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
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AUTHOR - Chris Fields
Email cjfields-at-uiuc-dot-eduAPPENDIX
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.