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Manual Reference Pages  -  BIO::SEARCHIO::ERPIN (3)

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NAME

Bio::SearchIO::erpin - SearchIO-based ERPIN parser

CONTENTS

SYNOPSIS



  # do not call this module directly. Use Bio::SearchIO.



DESCRIPTION

This is an experimental SearchIO-based parser for output from the erpin program. It currently parses erpin output for ERPIN versions 4.2.5 and above; older versions may work but will not be supported.

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::infernal->new();
 Function: Builds a new Bio::SearchIO::infernal object
 Returns : Bio::SearchIO::infernal
 Args    : -fh/-file     => cmsearch (infernal) filename
           -format       => erpin
           -algorithm    => algorithm (default Infernal)
           -query_acc    => query accession, eg. Rfam accession (default undef)
           -hsp_minscore => minimum HSP score cutoff
           -version      => ERPIN version (not reported in output)



    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



    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)



    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)



    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)



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perl v5.20.3 BIO::SEARCHIO::ERPIN (3) 2016-04-05

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