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.\" ========================================================================
.\"
.IX Title "Bio::SearchIO::rnamotif 3pm"
.TH Bio::SearchIO::rnamotif 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::SearchIO::rnamotif \- SearchIO\-based RNAMotif parser
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  # do not call this module directly. Use Bio::SearchIO.
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Chris Fields"
.IX Header "AUTHOR - Chris Fields"
Email cjfields-at-uiuc-dot-edu
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 10
\& 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       => \*(Aqrnamotif\*(Aq
\&           \-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)
.Ve
.SS "next_result"
.IX Subsection "next_result"
.Vb 5
\& 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
.Ve
.SS "start_element"
.IX Subsection "start_element"
.Vb 5
\& Title   : start_element
\& Usage   : $eventgenerator\->start_element
\& Function: Handles a start element event
\& Returns : none
\& Args    : hashref with at least 2 keys \*(AqData\*(Aq and \*(AqName\*(Aq
.Ve
.SS "end_element"
.IX Subsection "end_element"
.Vb 5
\& Title   : start_element
\& Usage   : $eventgenerator\->end_element
\& Function: Handles an end element event
\& Returns : none
\& Args    : hashref with at least 2 keys, \*(AqData\*(Aq and \*(AqName\*(Aq
.Ve
.SS "element"
.IX Subsection "element"
.Vb 5
\& Title   : element
\& Usage   : $eventhandler\->element({\*(AqName\*(Aq => $name, \*(AqData\*(Aq => $str});
\& Function: Convenience method that calls start_element, characters, end_element
\& Returns : none
\& Args    : Hash ref with the keys \*(AqName\*(Aq and \*(AqData\*(Aq
.Ve
.SS "element_hash"
.IX Subsection "element_hash"
.Vb 8
\& Title   : element
\& Usage   : $eventhandler\->element_hash({\*(AqHsp_hit\-from\*(Aq => $start,
\&                                        \*(AqHsp_hit\-to\*(Aq   => $end,
\&                                        \*(AqHsp_score\*(Aq    => $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
.Ve
.SS "characters"
.IX Subsection "characters"
.Vb 5
\& Title   : characters
\& Usage   : $eventgenerator\->characters($str)
\& Function: Send a character events
\& Returns : none
\& Args    : string
.Ve
.SS "within_element"
.IX Subsection "within_element"
.Vb 7
\& Title   : within_element
\& Usage   : if( $eventgenerator\->within_element($element) ) {}
\& Function: Test if we are within a particular element
\&           This is different than \*(Aqin\*(Aq because within can be tested
\&           for a whole block.
\& Returns : boolean
\& Args    : string element name
.Ve
.SS "in_element"
.IX Subsection "in_element"
.Vb 7
\& Title   : in_element
\& Usage   : if( $eventgenerator\->in_element($element) ) {}
\& Function: Test if we are in a particular element
\&           This is different than \*(Aqwithin\*(Aq because \*(Aqin\*(Aq only 
\&           tests its immediate parent.
\& Returns : boolean
\& Args    : string element name
.Ve
.SS "start_document"
.IX Subsection "start_document"
.Vb 5
\& Title   : start_document
\& Usage   : $eventgenerator\->start_document
\& Function: Handle a start document event
\& Returns : none
\& Args    : none
.Ve
.SS "end_document"
.IX Subsection "end_document"
.Vb 5
\& Title   : end_document
\& Usage   : $eventgenerator\->end_document
\& Function: Handles an end document event
\& Returns : Bio::Search::Result::ResultI object
\& Args    : none
.Ve
.SS "result_count"
.IX Subsection "result_count"
.Vb 5
\& Title   : result_count
\& Usage   : my $count = $searchio\->result_count
\& Function: Returns the number of results we have processed
\& Returns : integer
\& Args    : none
.Ve
.SS "descriptor"
.IX Subsection "descriptor"
.Vb 7
\& 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)
.Ve
.SS "model"
.IX Subsection "model"
.Vb 7
\& 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()
.Ve
.SS "database"
.IX Subsection "database"
.Vb 6
\& 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)
.Ve
.SS "query_accession"
.IX Subsection "query_accession"
.Vb 6
\& 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)
.Ve
.SS "algorithm_version"
.IX Subsection "algorithm_version"
.Vb 5
\& 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)
.Ve
.SS "hsp_minscore"
.IX Subsection "hsp_minscore"
.Vb 6
\& 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()
.Ve
.SS "hsp_maxscore"
.IX Subsection "hsp_maxscore"
.Vb 6
\& 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()
.Ve
.SS "structure_symbols"
.IX Subsection "structure_symbols"
.Vb 9
\& Title   : structure_symbols
\& Usage   : my $hashref = $parser\->structure_symbols();
\& Function: Get/Set RNA structure symbols
\& Returns : Hash ref of delimiters (5\*(Aq stem, 3\*(Aq stem, single\-strand, etc)
\&         : default = < (5\-prime)
\&                     > (3\-prime)
\&                     . (single\-strand)
\&                     ? (unknown) 
\& Args    : Hash ref of substitute delimiters, using above keys.
.Ve
.SS "_motif2meta"
.IX Subsection "_motif2meta"
.Vb 5
\& Title   : _motif2meta
\& Usage   : my ($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.
.Ve