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 0.7-1.1; older versions may work but will not be supported.

The latest version of Infernal is 1.1. The output has changed substantially relative to version 1.0. Versions 1.x are stable releases (and output has stabilized) therefore 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:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Chris Fields

Email cjfields-at-uiuc-dot-edu

CONTRIBUTORS

  Jeffrey Barrick, Michigan State University
  Paul Cantalupo, University of Pittsburgh

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; pre-v.1 versions of Infernal do 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; pre-v.1 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; pre-v1.1 Infernal 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; pre-v1.1 Infernal 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.