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Summary

Bio::EnsEMBL::Analysis::Runnable::EponineTSS

Package variables

Included modules

Inherit

Bio::EnsEMBL::Analysis::Runnable

Synopsis

  my $runnable = Bio::EnsEMBL::Analysis::Runnable::EponineTSS->new
  (
   -query => $slice,
   -program => 'java',
  );
  $runnable->run;
  my @simple_features = @{$runnable->output};

Description

EponineTSS expects to run the program EponineTSS and produces SimpleFeature
which can be stored in the simple_feature table in the core database

Methods

Methods description

  Arg [1]   : Bio::EnsEMBL::Analysis::Runnable::EponineTSS
  Arg [2]   : string , path to the eponine jar
  Function  : container
  Returntype: string
  Exceptions: none (find file will throw if it cant locate the file)
  Example   :

  Arg [1]   : Bio::EnsEMBL::Analysis::Runnable::EponineTSS
  Arg [2]   : string, path to the eponine jar
  Arg [3]   : int, threshold
  Function  : create a new Bio::EnsEMBL::Analysis::Runnable::EponineTSS
  Returntype: Bio::EnsEMBL::Analysis::Runnable::EponineTSS
  Exceptions: none
  Example   :

  Arg [1]   : Bio::EnsEMBL::Analysis::Runnable::EponineTSS
  Arg [2]   : string, filename
  Function  : to open and parse the results file
  Returntype: none
  Exceptions: throws on failure to open or close the results file
  or if the results file doesnt exist
  Example   :

  Arg [1]   : Bio::EnsEMBL::Analysis::Runnable::EponineTSS
  Arg [2]   : string, program name
  Function  : construct and open commandline for running
  eponine
  Returntype: none 
  Exceptions: throws if fail to run program
  Example   :

  Arg [1]   : Bio::EnsEMBL::Analysis::Runnable::EponineTSS
  Arg [2]   : int, threshold
  Function  : container
  Returntype: int
  Exceptions: 
  Example   :

  Arg [1]   : Bio::EnsEMBL::Analysis::Runnable::EponineTSS
  Arg [2]   : int, number to be truncated
  Function  : truncate a floating point number to three decimal places
  Returntype: 
  Exceptions: 
  Example   :

Methods code

sub epojar {

  my $self = shift;
  my $epojar = shift;
  if($epojar){
    if(! -e $epojar){
      my $temp = $self->find_file($epojar);
      $epojar = $temp;
    }
    $self->{'epojar'} = $epojar;
  }
  return $self->{'epojar'};

}

sub new {

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

  my ($epojar, $threshold) = rearrange(['EPOJAR', 'THRESHOLD'], @args);

  ##################
  #SETTING DEFAULTS#
  ##################
  if(!$self->program){
    $self->program('java');
  }
  $self->epojar('eponine-scan.jar');
  $self->threshold(50);
  ##################

  $self->epojar($epojar) if($epojar);
  $self->threshold($threshold) if($threshold);
  
  return $self;

}

sub parse_results {

  my ($self, $results) = @_;
  if(!$results){
    $results = $self->resultsfile;
  }
  my $ff = $self->feature_factory;
  if(!-e $results){
    throw("Can't parse an no existance results file ".$results.
          " EponineTSS:parse_results");
  }
  my @output;
  open(EponineTSS, $results) or throw("FAILED to open ".$results.
                                      " EponineTSS:parse_results");
 LINE:while(<EponineTSS>){
    if (! /^\#/){ #ignore introductory lines
      chomp;
      my @element = split;
      my ($name, $start, $end, $score, $temp_strand) =
        @element[0, 3, 4, 5, 6];
      my $strand = 1;
      if($temp_strand eq '-'){
        $strand = -1;
      }
      $score = $self->trunc_float_3($score);
      my $sf = $ff->create_simple_feature($start, $end, $strand, $score,
                                          '', $name, $self->query); 
      push(@output, $sf);
    }
  }
  $self->output(\@output);
  close(EponineTSS) or throw("FAILED to close ".$results.
                             " EponineTSS:parse_results");

}

sub run_analysis {

  my ($self, $program) = @_;
  if(!$program){
    $program = $self->program;
  }
  throw($program." is not executable EponineTSS::run_analysis ") 
    unless($program && -x $program);
  my $command = $program." -jar ".$self->epojar." -seq ".$self->queryfile.
    " -threshold ".$self->threshold." > ".$self->resultsfile;
  print "Running analysis ".$command."\n";
  system($command) == 0 or throw("FAILED to run ".$command);

}

sub threshold {

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

}

sub trunc_float_3 {

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

    # deal only with valid numbers
    # and only need cases of the form [+/-]xx.yyyyy
    return $arg unless $arg =~ /^[+-]?\d*\.\d+$/;

    return 0.001 * int (1000 * $arg);

}

General documentation

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