Bio::SearchIO::rnamotif(3)

NAME
Bio::SearchIO::rnamotif - SearchIO-based RNAMotif parser

SYNOPSIS
  # do not call this module directly. Use Bio::SearchIO.

DESCRIPTION
This is a highly experimental SearchIO-based parser for output from the rnamotif program (one of the programs in the RNAMotif suite). It currently parses only raw rnamotif output for RNAMotif versions 3.0 and above; older versions may work but will not be supported. rmfmt output will not be supported at this time.

FEEDBACK

  Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

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

  Support
Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

  Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Chris Fields
Email cjfields-at-uiuc-dot-edu

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

  new
 Title   : new
 Usage   : my $obj = Bio::SearchIO->new();
 Function: Builds a new Bio::SearchIO::rnamotif object
 Returns : Bio::SearchIO::rnamotif parser
 Args    : -fh/-file     => RNAMotif filename
           -format       => 'rnamotif'
           -model        => query model (or descriptor, in this case)
           -database     => database name (default undef)
           -query_acc    => query accession (default undef)
           -hsp_minscore => minimum HSP score cutoff
           -hsp_maxscore => maximum HSP score cutoff
           -symbols      => hash ref of structure symbols to use
                            (default symbols in %STRUCTURE_SYMBOLS hash)

  next_result
 Title   : next_result
 Usage   : my $hit = $searchio->next_result;
 Function: Returns the next Result from a search
 Returns : Bio::Search::Result::ResultI object
 Args    : none

  start_element
 Title   : start_element
 Usage   : $eventgenerator->start_element
 Function: Handles a start element event
 Returns : none
 Args    : hashref with at least 2 keys 'Data' and 'Name'

  end_element
 Title   : start_element
 Usage   : $eventgenerator->end_element
 Function: Handles an end element event
 Returns : none
 Args    : hashref with at least 2 keys, 'Data' and 'Name'

  element
 Title   : element
 Usage   : $eventhandler->element({'Name' => $name, 'Data' => $str});
 Function: Convenience method that calls start_element, characters, end_element
 Returns : none
 Args    : Hash ref with the keys 'Name' and 'Data'

  element_hash
 Title   : element
 Usage   : $eventhandler->element_hash({'Hsp_hit-from' => $start,
                                        'Hsp_hit-to'   => $end,
                                        'Hsp_score'    => $lastscore});
 Function: Convenience method that takes multiple simple data elements and
           maps to appropriate parameters
 Returns : none
 Args    : Hash ref with the mapped key (in %MAPPING) and value

  characters
 Title   : characters
 Usage   : $eventgenerator->characters($str)
 Function: Send a character events
 Returns : none
 Args    : string

  within_element
 Title   : within_element
 Usage   : if( $eventgenerator->within_element($element) ) {}
 Function: Test if we are within a particular element
           This is different than 'in' because within can be tested
           for a whole block.
 Returns : boolean
 Args    : string element name

  in_element
 Title   : in_element
 Usage   : if( $eventgenerator->in_element($element) ) {}
 Function: Test if we are in a particular element
           This is different than 'within' because 'in' only
           tests its immediate parent.
 Returns : boolean
 Args    : string element name

  start_document
 Title   : start_document
 Usage   : $eventgenerator->start_document
 Function: Handle a start document event
 Returns : none
 Args    : none

  end_document
 Title   : end_document
 Usage   : $eventgenerator->end_document
 Function: Handles an end document event
 Returns : Bio::Search::Result::ResultI object
 Args    : none

  result_count
 Title   : result_count
 Usage   : my $count = $searchio->result_count
 Function: Returns the number of results we have processed
 Returns : integer
 Args    : none

  descriptor
 Title   : descriptor
 Usage   : my $descr = $parser->descriptor();
 Function: Get/Set descriptor name.  Some versions of RNAMotif do not add the
           descriptor name to the output.  This also overrides any name found
           while parsing.
 Returns : String (name of model)
 Args    : [optional] String (name of model)

  model
 Title   : model
 Usage   : my $model = $parser->model();
 Function: Get/Set model; Infernal currently does not output
           the model name (Rfam ID)
 Returns : String (name of model)
 Args    : [optional] String (name of model)
 Note    : this is a synonym for descriptor()

  database
 Title   : database
 Usage   : my $database = $parser->database();
 Function: Get/Set database; Infernal currently does not output
           the database name
 Returns : String (database name)
 Args    : [optional] String (database name)

  query_accession
 Title   : query_accession
 Usage   : my $acc = $parser->query_accession();
 Function: Get/Set query (model) accession; RNAMotif currently does not output
           the accession number
 Returns : String (accession)
 Args    : [optional] String (accession)

  algorithm_version
 Title   : algorithm_version
 Usage   : my $ver = $parser->algorithm_version();
 Function: Get/Set algorithm version (not defined in RNAMotif output)
 Returns : String (accession)
 Args    : [optional] String (accession)

  hsp_minscore
 Title   : hsp_minscore
 Usage   : my $cutoff = $parser->hsp_minscore();
 Function: Get/Set min score cutoff (for generating Hits/HSPs).
 Returns : score (number)
 Args    : [optional] score (number)
 Note    : Cannot be set along with hsp_maxscore()

  hsp_maxscore
 Title   : hsp_maxscore
 Usage   : my $cutoff = $parser->hsp_maxscore();
 Function: Get/Set max score cutoff (for generating Hits/HSPs).
 Returns : score (number)
 Args    : [optional] score (number)
 Note    : Cannot be set along with hsp_minscore()

  structure_symbols
 Title   : structure_symbols
 Usage   : my $hashref = $parser->structure_symbols();
 Function: Get/Set RNA structure symbols
 Returns : Hash ref of delimiters (5' stem, 3' stem, single-strand, etc)
         : default = < (5-prime)
                     > (3-prime)
                     . (single-strand)
                     ? (unknown)
 Args    : Hash ref of substitute delimiters, using above keys.

  _motif2meta
 Title   : _motif2meta
 Usage   : my ($rna, $meta) = $parser->_motif2meta($str, $descr);
 Function: Creates meta string from sequence and descriptor
 Returns : array of sequence, meta strings
 Args    : Array of string data and descriptor data

 Note: This is currently a quick and simple way of making simple
 RNA structures (stem-loops, helices, etc) from RNAMotif descriptor
 data in the output file.  It does not currently work with pseudoknots,
 triplets, G-quartets, or other more complex RNA structural motifs.