simprot;
use vars qw(@ISA %VALIDVALUES $PROGRAMNAME $PROGRAM);
use strict;
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::SeqIO;
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);
# valid values for parameters, the default one is always
# the first one in the array
BEGIN {
%VALIDVALUES = (
'branch' => '1',
'eFactor' => '3',
'indelFrequncy' => '0.03',
'maxIndel' => '2048',
'subModel' => [ 2,0,1], # 0:PAM, 1:JTT, 2:PMB
'rootLength' => '50',
'alpha' => '1',
'Benner' => '0',
'interleaved' => '1',
'variablegamma' => '0',
'bennerk' => '-2',
);
}
=head2 program_name
Title : program_name
Usage : $factory->program_name()
Function: holds the program name
Returns: string
Args : None
=cut
sub program_name {
return 'simprot';
}
=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{SIMPROTDIR}) if $ENV{SIMPROTDIR};
}
=head2 new
Title : new
Usage : my $simprot = Bio::Tools::Run::Simprot->new();
Function: Builds a new Bio::Tools::Run::Simprot
Returns : Bio::Tools::Run::Simprot
Args : -alignment => the Bio::Align::AlignI object
-tree => the Bio::Tree::TreeI object
-save_tempfiles => boolean to save the generated tempfiles and
NOT cleanup after onesself (default FALSE)
-executable => where the simprot executable resides
-params => A reference to a hash where keys are parameter names
and hash values are the associated parameter values
See also: L<Bio::Tree::TreeI>, L<Bio::Align::AlignI>
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($aln, $tree, $st, $params, $exe,
$ubl) = $self->_rearrange([qw(TREE SAVE_TEMPFILES PARAMS EXECUTABLE)],
@args);
defined $tree && $self->tree($tree);
defined $st && $self->save_tempfiles($st);
defined $exe && $self->executable($exe);
$self->set_default_parameters();
if( defined $params ) {
if( ref($params) !~ /HASH/i ) {
$self->warn("Must provide a valid hash ref for parameter -FLAGS");
} else {
map { $self->set_parameter($_, $$params{$_}) } keys %$params;
}
}
return $self;
}
=head2 set_parameters
Title : set_parameters
Usage : $codeml->set_parameters($parameter, $value);
Function: (Re)set the SimProt parameters
Returns : none
Args : First argument is the parameter name
Second argument is the parameter value
=cut
sub set_parameter{
my ($self,$param,$value) = @_;
unless (defined $self->{'no_param_checks'} && $self->{'no_param_checks'} == 1) {
if ( ! defined $VALIDVALUES{$param} ) {
$self->warn("unknown parameter $param will not be set unless you force by setting no_param_checks to true");
return 0;
}
if ( ref( $VALIDVALUES{$param}) =~ /ARRAY/i &&
scalar @{$VALIDVALUES{$param}} > 0 ) {
unless ( grep { $value eq $_ } @{ $VALIDVALUES{$param} } ) {
$self->warn("parameter $param specified value $value is not recognized, please see the documentation and the code for this module or set the no_param_checks to a true value");
return 0;
}
}
}
$self->{'_simprotparams'}->{$param} = $value;
return 1;
}
=head2 set_default_parameters
Title : set_default_parameters
Usage : $codeml->set_default_parameters(0);
Function: (Re)set the default parameters from the defaults
(the first value in each array in the
%VALIDVALUES class variable)
Returns : none
Args : boolean: keep existing parameter values
=cut
sub set_default_parameters{
my ($self,$keepold) = @_;
$keepold = 0 unless defined $keepold;
while( my ($param,$val) = each %VALIDVALUES ) {
# skip if we want to keep old values and it is already set
next if( defined $self->{'_simprotparams'}->{$param} && $keepold);
if(ref($val)=~/ARRAY/i ) {
$self->{'_simprotparams'}->{$param} = $val->[0];
} else {
$self->{'_simprotparams'}->{$param} = $val;
}
}
}
=head2 get_parameters
Title : get_parameters
Usage : my %params = $self->get_parameters();
Function: returns the list of parameters as a hash
Returns : associative array keyed on parameter names
Args : none
=cut
sub get_parameters{
my ($self) = @_;
# we're returning a copy of this
return %{ $self->{'_simprotparams'} };
}
=head2 prepare
Title : prepare
Usage : my $rundir = $simprot->prepare();
Function: prepare the simprot analysis using the default or updated parameters
the alignment parameter and species tree must have been set
Returns : value of rundir
Args : L<Bio::Align::AlignI> object,
L<Bio::Tree::TreeI> object [optional]
=cut
sub prepare {
my ($self,$tree) = @_;
unless ( $self->save_tempfiles ) {
# brush so we don't get plaque buildup ;)
$self->cleanup();
}
$tree = $self->tree unless $tree;
if( ! $tree ) {
$self->warn("must have supplied a valid species tree file in order to run simprot");
return 0;
}
my ($tempdir) = $self->tempdir();
my ($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;
my %params = $self->get_parameters;
while( my ($param,$val) = each %params ) {
$self->{_simprot_params} .=" \-\-$param\=$val";
}
return $tempdir;
}
=head2 run
Title : run
Usage : my $nhx_tree = $simprot->run();
Function: run the simprot analysis using the default or updated parameters
the alignment parameter must have been set
Returns : L<Bio::Tree::TreeI> object [optional]
Args : L<Bio::Align::AlignI> object
L<Bio::Tree::TreeI> object
=cut
sub run {
my ($self,$tree) = @_;
$self->prepare($tree) unless (defined($self->{_prepared}));
my ($rc,$aln,$seq) = (1);
my ($tmpdir) = $self->tempdir();
my $outfile;
{
my $commandstring;
my $exit_status;
my $simprot_executable = $self->executable;
$commandstring .= $simprot_executable;
$commandstring .= $self->{_simprot_params};
$commandstring .= " --tree=". $self->{_temptreefile} . " ";
my ($tfh, $outfile) = $self->io->tempfile(-dir=>$self->tempdir());
close($tfh);
undef $tfh;
$self->outfile_name($outfile);
my $seqfile;
($tfh, $seqfile) = $self->io->tempfile(-dir=>$self->tempdir());
close($tfh);
undef $tfh;
$commandstring .= "--alignment=". $self->outfile_name . " ";
$commandstring .= "--sequence=". $seqfile . " ";
$self->throw("unable to find or run executable for 'simprot'")
unless $simprot_executable && -e $simprot_executable && -x _;
open(RUN, "$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 {
$aln = Bio::AlignIO->new(-file => "$outfile",-format => 'fasta');
$seq = Bio::SeqIO->new(-file => "$seqfile", -format => 'fasta');
};
if( $@ ) {
$self->warn($self->error_string);
}
}
unless ( $self->save_tempfiles ) {
$self->cleanup();
}
return ($rc,$aln,$seq);
}
=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 : $simprot->align($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 : $simprot->tree($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'};
}
=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 = $simprot->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 : $simprot->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