Provided by: libbio-perl-perl_1.6.901-2_all bug

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

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.