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#
# BioPerl module for Bio::Tools::Run::Phylo::Hyphy::Base
#
# 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::Base - Hyphy wrapping base methods
=head1 SYNOPSIS
FIXME
=head1 DESCRIPTION
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.
=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 - 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::Base;
use vars qw(@ISA @VALIDVALUES $PROGRAMNAME $PROGRAM);
use strict;
use Bio::Root::Root;
use Bio::AlignIO;
use Bio::TreeIO;
use Bio::Tools::Run::WrapperBase;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
=head2 Default Values
Valid and default values 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 {
$PROGRAMNAME = 'HYPHYMP' . ($^O =~ /mswin/i ?'.exe':'');
if( defined $ENV{'HYPHYDIR'} ) {
$PROGRAM = Bio::Root::IO->catfile($ENV{'HYPHYDIR'},$PROGRAMNAME). ($^O =~ /mswin/i ?'.exe':'');;
}
}
=head2 program_name
Title : program_name
Usage : $factory->program_name()
Function: holds the program name
Returns: string
Args : None
=cut
sub program_name {
return 'HYPHYMP';
}
=head2 program_dir
Title : program_dir
Usage : ->program_dir()
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
=cut
sub program_dir {
return Bio::Root::IO->catfile($ENV{HYPHYDIR}) if $ENV{HYPHYDIR};
}
=head2 new
Title : new
Usage : my $obj = Bio::Tools::Run::Phylo::Hyphy->new();
Function: Builds a new Bio::Tools::Run::Phylo::Hyphy object
Returns : Bio::Tools::Run::Phylo::Hyphy
Args : -alignment => the Bio::Align::AlignI object
-save_tempfiles => boolean to save the generated tempfiles and
NOT cleanup after onesself (default FALSE)
-tree => the Bio::Tree::TreeI object
-params => a hashref of parameters (all passed to set_parameter)
-executable => where the hyphy executable resides
See also: L<Bio::Tree::TreeI>, L<Bio::Align::AlignI>
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my $versionstring = $self->version();
return $self;
}
=head2 prepare
Title : prepare
Usage : my $rundir = $hyphy->prepare($aln);
Function: prepare the analysis using the default or updated parameters
the alignment parameter 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 ) {
$self->warn("must have supplied a valid alignment file in order to run hyphy");
return 0;
}
my ($tempdir) = $self->tempdir();
my ($tempseqFH,$tempalnfile);
if( ! ref($aln) && -e $aln ) {
$tempalnfile = $aln;
} else {
($tempseqFH,$tempalnfile) = $self->io->tempfile
('-dir' => $tempdir,
UNLINK => ($self->save_tempfiles ? 0 : 1));
$aln->set_displayname_flat(1);
my $alnout = Bio::AlignIO->new('-format' => 'fasta',
'-fh' => $tempseqFH);
$alnout->write_aln($aln);
$alnout->close();
undef $alnout;
close($tempseqFH);
}
$self->{'_params'}{'tempalnfile'} = $tempalnfile;
my $outfile = $self->outfile_name || "$tempdir/results.tsv";
$self->{'_params'}{'outfile'} = $outfile;
my ($temptreeFH,$temptreefile);
if( ! ref($tree) && -e $tree ) {
$temptreefile = $tree;
} else {
($temptreeFH,$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->{'_params'}{'temptreefile'} = $temptreefile;
$self->create_wrapper;
$self->{_prepared} = 1;
return $tempdir;
}
=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,$batchfile) = @_;
my $tempdir = $self->tempdir;
$self->update_ordered_parameters;
#check version of HYPHY:
my $versionstring = $self->version();
$versionstring =~ /.*?(\d+\.\d+).*/;
my $version = $1;
my $wrapper = "$tempdir/wrapper.bf";
open(WRAPPER, ">$wrapper") or $self->throw("cannot open $wrapper for writing");
print WRAPPER "stdinRedirect"," = ", "\{", "\};", "\n\n";
my $counter = sprintf("%02d", 0);
foreach my $elem (@{ $self->{'_updatedorderedparams'} }) {
my ($param,$val) = each %$elem;
print WRAPPER 'stdinRedirect ["';
print WRAPPER "$counter";
print WRAPPER '"] = "';
print WRAPPER "$val";
print WRAPPER '"',";\n";
$counter = sprintf("%02d",$counter+1);
}
# not exactly sure what version of HYPHY caused this change,
# but Github source changes suggest that it was sometime
# after version 0.9920060501 was required.
if ($version >= 0.9920060501) {
print WRAPPER qq{\nExecuteAFile (HYPHY_LIB_DIRECTORY + "TemplateBatchFiles" + DIRECTORY_SEPARATOR + "$batchfile", stdinRedirect);\n};
} else {
print WRAPPER qq{\nExecuteAFile (HYPHY_BASE_DIRECTORY + "TemplateBatchFiles" + DIRECTORY_SEPARATOR + "$batchfile", stdinRedirect);\n};
}
close(WRAPPER);
$self->{'_wrapper'} = $wrapper;
}
=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 alignment
Title : alignment
Usage : $hyphy->align($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 : $hyphy->tree($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 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->{'_hyphyparams'} };
}
=head2 set_parameter
Title : set_parameter
Usage : $hyphy->set_parameter($param,$val);
Function: Sets a hyphy parameter, will be validated against
the valid values as set in the %VALIDVALUES class variable.
The checks can be ignored if one turns off param checks like this:
$hyphy->no_param_checks(1)
Returns : boolean if set was success, if verbose is set to -1
then no warning will be reported
Args : $param => name of the parameter
$value => value to set the parameter to
See also: L<no_param_checks()>
=cut
sub set_parameter {
my ($self,$param,$value) = @_;
# FIXME - add validparams checking
$self->{'_hyphyparams'}{$param} = $value;
return 1;
}
=head2 update_ordered_parameters
Title : update_ordered_parameters
Usage : $hyphy->update_ordered_parameters(0);
Function: (Re)set the default parameters from the defaults
(the first value in each array in the
%VALIDVALUES class variable)
Returns : none
Args : boolean: keep existing parameter values
=cut
sub update_ordered_parameters {
my ($self,$keepold) = @_;
$keepold = 0 unless defined $keepold;
foreach my $elem (@{$self->{'_orderedparams'}}) {
my ($param,$val) = each %$elem;
my $composite_param = $param;
# skip if we want to keep old values and it is already set
if (ref($param) =~ /ARRAY/i ) {
push @{ $self->{'_updatedorderedsparams'} }, {$param, $self->{_params}{$param} || $val};
} elsif ( ref($val) =~ /HASH/i ) {
while (defined($val)) {
last unless (ref($val) =~ /HASH/i);
my ($param,$val) = each %{$val};
$composite_param .= $param;
}
push @{ $self->{'_updatedorderedparams'} }, {$param, $self->{_params}{$composite_param} || $val};
} else {
push @{ $self->{'_updatedorderedparams'} }, {$param, $self->{_params}{$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
sub no_param_checks {
my ($self,$value) = @_;
if( defined $value) {
$self->{'no_param_checks'} = $value;
}
return $self->{'no_param_checks'};
}
=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 = $hyphy->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
sub outfile_name {
my $self = shift;
if( @_ ) {
return $self->{'_params'}->{'outfile'} = shift @_;
}
return $self->{'_params'}->{'outfile'};
}
=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
# sub no_param_checks {
# my ($self,$value) = @_;
# if( defined $value) {
# $self->{'no_param_checks'} = $value;
# }
# return $self->{'no_param_checks'};
# }
=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 : $hyphy->cleanup();
Function: Will cleanup the tempdir directory after a run
Returns : none
Args : none
=cut
=head2 version
Title : version
Usage : $obj->version()
Function: Returns the version string from HYPHY
Returns : string
Args : none
=cut
sub version {
my $self = shift;
my $tempdir = $self->tempdir;
my $wrapper = "$tempdir/version.bf";
open(WRAPPER, ">$wrapper") or $self->throw("cannot open $wrapper for writing");
print WRAPPER qq{GetString (versionString, HYPHY_VERSION, 2);\nfprintf (stdout, versionString);};
close(WRAPPER);
my $exe = $self->executable();
unless ($exe && -e $exe && -x _) {
$self->throw("unable to find or run executable for 'HYPHY'");
}
my $commandstring = $exe . " BASEPATH=" . $self->program_dir . " " . $wrapper;
open(RUN, "$commandstring |") or $self->throw("Cannot open exe $exe");
my $output = <RUN>;
close(RUN);
$self->{'_version'} = $output;
return $output;
}
sub DESTROY {
my $self= shift;
unless ( $self->save_tempfiles ) {
$self->cleanup();
}
$self->SUPER::DESTROY();
}
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