Bio::SearchIO::rnamotif.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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.