/ 
BioPerl-1.7.8
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SearchIO::rnamotif

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.

_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.