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Bio::SearchIO::waba(3)User Contributed Perl DocumentatioBio::SearchIO::waba(3)

NAME
       Bio::SearchIO::waba - SearchIO parser for Jim Kent WABA program
       alignment output

SYNOPSIS
	   # do	not use	this object directly, rather through Bio::SearchIO

	   use Bio::SearchIO;
	   my $in = Bio::SearchIO->new(-format => 'waba',
				      -file   => 'output.wab');
	   while( my $result = $in->next_result	) {
	       while( my $hit =	$result->next_hit ) {
		   while( my $hsp = $result->next_hsp )	{

		   }
	       }
	   }

DESCRIPTION
       This parser will	process	the waba output	(NOT the human readable
       format).

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 - Jason Stajich
       Email jason-at-bioperl.org

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::waba->new();
	Function: Builds a new Bio::SearchIO::waba object
	Returns	: Bio::SearchIO::waba
	Args	: see Bio::SearchIO

   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: Convience method that	calls start_element, characters, end_element
	Returns	: none
	Args	: Hash ref with	the keys 'Name'	and 'Data'

   characters
	Title	: characters
	Usage	: $eventgenerator->characters($str)
	Function: Send a character events
	Returns	: none
	Args	: string

   _mode
	Title	: _mode
	Usage	: $obj->_mode($newval)
	Function:
	Example	:
	Returns	: value	of _mode
	Args	: newvalue (optional)

   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 'in' because within can be tested
		  for a	whole block.
	Returns	: boolean
	Args	: string element name

   start_document
	Title	: start_document
	Usage	: $eventgenerator->start_document
	Function: Handles 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

perl v5.32.1			  2019-12-07		Bio::SearchIO::waba(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

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