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Summary

Bio::EnsEMBL::Analysis::Runnable::Fungen

Package variables

Included modules

Inherit

Bio::EnsEMBL::Analysis::Runnable

Synopsis

Description

This module is the base class for Fungen Runnables.

Methods

Methods description

  Arg [1]     : Bio::EnsEMBL::Analysis::Runnable::Funcgen
  Description : parse analysis parameters
  Returntype  : hash ref with parameter names as keys
  Exceptions  : none
  Example     :

  Arg [1]     : Bio::EnsEMBL::Analysis::Runnable::Funcgen
  Arg [2]     : filename (string)
  Description : will hold a given filename or if one is requested but none
  defined it will use the create_filename method to create a filename
  Returntype  : string, filename
  Exceptions  : none
  Example     :

  Arg         : 
  Usage       : my $runnable = Bio::EnsEMBL::Analysis::Runnable::Funcgen->new()
  Description : Instantiates new Chipotle runnable
  Returns     : Bio::EnsEMBL::Analysis::Runnable::Funcgen::Nessie object
  Exceptions  : none

  Arg [1]     : Bio::EnsEMBL::Analysis::RunnableDB
  Arg [2]     : arrayref of output fields
  Description : container for outout fields
  Returntype  : arrayref
  Exceptions  : throws if no output field container is defined
  Example     :

  Arg [1]     : Bio::EnsEMBL::Analysis::Runnable::Funcgen
  Arg [2]     : filename (string)
  Decription  : open and parse resultsfile
  Returntype  : none
  Exceptions  : throws 
  Example     :

  Arg [1]     : Bio::EnsEMBL::Analysis::Runnable::Funcgen
  Arg [2]     : arrayref of result features
  Description : container for result features
  Returntype  : arrayref
  Exceptions  : throws if no probe feature container is defined
  Example     :

    Arg [1]     : Bio::EnsEMBL::Analysis::Runnable::Funcgen
    Arg [2]     : string, directory
    Description : Class specific run method. This checks the directory specifed
    to run it, write the data to file (tab-delimited), marks the query infile 
    and results file for deletion, runs the analysis, parses the results and 
    deletes any files
    Returntype  : 1
    Exceptions  : throws if no query sequence is specified
    Example     :

Methods code

sub get_parameters {

    my ($self) = @_;
    my %parameters = ();
    
    throw ("Object needs to be a Bio::EnsEMBL::Analysis::Runnable::Funcgen") 
        if (! $self->isa("Bio::EnsEMBL::Analysis::Runnable::Funcgen"));

    my @parameters = split(/\s+/, $self->analysis->parameters());
    map { throw("Parameter $_ has not the correct format.") 
              if (! m/^(.+)=(.+)/);
          $parameters{$1} = $2; } @parameters;

    #print Dumper %parameters;

    return\% parameters;

}

sub infile {

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

  if($filename){
    $self->{'infile'} = $filename;
  }
  if(!$self->{'infile'}){
    $self->{'infile'} = $self->create_filename
        ($self->analysis->module.'/'.$self->analysis->module, 'dat');
    (my $dir = $self->{'infile'}) =~ s,/[^/]+$,,;
    system("mkdir -p $dir") unless ( -d $dir );
  }

  return $self->{'infile'};

}

sub new {

    print "Analysis::Runnable::Funcgen::new\n";

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

    my ($result_features, $options, $workdir) = rearrange
        (['RESULT_FEATURES', 'OPTIONS', 'WORKDIR'], @args);

    $self->result_features($result_features);
    $self->workdir($workdir);
    $self->checkdir();

    warn("workdir ".$self->workdir()." OK!");

    #warn('RESULT_FEATURES: '.$self->result_features);

    #warn('OPTIONS:  '.$self->options);
    #warn('OPTIONS:  '.$options);
    #warn('A_PARAMS: '.$self->analysis->parameters);

    return $self;

}

sub output_fields {

    my ($self, $array) = @_;
    #print Dumper $array;
    if($array){
        $self->{'outfile_fields'} = $array;
    }
    throw("No outfile field string set in Runnable.") 
        if (!$self->{'outfile_fields'});
    return $self->{'outfile_fields'};

}

sub parse_results {

    my ($self, $resultsfile) = @_;
    
    if (! defined $resultsfile) {
        $resultsfile = $self->resultsfile;
    }
    throw ('No resultsfile defined in instance!')
        if(! defined $resultsfile);
    
    throw("parse_results: results file ".$resultsfile." does not exist.")
        if (! -e $resultsfile);
    
    warn('Resultsfile: '.$resultsfile);
    
    throw("parse_results: can't open file ".$resultsfile.": ". $!)
        unless (open(F, $resultsfile));
    
    my @output = ();
    
    while (<F>) {
        s/\"//g;
        s/^chr//;
        next unless (/^[0-9XYM]+\s/);
        
        chomp;
        my @ft = split;
        push(@output, [ @ft[@{$self->output_fields()}] ]);
        
    }
    
    $self->output(\@output);
    #print Dumper $self->output();
    
    throw("parse_results: can't close file ".$resultsfile.".")
        unless (close(F));

}

sub query {

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

    if ( $query ) {
        
        throw("Must pass RunnableDB:Funcgen:query a array ref not a ".
              ref($query)) unless (ref($query) eq 'ARRAY');

        map { 
            throw($_->name . " is not a Bio::EnsEMBL::Slice")
                unless ($_->isa("Bio::EnsEMBL::Slice"));
        } @$query;

        $self->{'query'} = $query;
    }

    return $self->{'query'};

}

1;

}

sub result_features {

    my ($self, $features) = @_;
    if($features){
        $self->{'result_features'} = $features;
    }
    #throw("No result features available in Runnable.") 
    #    if (!$self->{'result_features'});
    return $self->{'result_features'};

}

sub run {

    print "Bio::EnsEMBL::Analysis::Runnable::Funcgen::run\n";
    my ($self, $dir) = @_;
  
    #print Dumper $self->options;

    #throw("Can't run ".$self." without result features") 
    #    unless($self->result_features);
    #print Dumper $self->probe_features;
   
    $self->write_infile();

    warn("infile: ".$self->infile);

    throw("Input file ".$self->infile." is empty.") if (-z $self->infile);
    $self->files_to_delete($self->infile);
	
    $self->run_analysis();

    #print "Parsing results ... ";
    $self->parse_results();
    #print "done!\n";

    #$self->delete_files;
    return 1;

}

General documentation

This code is distributed under an Apache style licence. Please see
/info/about/code_licence.html for details.

Stefan Graf, Ensembl Functional Genomics -

Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk