Base documentation.

 Title   : program_name
 Usage   : $factory->program_name()
 Function: holds the program name
 Returns:  string
 Args    : None

program_dir

 Title   : program_dir
 Usage   : ->program_dir()
 Function: returns the program directory, obtained from ENV variable.
 Returns:  string
 Args    :

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

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    : Bio::Align::AlignI object,
	   Bio::Tree::TreeI object [optional]

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    :

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)

alignment

 Title   : alignment
 Usage   : $hyphy->align($aln);
 Function: Get/Set the Bio::Align::AlignI object
 Returns : Bio::Align::AlignI object
 Args    : [optional] Bio::Align::AlignI
 Comment : We could potentially add support for running directly on a file
           but we shall keep it simple
 See also: Bio::SimpleAlign

tree

 Title   : tree
 Usage   : $hyphy->tree($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

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

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: no_param_checks()

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

no_param_checks(2)

 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)

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

Methods code

BEGIN

BEGIN {

     $PROGRAMNAME = 'HYPHYMP' . ($^O =~ /mswin/i ?'.exe':'');
    if( defined $ENV{'HYPHYDIR'} ) {
	$PROGRAM = Bio::Root::IO->catfile($ENV{'HYPHYDIR'},$PROGRAMNAME). ($^O =~ /mswin/i ?'.exe':'');;

}

program_name

sub program_name {

        return 'HYPHYMP';

}

program_dir

sub program_dir {

        return Bio::Root::IO->catfile($ENV{HYPHYDIR}) if $ENV{HYPHYDIR};

}

new

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);

  return $self;

}

prepare

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;

}

create_wrapper

sub create_wrapper {

   my ($self,$batchfile) = @_;

   my $tempdir = $self->tempdir;
   $self->update_ordered_parameters;
   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);
   }
   print WRAPPER "\n",'ExecuteAFile (HYPHY_BASE_DIRECTORY + "TemplateBatchFiles" + DIRECTORY_SEPARATOR  + "', $batchfile ,'", stdinRedirect);', "\n";

   close(WRAPPER);
   $self->{'_wrapper'} = $wrapper;

}

error_string

sub error_string {

   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'error_string'} = $value;
    }
    return $self->{'error_string'};

}

alignment

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'};

}

tree

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'};

}

get_parameters

sub get_parameters {

   my ($self) = @_;
   # we're returning a copy of this
   return @{ $self->{'_hyphyparams'} };

}

set_parameter

sub set_parameter {

   my ($self,$param,$value) = @_;

   # FIXME - add validparams checking
   $self->{'_hyphyparams'}{$param} = $value;
   return 1;

}

update_ordered_parameters

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};
       }
   }

}

no_param_checks

sub no_param_checks {

   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'no_param_checks'} = $value;
    }
    return $self->{'no_param_checks'};

}

outfile_name

sub outfile_name {

    my $self = shift;
    if( @_ ) {
	return $self->{'_params'}->{'outfile'} = shift @_;
    }
    return $self->{'_params'}->{'outfile'};

}

DESTROY

description

sub DESTROY {

    my $self= shift;
    unless ( $self->save_tempfiles ) {
	$self->cleanup();
    }
    $self->SUPER::DESTROY();
}

1;

}

General documentation

FEEDBACK

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

Support

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.

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/

AUTHOR - Albert Vilella

Email avilella-at-gmail-dot-com

CONTRIBUTORS

Additional contributors names and emails here

APPENDIX

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _

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

Bio::Tools::Run::WrapperBase methods

save_tempfiles

 Title   : save_tempfiles
 Usage   : $obj->save_tempfiles($newval)
 Function: 
 Returns : value of save_tempfiles
 Args    : newvalue (optional)

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

cleanup

 Title   : cleanup
 Usage   : $hyphy->cleanup();
 Function: Will cleanup the tempdir directory after a run
 Returns : none
 Args    : none