NAME

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

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)

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq