Bio::SearchIO::erpin man page on Pidora

Man page or keyword search:  
man Server   31170 pages
apropos Keyword Search (all sections)
Output format
Pidora logo
[printable version]

Bio::SearchIO::erpin(3User Contributed Perl DocumentatiBio::SearchIO::erpin(3)

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:

	 http://bugzilla.open-bio.org/

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 v5.14.1			  2011-07-22	       Bio::SearchIO::erpin(3)
[top]

List of man pages available for Pidora

Copyright (c) for man pages and the logo by the respective OS vendor.

For those who want to learn more, the polarhome community provides shell access and support.

[legal] [privacy] [GNU] [policy] [cookies] [netiquette] [sponsors] [FAQ]
Tweet
Polarhome, production since 1999.
Member of Polarhome portal.
Based on Fawad Halim's script.
....................................................................
Vote for polarhome
Free Shell Accounts :: the biggest list on the net