Build a Profile factory
 # $paramfile is the full path to the seg binary file

 my @params = ('DB',$dbfile,'PROGRAM',$paramfile);
 my $factory = Bio::Tools::Run::Profile->new($param);

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

 Wrapper module for the pfscan program

    @PROFILE_PARAMS=qw(DB PROGRAM VERBOSE);
    foreach my $attr ( @PROFILE_PARAMS)
    { $OK_FIELD{$attr}++;

    return 'pfscan';

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

       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};

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

	return shift->run(@_);

    my ($self,$seq) = @_;
    my @feats;

     if (ref($seq) ) {
         
         if (ref($seq) =~ /GLOB/) {
             $self->throw("cannot use filehandle");
         }
         
        my $display_id = $seq->display_id;
        
        my $infile1 = $self->_writeSeqFile($seq);
        
        $self->_input($infile1);
        
         @feats = $self->_run($display_id);
         unlink $infile1;
       
    }
    else {
        #The clone object is not a seq object but a 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 ($self,$display_id)= @_;
     my ($tfh,$outfile) = $self->io->tempfile(-dir=>$self->tempdir());
     close($tfh);
     undef $tfh;
     my $str =$self->executable.' -fz '.$self->_input." ".$self->DB." > ".$outfile;
     my $status = system($str);
     $self->throw( "Profile call ($str) crashed: $?\n ") unless $status==0;
     
     my $filehandle;
     if (ref ($outfile) !~ /GLOB/) {
        open (PROFILE, "<".$outfile) or $self->throw ("Couldn't open file ".$outfile.": $!\n");
        $filehandle =\* PROFILE;
     }
     else {
        $filehandle = $outfile;
     }
     my $profile_parser = Bio::Tools::Profile->new(-fh=>$filehandle);

     my @profile_feat;

     while(my $profile_feat = $profile_parser->next_result){

        $profile_feat->seq_id($display_id); 
         push @profile_feat, $profile_feat;
     }
     
     $self->cleanup();
     
     unlink $outfile;
     return @profile_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);
    $in->close();
    undef $in;
    close($tfh);
    undef $tfh;
    return $inputfile;

}
1;

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 Email: fugui@worf.fugu-sg.org

 The rest of the documentation details each of the object
 methods. Internal methods are usually preceded with a _

 Title   :   _input
 Usage   :   $factory->_input($seqFile)
 Function:   get/set for input file
 Returns :
 Args    :