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FEL.pm
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# $Id$
#
# BioPerl module for Bio::Tools::Run::Phylo::Hyphy::FEL
#
# 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::Hyphy::FEL - Wrapper around the Hyphy FEL analysis
=head1 SYNOPSIS
use Bio::Tools::Run::Phylo::Hyphy::FEL;
use Bio::AlignIO;
use Bio::TreeIO;
my $alignio = Bio::AlignIO->new(-format => 'fasta',
-file => 't/data/hyphy1.fasta');
my $aln = $alignio->next_aln;
my $treeio = Bio::TreeIO->new(
-format => 'newick', -file => 't/data/hyphy1.tree');
my $fel = Bio::Tools::Run::Phylo::Hyphy::FEL->new();
$fel->alignment($aln);
$fel->tree($tree);
my ($rc,$results) = $fel->run();
=head1 DESCRIPTION
This is a wrapper around the FEL analysis of HyPhy ([Hy]pothesis
Testing Using [Phy]logenies) package of Sergei Kosakowsky Pond,
Spencer V. Muse, Simon D.W. Frost and Art Poon. See
http://www.hyphy.org for more information.
This module will generate the correct list of options for interfacing
with TemplateBatchFiles/Ghostrides/Wrapper.bf.
=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://bugzilla.open-bio.org/
=head1 AUTHOR - Albert Vilella
Email avilella-at-gmail-dot-com
=head1 CONTRIBUTORS
Additional contributors names and emails here
=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::Hyphy::FEL;
use vars qw(@ISA @VALIDVALUES $PROGRAMNAME $PROGRAM);
use strict;
use Bio::Root::Root;
use Bio::AlignIO;
use Bio::TreeIO;
use Bio::Tools::Run::Phylo::Hyphy::Base;
use Bio::Tools::Run::WrapperBase;
@ISA = qw(Bio::Tools::Run::Phylo::Hyphy::Base);
=head2 Default Values
Valid and default values for FEL are listed below. The default
values are always the first one listed. These descriptions are
essentially lifted from the python wrapper or provided by the author.
INCOMPLETE DOCUMENTATION OF ALL METHODS
=cut
BEGIN {
@VALIDVALUES =
(
{'geneticCode' => [ "Universal","VertebratemtDNA","YeastmtDNA","Mold/ProtozoanmtDNA",
"InvertebratemtDNA","CiliateNuclear","EchinodermmtDNA","EuplotidNuclear",
"Alt.YeastNuclear","AscidianmtDNA","FlatwormmtDNA","BlepharismaNuclear"]},
{'New/Restore' => [ "New Analysis", "Restore"]},
{'tempalnfile' => undef }, # aln file goes here
{'Model Options' => [ { "Custom" => '010010' },
{ "Default" => undef } ]
},
{'temptreefile' => undef }, # tree file goes here
{'Model Fit Results' => [ '/dev/null'] }, # this will not work under Windows
{'dN/dS bias parameter' => [ { "Estimate dN/dS only" => undef },
{ "Neutral" => undef },
{ "Estimate" => undef },
{ "Estimate + CI" => undef },
{ "User" => '3' } ] },
{'Ancestor Counting' => [ 'Two rate FEL','Single Ancestor Counting','Weighted Ancestor Counting',
'Sample Ancestal States','Process Sampled Ancestal States',
'One rate FEL','Rate Distribution',
'Full site-by-site LRT','Multirate FEL'] },
{'Significance level' => '0.05' },
{'Branch Options' => ['Internal Only','All','A Subtree only','Custom subset'] },
{'outfile' => undef }, # outfile goes here
);
}
=head2 program_name
Title : program_name
Usage : $factory->program_name()
Function: holds the program name
Returns: string
Args : None
=cut
=head2 program_dir
Title : program_dir
Usage : ->program_dir()
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
=cut
=head2 new
Title : new
Usage : my $obj = Bio::Tools::Run::Phylo::Hyphy::FEL->new();
Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::FEL object
Returns : Bio::Tools::Run::Phylo::Hyphy::FEL
Args : -alignment => the Bio::Align::AlignI object
-save_tempfiles => boolean to save the generated tempfiles and
NOT cleanup after onesself (default FALSE)
-tree => the Bio::Tree::TreeI object
-params => a hashref of parameters (all passed to set_parameter)
-executable => where the hyphy executable resides
See also: L<Bio::Tree::TreeI>, L<Bio::Align::AlignI>
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($aln, $tree, $st, $params, $exe,
$ubl) = $self->_rearrange([qw(ALIGNMENT TREE SAVE_TEMPFILES
PARAMS EXECUTABLE)],
@args);
defined $aln && $self->alignment($aln);
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 $self;
}
=head2 run
Title : run
Usage : my ($rc,$results) = $fel->run($aln);
Function: run the fel analysis using the default or updated parameters
the alignment parameter must have been set
Returns : Return code, Hash
Args : L<Bio::Align::AlignI> object,
L<Bio::Tree::TreeI> object [optional]
=cut
sub run {
my ($self,$aln,$tree) = @_;
$self->prepare($aln,$tree) unless (defined($self->{'_prepared'}));
my ($rc,$results) = (1);
{
my $commandstring;
my $exit_status;
my $tempdir = $self->tempdir;
my $felexe = $self->executable();
$self->throw("unable to find or run executable for 'HYPHY'") unless $felexe && -e $felexe && -x _;
$commandstring = $felexe . " BASEPATH=" . $self->program_dir . " " . $self->{'_wrapper'};
open(RUN, "$commandstring |") or $self->throw("Cannot open exe $felexe");
my @output = <RUN>;
$exit_status = close(RUN);
$self->error_string(join('',@output));
if( (grep { /\berr(or)?: /io } @output) || !$exit_status) {
$self->warn("There was an error - see error_string for the program output");
$rc = 0;
}
my $outfile = $self->outfile_name;
eval {
open(OUTFILE, "$outfile") or $self->throw("cannot open $outfile for reading");
my $readed_header = 0;
my @elems;
while (<OUTFILE>) {
if ($readed_header) {
# FEL results are csv
my @values = split("\,",$_);
for my $i (0 .. (scalar(@values)-1)) {
$elems[$i] =~ s/\n//g;
push @{$results->{$elems[$i]}}, $values[$i];
}
} else {
@elems = split("\,",$_);
$readed_header = 1;
}
}
};
if( $@ ) {
$self->warn($self->error_string);
}
}
unless ( $self->save_tempfiles ) {
unlink($self->{'_wrapper'});
$self->cleanup();
}
return ($rc,$results);
}
=head2 create_wrapper
Title : create_wrapper
Usage : $self->create_wrapper
Function: It will create the wrapper file that interfaces with the analysis bf file
Example :
Returns :
Args :
=cut
sub create_wrapper {
my $self = shift;
my $batchfile = 'QuickSelectionDetection.bf';
$self->SUPER::create_wrapper($batchfile);
}
=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
=head2 set_default_parameters
Title : set_default_parameters
Usage : $fel->set_default_parameters(0);
Function: (Re)set the default parameters from the defaults
(the first value in each array in the
%VALIDVALUES class variable)
Returns : none
Args : boolean: keep existing parameter values
=cut
sub set_default_parameters {
my ($self,$keepold) = @_;
$keepold = 0 unless defined $keepold;
foreach my $elem (@VALIDVALUES) {
my ($param,$val) = each %$elem;
# skip if we want to keep old values and it is already set
if (ref($val)=~/ARRAY/i ) {
unless (ref($val->[0])=~/HASH/i) {
push @{ $self->{'_orderedparams'} }, {$param, $val->[0]};
} else {
$val = $val->[0];
}
}
if ( ref($val) =~ /HASH/i ) {
my $prevparam;
while (defined($val)) {
last unless (ref($val) =~ /HASH/i);
last unless (defined($param));
$prevparam = $param;
($param,$val) = each %{$val};
push @{ $self->{'_orderedparams'} }, {$prevparam, $param};
push @{ $self->{'_orderedparams'} }, {$param, $val} if (defined($val));
}
} elsif (ref($val) !~ /HASH/i && ref($val) !~ /ARRAY/i) {
push @{ $self->{'_orderedparams'} }, {$param, $val};
}
}
}
=head1 Bio::Tools::Run::WrapperBase 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 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 : $fel->cleanup();
Function: Will cleanup the tempdir directory after a run
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;