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BioPerl-1.007002
River stage two • 60 direct dependents • 65 total dependents
/ Bio::SearchIO::infernal

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.