Mailing Lists¶

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

Support¶

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¶

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

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.