Bio::Tools::Run::Phylo::Hyphy Modeltest
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::Tools::Run::Phylo::Hyphy::Modeltest - Wrapper around the Hyphy Modeltest analysis
Package variables
No package variables defined.
Included modules
Bio::AlignIO
Bio::Root::Root
Bio::Tools::Run::Phylo::Hyphy::Base
Bio::Tools::Run::WrapperBase
Bio::TreeIO
Inherit
Bio::Root::Root Bio::Tools::Run::Phylo::Hyphy::Base
Synopsis
  use Bio::Tools::Run::Phylo::Hyphy::Modeltest;
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 $modeltest = Bio::Tools::Run::Phylo::Hyphy::Modeltest->new(); $modeltest->alignment($aln); $modeltest->tree($tree); my ($rc,$results) = $modeltest->run();
Description
This is a wrapper around the Modeltest 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/Modeltestwrapper.bf.
Methods
BEGIN Code
newDescriptionCode
runDescriptionCode
create_wrapperDescriptionCode
set_default_parametersDescriptionCode
DESTROY
No description
Code
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Tools::Run::Phylo::Hyphy::Modeltest->new();
Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::Modeltest object
Returns : Bio::Tools::Run::Phylo::Hyphy::Modeltest
Args : -alignment => the Bio::Align::AlignI object
-save_tempfiles => boolean to save the generated tempfiles and
NOT cleanup after onesself (default FALSE)
-tree => the Bio::Tree::TreeI object
-params => a hashref of parameters (all passed to set_parameter)
-executable => where the hyphy executable resides
See also: Bio::Tree::TreeI, Bio::Align::AlignI
runcodeprevnextTop
 Title   : run
Usage : my ($rc,$results) = $modeltest->run($aln);
Function: run the modeltest analysis using the default or updated parameters
the alignment parameter must have been set
Returns : Return code, Hash
Args : Bio::Align::AlignI object,
Bio::Tree::TreeI object [optional]
create_wrappercodeprevnextTop
 Title   : create_wrapper
Usage : $self->create_wrapper
Function: It will create the wrapper file that interfaces with the analysis bf file
Example :
Returns :
Args :
set_default_parameterscodeprevnextTop
 Title   : set_default_parameters
Usage : $modeltest->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
Methods code
BEGINTop
BEGIN {
     $PROGRAMNAME = 'HYPHYMP' . ($^O =~ /mswin/i ?'.exe':'');
    if( defined $ENV{'HYPHYDIR'} ) {
	$PROGRAM = Bio::Root::IO->catfile($ENV{'HYPHYDIR'},$PROGRAMNAME). ($^O =~ /mswin/i ?'.exe':'');;
    }

    @VALIDVALUES = 
        (
         {'tempalnfile' => undef }, # aln file goes here
{'temptreefile' => undef }, # tree file goes here
{'Number of Rate Classes' => [ '4' ] }, {'Model Selection Method' => [ 'Both', 'Hierarchical Test', 'AIC Test'] }, {'Model rejection level' => '0.05' }, );
}
newdescriptionprevnextTop
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 $self;
}
rundescriptionprevnextTop
sub run {
   my ($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 $modeltestexe = $self->executable();
       $self->throw("unable to find or run executable for 'HYPHY'") unless $modeltestexe && -e $modeltestexe && -x _;
       $commandstring = $modeltestexe . " BASEPATH=" . $self->program_dir . " " . $self->{'_wrapper'};
       open(RUN, "$commandstring |") or $self->throw("Cannot open exe $modeltestexe");
       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 writing");
           # FIXME -- needs output parsing -- ask hyphy to clean that up into a tsv?
foreach my $output (@output) { print OUTFILE $output; $results .= sprintf($output); } close(OUTFILE); }; if( $@ ) { $self->warn($self->error_string); } } unless ( $self->save_tempfiles ) { unlink($self->{'_wrapper'}); $self->cleanup(); } return ($rc,$results);
}
create_wrapperdescriptionprevnextTop
sub create_wrapper {
   my $self = shift;

   my $batchfile = 'ModelTest.bf';
   $self->SUPER::create_wrapper($batchfile);
}
set_default_parametersdescriptionprevnextTop
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}; } }
}
DESTROYdescriptionprevnextTop
sub DESTROY {
    my $self= shift;
    unless ( $self->save_tempfiles ) {
	$self->cleanup();
    }
    $self->SUPER::DESTROY();
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
 
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 BugsTop
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/
AUTHOR - Albert VilellaTop
Email avilella-at-gmail-dot-com
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Default ValuesTop
Valid and default values for Modeltest 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 methodsTop
save_tempfilesTop
 Title   : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)
tempdirTop
 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
cleanupTop
 Title   : cleanup
Usage : $modeltest->cleanup();
Function: Will cleanup the tempdir directory after a run
Returns : none
Args : none
ioTop
 Title   : io
Usage : $obj->io($newval)
Function: Gets a Bio::Root::IO object
Returns : Bio::Root::IO
Args : none