Bio::Tools::Run::Phylo::Hyphy SLAC
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Summary
Bio::Tools::Run::Phylo::Hyphy::SLAC - Wrapper around the Hyphy SLAC 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::Tools::Run::Phylo::Hyphy::Base
Synopsis
  use Bio::Tools::Run::Phylo::Hyphy::SLAC;
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 $slac = Bio::Tools::Run::Phylo::Hyphy::SLAC->new(); $slac->alignment($aln); $slac->tree($tree); my ($rc,$results) = $slac->run();
Description
This is a wrapper around the SLAC 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.
Methods
BEGIN Code
newDescriptionCode
runDescriptionCode
create_wrapperDescriptionCode
set_default_parametersDescriptionCode
DESTROY
No description
Code
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Tools::Run::Phylo::Hyphy::SLAC->new();
Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::SLAC object
Returns : Bio::Tools::Run::Phylo::Hyphy::SLAC
Args : -alignment => the Bio::Align::AlignI object
-save_tempfiles => boolean to save the generated tempfiles and
NOT cleanup after onesself (default FALSE)
-tree => the Bio::Tree::TreeI object
-params => a hashref of parameters (all passed to set_parameter)
-executable => where the hyphy executable resides
See also: Bio::Tree::TreeI, Bio::Align::AlignI
runcodeprevnextTop
 Title   : run
Usage : my ($rc,$results) = $slac->run($aln);
Function: run the slac 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_parameters(2)codeprevnextTop
 Title   : set_default_parameters
Usage : $slac->set_default_parameters(0);
Function: (Re)set the default parameters from the defaults
(the first value in each array in the
%VALIDVALUES class variable)
Returns : none
Args : boolean: keep existing parameter values
Methods code
BEGINTop
BEGIN {
     @VALIDVALUES = 
        (
         {'geneticCode' => [ "Universal","VertebratemtDNA","YeastmtDNA","Mold/ProtozoanmtDNA",
                             "InvertebratemtDNA","CiliateNuclear","EchinodermmtDNA","EuplotidNuclear",
                             "Alt.YeastNuclear","AscidianmtDNA","FlatwormmtDNA","BlepharismaNuclear"]},
         {'New/Restore' => [ "New Analysis", "Restore"]},
         {'tempalnfile' => undef }, # aln file goes here
{'Model Options' => [ { "Custom" => '010010' }, { "Default" => undef } ] }, {'temptreefile' => undef }, # tree file goes here
{'Model Fit Results' => [ '/dev/null'] }, # this will not work under Windows
{'dN/dS bias parameter' => [ { "Estimate dN/dS only" => undef }, { "Neutral" => undef }, { "Estimate" => undef }, { "Estimate + CI" => undef }, { "User" => '3' } ] }, {'Ancestor Counting' => [ 'Single Ancestor Counting','Weighted Ancestor Counting', 'Sample Ancestal States','Process Sampled Ancestal States', 'One rate FEL','Two rate FEL','Rate Distribution', 'Full site-by-site LRT','Multirate FEL'] }, {'SLAC Options' => ['Full tree','Tips vs Internals'] }, {'Treatment of Ambiguities' => ['Resolved','Averaged'] }, {'Test Statistic' => ['Approximate','Simulated Null'] }, {'Significance level' => '0.05' }, {'Output options' => 'Export to File' }, #we force a tsv file here
{'outfile' => undef }, # outfile goes here
{'Rate class estimator' => [ 'Skip','Count'] }, );
}
newdescriptionprevnextTop
sub new {
  my($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 $slacexe = $self->executable();
       $self->throw("unable to find or run executable for 'HYPHY'") unless $slacexe && -e $slacexe && -x _;
       $commandstring = $slacexe . " BASEPATH=" . $self->program_dir . " " . $self->{'_wrapper'};
       open(RUN, "$commandstring |") or $self->throw("Cannot open exe $slacexe");
       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 tsv
my @values = split("\t",$_); for my $i (0 .. (scalar(@values)-1)) { $elems[$i] =~ s/\n//g; push @{$results->{$elems[$i]}}, $values[$i]; } } else { @elems = split("\t",$_); $readed_header = 1; } } }; 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 = 'QuickSelectionDetection.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 SLAC 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::Phylo::Hyphy::Base methodsTop
program_nameTop
 Title   : program_name
Usage : $factory->program_name()
Function: holds the program name
Returns: string
Args : None
program_dirTop
 Title   : program_dir
Usage : ->program_dir()
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
prepareTop
 Title   : prepare
Usage : my $rundir = $slac->prepare($aln);
Function: prepare the slac 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]
error_stringTop
 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)
alignmentTop
 Title   : alignment
Usage : $slac->align($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
treeTop
 Title   : tree
Usage : $slac->tree($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_parametersTop
 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_parameterTop
 Title   : set_parameter
Usage : $slac->set_parameter($param,$val);
Function: Sets a slac 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:
$slac->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_parametersTop
 Title   : update_ordered_parameters
Usage : $slac->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
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 : $slac->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