# Build a Coil factory
  my $factory = Bio::Tools::Run::Coil->new($params);

  # Pass the factory a Bio::Seq object
  # @feats is an array of Bio::SeqFeature::Generic objects
  my @feats = $factory->run($seq);

       @COIL_PARAMS=qw(PROGRAM VERBOSE QUIET SILENT);
       foreach my $attr ( @COIL_PARAMS)
                        { $OK_FIELD{$attr}++;

       my $self = shift;
       my $attr = $AUTOLOAD;
       $attr =~ s/.*:://;
       $attr = uc $attr;
       $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
       $self->{$attr} = shift if @_;
       return $self->{$attr};

    return 'ncoils';

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

       my ($class,@args) = @_;
       my $self = $class->SUPER::new(@args); 
       my ($attr, $value);
       while (@args)  {
           $attr =   shift @args;
           $value =  shift @args;
           next if( $attr =~ /^-/ ); # don't want named parameters
           if ($attr =~/PROGRAM/i) {
              $self->executable($value);
              next;
           }
           $self->$attr($value);
       }
       return $self;

	return shift->run(@_);

    my ($self,$seq) = @_;
    my @feats;
    
    if (ref($seq) ) { # it is an object
        if (ref($seq) =~ /GLOB/) {
            $self->throw("cannot use filehandle");
        }
        
        my $infile1 = $self->_writeSeqFile($seq);
        
        $self->_input($infile1);
        
        @feats = $self->_run();
        unlink $infile1;
    }
    else {
        #The argument is not a seq object but a sequence in a fasta file.
        #Perhaps should check here or before if this file is fasta format...if not die
        #Here the file does not need to be created or deleted. Its already written and may be used by other runnables.

        $self->_input($seq);

        @feats = $self->_run();
        
    }
   
    return @feats;

    my ($self,$infile1) = @_;
    if(defined $infile1){
	
	$self->{'input'}=$infile1;
     }
    return $self->{'input'};

     my ($self)= @_;
     
     my ($tfh1,$outfile) = $self->io->tempfile(-dir=>$self->tempdir());
     my $str =$self->executable." -f < ".$self->{'input'}." > ".$outfile;
     if($self->quiet || $self->verbose <=0 || $self->silent){
         $str.=" 2>/dev/null";
     }
     my $status = system($str);
     $self->throw( "Coil call ($str) crashed: $?\n ") unless $status==0;
     
     my $coil_parser = Bio::Tools::Coil->new();
     my $filehandle;
     if (ref ($outfile) !~ /GLOB/) {
        open (COIL, "<".$outfile) or $self->throw ("Couldn't open file ".$outfile.": $!\n");
        $filehandle =\* COIL;
     }
     else {
        $filehandle = $outfile;
     }

     my @coil_feat; 
      
     while(my $coil_feat = $coil_parser->next_result($filehandle)){

          push @coil_feat, $coil_feat;
     }
     
     $self->cleanup();
     close($tfh1);
     undef $tfh1;

     unlink $outfile;
     return @coil_feat;

    my ($self,$seq) = @_;
    my ($tfh,$inputfile) = $self->io->tempfile(-dir=>$self->tempdir());
    my $in  = Bio::SeqIO->new(-fh => $tfh , '-format' => 'Fasta');
    $in->write_seq($seq);

    return $inputfile;

}
1;

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  http://redmine.open-bio.org/projects/bioperl/

 Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil
 originally written by Marc Sohrmann (ms2@sanger.ac.uk)

 Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org>

 Title   :   _input
 Usage   :   obj->_input($seqFile)
 Function:   Internal(not to be used directly)
 Returns :
 Args    :