use Bio::Tools::RNAMotif;
  my $parser = Bio::Tools::RNAMotif->new(-file => $rna_output,
                                        -motiftag => 'protein_bind'
                                        -desctag => 'TRAP_binding');
  #parse the results
  while( my $motif = $parser->next_prediction) {
    # do something here
  }

  my ($score) = $feature->score; 

  my ($entry) = $feature->get_Annotations('secstructure');

   descline     - entire description line (in case the regex used for
                  sequence ID doesn't adequately catch the name
   descfile     - name of the descriptor file (may include path to file)
   secstrucure  - contains structural information from the descriptor
                  used as a query
   sequence     - sequence of motif, separated by spaces according to
                  matches to the structure in the descriptor (in
                  SecStructure).

  $list = $obj->clean_features(20); 

  $list = $obj->clean_features(-20);

  $list = $obj->clean_features(10000000);

  @sf = $list->get_all_features;
  for my $f (@sf) {
    # do crazy things here
  }

  my($self,@args) = @_;
  $self->warn('Use of this module is deprecated.  Use Bio::SearchIO::rnamotif instead');
  $self->SUPER::_initialize(@args);
  my ($motiftag,$desctag,$srctag) =  $self->SUPER::_rearrange([qw(MOTIFTAG
                                                                  DESCTAG
                                                                  SRCTAG
                                 )],
                                  @args);
  $self->motif_tag(defined $motiftag ? $motiftag : $MotifTag);
  $self->source_tag(defined $srctag ? $srctag : $SrcTag);
  $self->desc_tag(defined $desctag ? $desctag : $DescTag);
  $self->{'_sec_structure' => '',
          '_dfile' => ''};

    my $self = shift;

    return $self->{'motif_tag'} = shift if @_;
    return $self->{'motif_tag'};

    my $self = shift;

    return $self->{'source_tag'} = shift if @_;
    return $self->{'source_tag'};

    my $self = shift;

    return $self->{'desc_tag'} = shift if @_;
    return $self->{'desc_tag'};

 #-------------
    my ($self, $method) = @_;  
    if($method && ($method !~ /RNAMotif/i)) {
    $self->throw("method $method not supported in " . ref($self));
    }
    return $self->SUPER::analysis_method($method);

    my ($self,@args) = @_;
    # even though next_prediction doesn't expect any args (and this method
    # does neither), we pass on args in order to be prepared if this changes
    # ever
    return $self->next_prediction(@args);

    my ($self) = @_;
    my ($motiftag,$srctag,$desctag) = ( $self->motif_tag,
                       $self->source_tag,
                       $self->desc_tag);
    my ($score, $strand, $start, $length, $sequence, $end, $seqid, $description)=0;
    while($_ = $self->_readline) {
        while($_ =~ /^#RM/) { # header line
            if(/^#RM\sdescr\s(.*)$/) { # contains sec structure
                $self->{'_sec_structure'}=$1;
            }
            if(/^#RM\sdfile\s(.*)$/) { # contains dfile
                $self->{'_dfile'}=$1;
            }
            $_ = $self->_readline;
        }
        if(m/^>((\S*)\s.*)$/) {
            $seqid = $2;
            $description = $1; # contains entire description line if needed
            if($seqid =~  /(gb|emb|dbj|sp|pdb|bbs|ref|lcl)\|(.*)\|/) {
                $seqid = $2; # pulls out gid
            }
        }
        # start pulling out hit information...
        # regex is m/^\S+\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s(.*)$/
        # m/^\S+\s+     # seqID, not needed
        # (.+)\s+       # score, or extra info using sprintf()
        # (\d+)\s+      # strand
        # (\d+)\s+      # start
        # (\d+)\s       # length
        # (.*)$/        # sequence, divided according to descriptor
        if(m/^\S+\s+(.+)\s+(\d+)\s+(\d+)\s+(\d+)\s(.*)$/) {
            ($score, $strand, $start, $length, $sequence, $end)=
                ($1, $2, $3, $4, $5, 0);
            if( $strand==0 ) {
                $end = $start + $length -1;
                $strand = 1;
            } else {
                $end = $start - $length + 1;
                ($start, $end, $strand) = ($end, $start, -1);
            }
            my $gene = Bio::SeqFeature::Generic->new(-seq_id => $seqid,
                                                      -start  => $start,
                                                      -end    => $end,
                                                      -strand => $strand,
                                                      -score  => $score,
                                                      -primary_tag => $motiftag,
                                                      -source_tag  => $srctag,
                                                      -display_name => $desctag,
                                                      -tag     => {
                                                        'descline'       => $description,
                                                        'descfile'      => $self->{'_dfile'},
                                                        'secstructure'  => $self->{'_sec_structure'},
                                                        'sequence'       => $sequence});
            return $gene;
        }
    }

    my $self = shift;
    my $bp = shift;
    $self->throw("No arg, need pos. or neg. integer") if !$bp;
    $self->throw("Need pos. or neg. integer") if ($bp !~ /\-?\d/ || $bp =~ /\./);
    my ($b, $sf2);
    my @list = ();
    my @features = ();
    while (my $pred = $self->next_prediction) {
        push @features, $pred;
    }
    while (@features) {
        $b = shift @features if !defined($b);
        $sf2 = shift @features;
        # from same sequence?
        if ($sf2) { # if there is no feature, then...
            if ($b->seq_id == $sf2->seq_id) {
                # close starts (probable redundant hit)?
                if(abs(($b->start)-($sf2->start)) <= abs($bp)) {
                    # which score is better?
                    if( (($bp < 0) && ($b->score > $sf2->score))  ||  # lowest score
                        (($bp > 0) && ($b->score < $sf2->score)) ){   # highest score
                        $b = $sf2;
                        next;
                    } else {
                        next;
                    }
                }
                push @list, $b;
                $b = $sf2;
            }
        }
    }
    push @list, $b if $b;
    my $col = Bio::SeqFeature::Collection->new;
    $col->add_features(\@list);
    return $col;
}

1;

  bioperl-l@bioperl.org                  - General discussion
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  https://redmine.open-bio.org/projects/bioperl/

 Title   : new
 Usage   : my $obj = Bio::Tools::RNAMotif->new();
 Function: Builds a new Bio::Tools::RNAMotif object 
 Returns : an instance of Bio::Tools::RNAMotif
 Args    : -fh/-file for input filename
           -motiftag => primary tag used in gene features (default 'misc_binding')
           -desctag => tag used for display_name name (default 'rnamotif')
           -srctag  => source tag used in all features (default 'RNAMotif')