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

NAME
       Bio::SearchIO::fasta - A	SearchIO parser	for FASTA results

SYNOPSIS
	 # Do not use this object directly, use	it through the SearchIO	system
	  use Bio::SearchIO;
	  my $searchio = Bio::SearchIO->new(-format => 'fasta',
			   -file   => 'report.FASTA');
	  while( my $result = $searchio->next_result ) {
	   # ... do what you would normally doi	with Bio::SearchIO.
	  }

DESCRIPTION
       This object contains the	event based parsing code for FASTA format
       reports.	 It creates Bio::Search::HSP::FastaHSP objects instead of
       Bio::Search::HSP::GenericHSP for	the HSP	objects.

       This module will	parse -m 9 -d 0	output as well as default m 1 output
       from FASTA as well as SSEARCH.

       Also see	the SearchIO HOWTO:
       <http://bioperl.open-bio.org/wiki/HOWTO:SearchIO>.

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,	Aaron Mackey, William Pearson
       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::fasta->new();
	Function: Builds a new Bio::SearchIO::fasta object
	Returns	: Bio::SearchIO::fasta
	Args	: -idlength - set ID length to something other
			      than the default (6), this is only
			      necessary	if you have compiled FASTA
			      with a new default id length to display
			      in the HSP alignment blocks

   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

   idlength
	Title	: idlength
	Usage	: $obj->idlength($newval)
	Function: Internal storage of the length of the	ID desc
		  in the HSP alignment blocks.	Defaults to
		  $IDLENGTH class variable value
	Returns	: value	of idlength
	Args	: newvalue (optional)

   result_count
	Title	: result_count
	Usage	: my $count = $searchio->result_count
	Function: Returns the number of	results	we have	processed
	Returns	: integer
	Args	: none

   _will_handle
	Title	: _will_handle
	Usage	: Private method. For internal use only.
		     if( $self->_will_handle($type) ) {	... }
	Function: Provides an optimized	way to check whether or	not an element of a
		  given	type is	to be handled.
	Returns	: Reference to EventHandler object if the element type is to be	handled.
		  undef	if the element type is not to be handled.
	Args	: string containing type of element.

       Optimizations:

       1.
	 Using the cached pointer to the EventHandler to minimize repeated
	 lookups.

       2.
	 Caching the will_handle status	for each type that is encountered so
	 that it only need be checked by calling handler->will_handle($type)
	 once.

       This does not lead to a major savings by	itself (only 5-10%).  In
       combination with	other optimizations, or	for large parse	jobs, the
       savings good be significant.

       To test against the unoptimized version,	remove the parentheses from
       around the third	term in	the ternary " ?	: " operator and add two calls
       to $self->_eventHandler().

   _processHits
	Title	: _processHits
	Usage	: Private method. For internal use only.
	Function: Process/report any hits/hsps we saw in the top table,	not in alignments.
	Returns	: nothing.
	Args	: array	of hits	to process.

perl v5.24.1			  2017-07-08	       Bio::SearchIO::fasta(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich, Aaron Mackey, William Pearson | APPENDIX

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