Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::Search::Result::BUserRContributed PerlBio::Search::Result::BlastResult(3)

NAME
       Bio::Search::Result::BlastResult	- Blast-specific subclass of
       Bio::Search::Result::GenericResult

SYNOPSIS
	   # Working with iterations (PSI-BLAST	results)

	   $result->next_iteration();
	   $result->num_iterations();
	   $result->iteration();
	   $result->iterations();

       # See Bio::Search::Result::GenericResult	for information	about working
       with Results.

       # See Bio::Search::Iteration::IterationI	# for details about working
       with iterations.

       # TODO: #     * Show how	to configure a SearchIO	stream so that it
       generates #	 BlastResult objects.

DESCRIPTION
       This object is a	subclass of Bio::Search::Result::GenericResult and
       provides	some operations	that facilitate	working	with BLAST and PSI-
       BLAST results.

       For general information about working with Results, see
       Bio::Search::Result::GenericResult.

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 - Steve Chervitz
       Email sac@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::Search::Result::BlastResult->new();
	Function: Builds a new Bio::Search::Result::BlastResult	object
	Returns	: Bio::Search::Result::BlastResult
	Args	: See Bio::Search::Result::GenericResult();
		  The following	parameters are specific	to BlastResult:
		    -iterations	 => array ref of Bio::Search::Iteration::IterationI objects
		    -inclusion_threshold => e-value threshold for inclusion in the
					    PSI-BLAST score matrix model (blastpgp)

   hits
	Title	: hits
	Usage	: my @hits = $result->hits
	Function: Returns the available	hits for this Result
	Returns	: Array	of L<Bio::Search::Hit::HitI> objects
	Args	: none
	Note	: This method overrides	L<Bio::Search::Result::GenericResult::hits> to
		  take into account the	possibility of multiple	iterations, as occurs
		  in PSI-BLAST reports.
		  If there are multiple	iterations, all	'new' hits for all iterations
		  are returned.	These are the hits that	did not	occur in a previous
		  iteration.

		  See Also: L<Bio::Search::Result::GenericResult::hits>

   next_hit
	Title	: next_hit
	Usage	: while( $hit =	$result->next_hit()) { ... }
	Function: Returns the next available Hit object, representing potential
		  matches between the query and	various	entities from the database.
	Returns	: a Bio::Search::Hit::HitI object or undef if there are	no more.
	Args	: none
	Note	: This method overrides	L<Bio::Search::Result::GenericResult::next_hit>
		  to take into account the possibility of multiple iterations, as
		  occurs in PSI-BLAST reports.

		  If there are multiple	iterations, calling next_hit() traverses the
		  all of the hits, old and new,	for each iteration, calling next_hit()
		  on each iteration.

		  See Also: L<Bio::Search::Iteration::GenericIteration::next_hit>

   num_hits
	Title	: num_hits
	Usage	: my $hitcount=	$result->num_hits
	Function: returns the number of	hits for this query result
	Returns	: integer
	Args	: none
	Note	: This method overrides	L<Bio::Search::Result::GenericResult::num_hits>
		  to take into account the possibility of multiple iterations, as
		  occurs in PSI-BLAST reports.

		  If there are multiple	iterations, calling num_hits() returns the
		  number of 'new' hits for each	iteration. These are the hits that did
		  not occur in a previous iteration.

		  See Also: L<Bio::Search::Result::GenericResult::num_hits>

   add_hit
	Title	: add_hit
	Usage	: $report->add_hit($hit)
	Function: Adds a HitI to the stored list of hits
	Returns	: Number of HitI currently stored
	Args	: Bio::Search::Hit::HitI

   add_iteration
	Title	: add_iteration
	Usage	: $report->add_iteration($iteration)
	Function: Adds a IterationI to the stored list of iterations
	Returns	: Number of IterationI currently stored
	Args	: Bio::Search::Iteration::IterationI

   next_iteration
	Title	: next_iteration
	Usage	: while( $it = $result->next_iteration()) { ...	}
	Function: Returns the next Iteration object, representing all hits
		  found	within a given PSI-Blast iteration.
	Returns	: a Bio::Search::Iteration::IterationI object or undef if there	are no more.
	Args	: none

   iteration
	Usage	  : $iteration = $blast->iteration( $number );
	Purpose	  : Get	an IterationI object for the specified iteration
		    in the search result (PSI-BLAST).
	Returns	  : Bio::Search::Iteration::IterationI object
	Throws	  : Bio::Root::NoSuchThing exception if	$number	is not within
		    range of the number	of iterations in this report.
	Argument  : integer (optional, if not specified	get the	last iteration)
		    First iteration = 1

   num_iterations
	Usage	  : $num_iterations = $blast->num_iterations;
	Purpose	  : Get	the number of iterations in the	search result (PSI-BLAST).
	Returns	  : Total number of iterations in the report
	Argument  : none (read-only)

   number_of_iterations
	Usage	  : $num_iterations = $blast->number_of_iterations;
	Purpose	  : Get	the number of iterations in the	search result (PSI-BLAST).
	Returns	  : Total number of iterations in the report
	Argument  : none (read-only)
	Note	  : Alias of L<num_iterations>.

   round
	Usage	  : $round = $blast->round( $number );
	Purpose	  : Get	an IterationI object for the specified iteration
		    in the search result (PSI-BLAST).
	Returns	  : Bio::Search::Iteration::IterationI object
	Throws	  : Bio::Root::NoSuchThing exception if	$number	is not within
		    range of the number	of iterations in this report.
	Argument  : integer (optional, if not specified	get the	last iteration)
		    First iteration = 1
	Note	  : Alias of L<iteration>.

   iterations
	Title	: iterations
	Usage	: my @iterations = $result->iterations
	Function: Returns the IterationI objects contained within this Result
	Returns	: Array	of L<Bio::Search::Iteration::IterationI> objects
	Args	: none

   psiblast
	Usage	  : if(	$blast->psiblast ) { ... }
	Purpose	  : Set/get a boolean indicator	whether	or not the report
		    is a PSI-BLAST report.
	Returns	  : 1 if PSI-BLAST, undef if not.
	Argument  : 1 (when setting)

   no_hits_found
	Usage	  : $nohits = $blast->no_hits_found( $iteration_number );
	Purpose	  : Get	boolean	indicator indicating whether or	not any	hits
		    were present in the	report.

		    This is NOT	the same as determining	the number of hits via
		    the	hits() method, which will return zero hits if there were no
		    hits in the	report or if all hits were filtered out	during the parse.

		    Thus, this method can be used to distinguish these possibilities
		    for	hitless	reports	generated when filtering.

	Returns	  : Boolean
	Argument  : (optional) integer indicating the iteration	number (PSI-BLAST)
		    If iteration number	is not specified and this is a PSI-BLAST result,
		    then this method will return true only if all iterations had
		    no hits found.

   set_no_hits_found
	Usage	  : $blast->set_no_hits_found( $iteration_number );
	Purpose	  : Set	boolean	indicator indicating whether or	not any	hits
		    were present in the	report.
	Returns	  : n/a
	Argument  : (optional) integer indicating the iteration	number (PSI-BLAST)

   _next_iteration_index
	Title	: _next_iteration_index
	Usage	: private

   rewind
	Title	: rewind
	Usage	: $result->rewind;
	Function: Allow	one to reset the Iteration iterator to the beginning
		  Since	this is	an in-memory implementation
	Returns	: none
	Args	: none

   inclusion_threshold
	Title	: inclusion_threshold
	Usage	: my $incl_thresh = $result->inclusion_threshold; (read-only)
	Function: Gets the e-value threshold for inclusion in the PSI-BLAST
		  score	matrix model (blastpgp)	that was used for generating the report
		  being	parsed.
	Returns	: number (real)	or undef if not	a PSI-BLAST report.
	Args	: none

perl v5.24.1			  2017-07-0Bio::Search::Result::BlastResult(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Steve Chervitz | APPENDIX

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::Search::Result::BlastResult&sektion=3&manpath=FreeBSD+12.1-RELEASE+and+Ports>

home | help