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 = $parser->structure_symbols();
Function: Get/Set RNA structure symbols
Returns : Hash ref of delimiters (5' stem, 3' stem, single-strand, etc)
: default = < (5-prime)
> (3-prime)
. (single-strand)
? (unknown)
Args : Hash ref of substitute delimiters, using above keys.
Title : _motif2meta
Usage : my ($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.