Bio::Tools::Run
Simprot
Toolbar
Summary
Bio::Tools::Run::Simprot - Wrapper around the Simprot program. Wrapper for the calculation of a multiple sequence alignment from a phylogenetic tree
Package variables
No package variables defined.
Included modules
Bio::AlignIO
Bio::Root::IO
Bio::Root::Root
Bio::SeqIO
Bio::SimpleAlign
Bio::Tools::Run::WrapperBase
Bio::TreeIO
Inherit
Bio::Root::Root Bio::Tools::Run::WrapperBase
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) = $simprot->run();
Description
This is a wrapper around the Simprot program by Andy Pang, Andrew D
Smith, Paulo AS Nuin and Elisabeth RM Tillier.
Simprot allows for several models of amino acid substitution (PAM, JTT
and PMB), allows for gamma distributed sites rates according to Yang's
model, and implements a parameterised Qian and Goldstein distribution
model for insertion and deletion.
See
http://www.uhnres.utoronto.ca/labs/tillier/software.htm for more
information.
You will need to enable SIMPROTDIR to find the simprot program. This can be
done in (at least) three ways:
1. Make sure the simprot executable is in your path (i.e.
'which simprot' returns a valid program
2. define an environmental variable SIMPROTDIR which points to a
directory containing the 'simprot' app:
In bash
export SIMPROTDIR=/home/progs/simprot or
In csh/tcsh
setenv SIMPROTDIR /home/progs/simprot
3. include a definition of an environmental variable SIMPROTDIR
in every script that will
BEGIN {$ENV{SIMPROTDIR} = '/home/progs/simprot'; }
use Bio::Tools::Run::Simprot;
Methods
Methods description
Title : program_name
Usage : $factory->program_name()
Function: holds the program name
Returns: string
Args : None |
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args : |
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: Bio::Tree::TreeI, Bio::Align::AlignI |
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 |
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 |
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 : Bio::Align::AlignI object,
Bio::Tree::TreeI object [optional] |
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 : Bio::Tree::TreeI object [optional]
Args : Bio::Align::AlignI object
Bio::Tree::TreeI object |
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) |
Title : version
Usage : exit if $prog->version() < 1.8
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none |
Title : tree
Usage : $simprot->tree($tree, %params);
Function: Get/Set the Bio::Tree::TreeI object
Returns : Bio::Tree::TreeI
Args : [optional] $tree => Bio::Tree::TreeI,
[optional] %parameters => hash of tree-specific parameters
Comment : We could potentially add support for running directly on a file
but we shall keep it simple
See also: Bio::Tree::Tree |
Methods code
BEGIN { %VALIDVALUES = (
'branch' => '1',
'eFactor' => '3',
'indelFrequncy' => '0.03',
'maxIndel' => '2048',
'subModel' => [ 2,0,1],
'rootLength' => '50',
'alpha' => '1',
'Benner' => '0',
'interleaved' => '1',
'variablegamma' => '0',
'bennerk' => '-2',
);} | sub program_name
{ return 'simprot'; } | sub program_dir
{ return Bio::Root::IO->catfile($ENV{SIMPROTDIR}) if $ENV{SIMPROTDIR};} | sub new
{ my($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 $self;} | sub set_parameter
{ my ($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} = $value;
return 1;} | sub set_default_parameters
{ my ($self,$keepold) = @_;
$keepold = 0 unless defined $keepold;
while( my ($param,$val) = each %VALIDVALUES ) {
next if( defined $self->{'_simprotparams'}->{$param} && $keepold);
if(ref($val)=~/ARRAY/i ) {
$self->{'_simprotparams'}->{$param} = $val->[0];
} else {
$self->{'_simprotparams'}->{$param} = $val;
}
}} | sub get_parameters
{ my ($self) = @_;
return %{ $self->{'_simprotparams'} }; } | sub prepare
{ my ($self,$tree) = @_;
unless ( $self->save_tempfiles ) {
$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 $tempdir;} | sub run
{ my ($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);} | sub error_string
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'error_string'} = $value;
}
return $self->{'error_string'};} | sub version
{ my ($self) = @_;
my $exe;
return undef unless $exe = $self->executable;
my $string = `$exe 2>&1` ;
$string =~ /Version\:\s+(\d+.\d+.\d+)/m;
return $1 || undef;} | sub alignment
{ my ($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 $self->{'_alignment'};} | sub tree
{ my ($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'};} | sub DESTROY
{ my $self= shift;
unless ( $self->save_tempfiles ) {
$self->cleanup();
}
$self->SUPER::DESTROY();
}
1;
} | General documentation
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
Please direct usage questions or support issues to the mailing list:
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.
| AUTHOR - Albert Vilella | Top |
Email avilella-at-gmail-dot-com
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
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
| Bio::Tools::Run::BaseWrapper methods | Top |
Title : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)
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
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
Title : cleanup
Usage : $simprot->cleanup();
Function: Will cleanup the tempdir directory
Returns : none
Args : none