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bio::searchio::erpin(3pm) [debian man page]

Bio::SearchIO::erpin(3pm)				User Contributed Perl Documentation				 Bio::SearchIO::erpin(3pm)

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://redmine.open-bio.org/projects/bioperl/ 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) perl v5.14.2 2012-03-02 Bio::SearchIO::erpin(3pm)
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