# something like this
  my $query = new Bio::Seq(-file   => $queryfile,
			   -format => 'Fasta');

  my $hmm =  Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Genes3d->new 
    ('-query'          => $query,
     '-program'        => 'hmmpfam' or '/usr/local/pubseq/bin/hmmpfam',
     '-database'       => 'Pfam');

  $hmm->workdir ($workdir);
  $hmm->run;
  my @results = $hmm->output;

  Blast takes a Bio::Seq (or Bio::PrimarySeq) object and runs hmmpfam.
  The resulting output file is parsed to produce a set of Bio::EnsEMBL::FeaturePairs.

    my ($self) = @_;

    my $filehandle;
    my $resfile = $self->resultsfile();
    my @fps;
		

    if (-e $resfile) {
	if (-z $resfile) {  
	    print STDERR "Genes3D didn't find any hits\n";
	    return; }       
	else {
	    open (CPGOUT, "<$resfile") or $self->throw("Error opening ", $resfile, "\n ");#
	    }
    }

   


#First parse what comes from the ls mode matches. Every match in that case is taken
    my $id;
    while (<CPGOUT>) {
	chomp;
        last if /^Alignments of top-scoring domains/;
        next if (/^Model/ || /^\-/ || /^$/);
        if (/^Query sequence:\s+(\S+)/) {
            $id = $1;
	}
	
        if (my ($hid, $start, $end, $hstart, $hend, $score, $evalue) = /^(\S+)\s+\S+\s+(\d+)\s+(\d+)\s+\S+\s+(\d+)\s+(\d+)\s+\S+\s+(\S+)\s+(\S+)/) {
	   my $fp= $self->create_protein_feature($start,$end,$score,$id,$hstart,$hend,$hid,$self->analysis, sprintf("%.3e", $evalue),0);
	   push @fps,$fp;
	}
    }
    close (CPGOUT); 
    $self->output(\@fps);
}

1;

    my ($self) = @_;

    # run program
    print STDERR "running ".$self->program." against ".$self->database."\n";

    # some of these options require HMMER 2.2g (August 2001)
    
    my @dbfiles = split(/;/,$self->analysis->db_file);

    print STDERR "FILENAME: ".$self->queryfile."\n";
 
    my $cmd = $self->program .' '.
	        '--acc -E 59.5 -A 100 '.
	        $self->options .' '.
	        $dbfiles[0]      .' '.
	        $self->queryfile.' > '.
		$self->resultsfile;
    print STDERR "$cmd\n";   
    $self->throw ("Error running ".$self->program." on ".$self->filename." against ".$dbfiles[0]) 
     unless ((system ($cmd)) == 0);

   Marc Sohrmann: ms2@sanger.ac.uk

 Title    : run_program
 Usage    : $self->program
 Function : makes the system call to program
 Example  :
 Returns  : 
 Args     :
 Throws   :