Bio::SearchIO::infernal.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::SearchIO::infernal - SearchIO-based Infernal parser

SYNOPSIS

   my $parser = Bio::SearchIO->new(-format => 'infernal',
                                   -file => 'purine.inf');
   while( my $result = $parser->next_result ) {
         # general result info, such as model used, Infernal version
         while( my $hit = $result->next_hit ) {
             while( my $hsp = $hit->next_hsp ) {
                 # ...
             }
         }
   }
 
 

DESCRIPTION

This is a SearchIO-based parser for Infernal output from the cmsearch program. It currently parses cmsearch output for Infernal versions 0.7-1.0; older versions may work but will not be supported.

As the first stable version has been released (and output has stabilized) it is highly recommended that users upgrade to using the latest Infernal release. Support for the older pre-v.1 developer releases will be dropped for future core 1.6 releases.

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

CONTRIBUTORS

   Jeffrey Barrick, Michigan State University
 
 

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::infernal->new();
  Function: Builds a new Bio::SearchIO::infernal object 
  Returns : Bio::SearchIO::infernal
  Args    : -fh/-file      => cmsearch (infernal) filename
            -format        => 'infernal'
            -model         => query model (Rfam ID) (default undef)
            -database      => database name (default undef)
            -query_acc     => query accession, eg. Rfam accession RF####
            -query_desc    => query description, eg. Rfam description
            -hsp_minscore  => minimum HSP score cutoff
            -convert_meta  => boolean, set to convert meta string to simple WUSS format
            -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
 
 

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)
 
 

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)
 
 

algorithm

  Title   : algorithm
  Usage   : my $algorithm = $parser->algorithm();
  Function: Get/Set algorithm; current versions of Infernal do not output
            the algorithm name
  Returns : String (algorithm name)
  Args    : [optional] String (algorithm name)
 
 

query_accession

  Title   : query_accession
  Usage   : my $acc = $parser->query_accession();
  Function: Get/Set query (model) accession; Infernal currently does not output
            the accession number (Rfam accession #)
  Returns : String (accession)
  Args    : [optional] String (accession)
 
 

query_description

  Title   : query_description
  Usage   : my $acc = $parser->query_description();
  Function: Get/Set query (model) description; Infernal currently does not output
            the Rfam description
  Returns : String (description)
  Args    : [optional] String (description)
 
 

hsp_minscore

  Title   : hsp_minscore
  Usage   : my $cutoff = $parser->hsp_minscore();
  Function: Get/Set min bit score cutoff (for generating Hits/HSPs)
  Returns : score (number)
  Args    : [optional] score (number)
 
 

convert_meta

  Title   : convert_meta
  Usage   : $parser->convert_meta(1);
  Function: Get/Set boolean flag for converting Infernal WUSS format
            to a simple bracketed format (simple WUSS by default) 
  Returns : boolean flag (TRUE or FALSE)
  Args    : [optional] boolean (eval's to TRUE or FALSE)
 
 

version

  Title   : version
  Usage   : $parser->version();
  Function: Set the Infernal cmsearch version
  Returns : version
  Args    : [optional] version
 
 

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)
                      . (gap)
  Args    : Hash ref of substitute delimiters, using above keys.
 
 

simple_meta

  Title   : simple_meta
  Usage   : my $string = $parser->simple_meta($str);
  Function: converts more complex WUSS meta format into simple bracket format
            using symbols defined in structure_symbols()
  Returns : converted string
  Args    : [required] string to convert
  Note    : This is a very simple conversion method to get simple bracketed
            format from Infernal data.  If the convert_meta() flag is set,
            this is the method used to convert the strings.