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Bio::Search::Hit::HitIUser Contributed Perl DocumentaBio::Search::Hit::HitI(3)

NAME
       Bio::Search::Hit::HitI -	Interface for a	hit in a similarity search
       result

SYNOPSIS
       # Bio::Search::Hit::HitI	objects	should not be instantiated since this
       # module	defines	a pure interface.

       # Given an object that implements the Bio::Search::Hit::HitI
       interface, # you	can do the following things with it:

	   # Get a HitI	object from a SearchIO stream:
	   use Bio::SeachIO;
	   my $searchio	= Bio::SearchIO->new(-format =>	'blast', -file => 'result.bls');
	   my $result =	$searchio->next_result;
	   my $hit    =	$result->next_hit;

	   $hit_name = $hit->name();

	   $desc = $hit->description();

	   $len	= $hit->length

	   $alg	= $hit->algorithm();

	   $score = $hit->raw_score();

	   $significance = $hit->significance();

	   $rank = $hit->rank(); # the Nth hit for a specific query

	   while( $hsp = $obj->next_hsp()) { ... } # process in	iterator fashion

	   for my $hsp ( $obj->hsps()()) { ... } # process in list fashion

DESCRIPTION
	   Bio::Search::Hit::* objects are data	structures that	contain	information
       about specific hits obtained during a library search.  Some information will
       be algorithm-specific, but others will be generally defined.

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 one
       of the Bioperl mailing lists.  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
       the bugs	and their resolution.  Bug reports can be submitted via	the
       web:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR - Aaron Mackey, Steve Chervitz
       Email amackey@virginia.edu  (original author) Email sac@bioperl.org

COPYRIGHT
       Copyright (c) 1999-2001 Aaron Mackey, Steve Chervitz. All Rights
       Reserved.

DISCLAIMER
       This software is	provided "as is" without warranty of any kind.

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   name
	Title	: name
	Usage	: $hit_name = $hit->name();
	Function: returns the name of the Hit sequence
	Returns	: a scalar string
	Args	: none

       The name	of a hit is unique within a Result or within an	Iteration.

   description
	Title	: description
	Usage	: $desc	= $hit->description();
	Function: Retrieve the description for the hit
	Returns	: a scalar string
	Args	: none

   accession
	Title	: accession
	Usage	: $acc = $hit->accession();
	Function: Retrieve the accession (if available)	for the	hit
	Returns	: a scalar string (empty string	if not set)
	Args	: none

   locus
	Title	: locus
	Usage	: $acc = $hit->locus();
	Function: Retrieve the locus(if	available) for the hit
	Returns	: a scalar string (empty string	if not set)
	Args	: none

   length
	Title	: length
	Usage	: my $len = $hit->length
	Function: Returns the length of	the hit
	Returns	: integer
	Args	: none

   algorithm
	Title	: algorithm
	Usage	: $alg = $hit->algorithm();
	Function: Gets the algorithm specification that	was used to obtain the hit
		  For BLAST, the algorithm denotes what	type of	sequence was aligned
		  against what (BLASTN:	dna-dna, BLASTP	prt-prt, BLASTX	translated
		  dna-prt, TBLASTN prt-translated dna, TBLASTX translated
		  dna-translated dna).
	Returns	: a scalar string
	Args	: none

   raw_score
	Title	: raw_score
	Usage	: $score = $hit->raw_score();
	Function: Gets the "raw	score" generated by the	algorithm.  What
		  this score is	exactly	will vary from algorithm to algorithm,
		  returning undef if unavailable.
	Returns	: a scalar value
	Args	: none

   score
       Equivalent to raw_score()

   significance
	Title	: significance
	Usage	: $significance	= $hit->significance();
	Function: Used to obtain the E or P value of a hit, i.e. the probability that
		  this particular hit was obtained purely by random chance.  If
		  information is not available (nor calculatable from other
		  information sources),	return undef.
	Returns	: a scalar value or undef if unavailable
	Args	: none

   bits
	Usage	  : $hit_object->bits();
	Purpose	  : Gets the bit score of the best HSP for the current hit.
	Example	  : $bits = $hit_object->bits();
	Returns	  : Integer or double for FASTA	reports
	Argument  : n/a
	Comments  : For	BLAST1,	the non-bit score is listed in the summary line.

       See Also	  : score()

   next_hsp
	Title	 : next_hsp
	Usage	 : while( $hsp = $obj->next_hsp()) { ... }
	Function : Returns the next available High Scoring Pair
	Example	 :
	Returns	 : L<Bio::Search::HSP::HSPI> object or null if finished
	Args	 : none

   hsps
	Usage	  : $hit_object->hsps();
	Purpose	  : Get	a list containing all HSP objects.
		  : Get	the numbers of HSPs for	the current hit.
	Example	  : @hsps = $hit_object->hsps();
		  : $num  = $hit_object->hsps();  # alternatively, use num_hsps()
	Returns	  : Array context : list of L<Bio::Search::HSP::BlastHSP> objects.
		  : Scalar context: integer (number of HSPs).
		  :		    (Equivalent	to num_hsps()).
	Argument  : n/a. Relies	on wantarray
	Throws	  : Exception if the HSPs have not been	collected.

       See Also	  : hsp(), num_hsps()

   num_hsps
	Usage	  : $hit_object->num_hsps();
	Purpose	  : Get	the number of HSPs for the present Blast hit.
	Example	  : $nhsps = $hit_object->num_hsps();
	Returns	  : Integer
	Argument  : n/a
	Throws	  : Exception if the HSPs have not been	collected.

       See Also	  : hsps()

   seq_inds
	Usage	  : $hit->seq_inds( seq_type, class, collapse );
	Purpose	  : Get	a list of residue positions (indices) across all HSPs
		  : for	identical or conserved residues	in the query or	sbjct sequence.
	Example	  : @s_ind = $hit->seq_inds('query', 'identical');
		  : @h_ind = $hit->seq_inds('hit', 'conserved');
		  : @h_ind = $hit->seq_inds('hit', 'conserved',	1);
	Returns	  : Array of integers
		  : May	include	ranges if collapse is non-zero.
	Argument  : [0]	seq_type  = 'query' or 'hit' or	'sbjct'	 (default = 'query')
		  :		    ('sbjct' is	synonymous with	'hit')
		  : [1]	class	  = 'identical'	or 'conserved' (default	= 'identical')
		  :		 (can be shortened to 'id' or 'cons')
		  :		 (actually, anything not 'id' will evaluate to 'conserved').
		  : [2]	collapse  = boolean, if	non-zero, consecutive positions	are merged
		  :		using a	range notation,	e.g., "1 2 3 4 5 7 9 10	11"
		  :		collapses to "1-5 7 9-11". This	is useful for
		  :		consolidating long lists. Default = no collapse.
	Throws	  : n/a.

       See Also	  : Bio::Search::HSP::HSPI::seq_inds()

   rewind
	Title	: rewind
	Usage	: $hit->rewind;
	Function: Allow	one to reset the HSP iterator to the beginning
		  if possible
	Returns	: none
	Args	: none

   overlap
	Usage	  : $hit_object->overlap( [integer] );
	Purpose	  : Gets/Sets the allowable amount overlap between different HSP sequences.
	Example	  : $hit_object->overlap(5);
		  : $overlap = $hit_object->overlap;
	Returns	  : Integer.
	Argument  : integer.
	Throws	  : n/a
	Status	  : Experimental
	Comments  : Any	two HSPs whose sequences overlap by less than or equal
		  : to the overlap() number of resides will be considered separate HSPs
		  : and	will not get tiled by L<Bio::Search::BlastUtils::_adjust_contigs()>.

       See Also	  : Bio::Search::BlastUtils::_adjust_contigs(),	BUGS

   n
	Usage	  : $hit_object->n();
	Purpose	  : Gets the N number for the current Blast hit.
		  : This is the	number of HSPs in the set which	was ascribed
		  : the	lowest P-value (listed on the description line).
		  : This number	is not the same	as the total number of HSPs.
		  : To get the total number of HSPs, use num_hsps().
	Example	  : $n = $hit_object->n();
	Returns	  : Integer
	Argument  : n/a
	Throws	  : Exception if HSPs have not been set	(BLAST2	reports).
	Comments  : Note that the N parameter is not reported in gapped	BLAST2.
		  : Calling n()	on such	reports	will result in a call to num_hsps().
		  : The	num_hsps() method will count the actual	number of
		  : HSPs in the	alignment listing, which may exceed N in
		  : some cases.

       See Also	  : num_hsps()

   p
	Usage	  : $hit_object->p( [format] );
	Purpose	  : Get	the P-value for	the best HSP of	the given BLAST	hit.
		  : (Note that P-values	are not	provided with NCBI Blast2 reports).
	Example	  : $p =  $sbjct->p;
		  : $p =  $sbjct->p('exp');  # get exponent only.
		  : ($num, $exp) =  $sbjct->p('parts');	 # split sci notation into parts
	Returns	  : Float or scientific	notation number	(the raw P-value, DEFAULT).
		  : Integer if format == 'exp' (the magnitude of the base 10 exponent).
		  : 2-element list (float, int)	if format == 'parts' and P-value
		  :		   is in scientific notation (See Comments).
	Argument  : format: string of 'raw' | 'exp' | 'parts'
		  :    'raw' returns value given in report. Default. (1.2e-34)
		  :    'exp' returns exponent value only (34)
		  :    'parts' returns the decimal and exponent	as a
		  :	       2-element list (1.2, -34) (See Comments).
	Throws	  : Warns if no	P-value	is defined. Uses expect	instead.
	Comments  : Using the 'parts' argument is not recommended since	it will	not
		  : work as expected if	the P-value is not in scientific notation.
		  : That is, floats are	not converted into sci notation	before
		  : splitting into parts.

       See Also	  : expect(), signif(),
       Bio::Search::BlastUtils::get_exponent()

   hsp
	Usage	  : $hit_object->hsp( [string] );
	Purpose	  : Get	a single HSPI object for the present HitI object.
	Example	  : $hspObj  = $hit_object->hsp;  # same as 'best'
		  : $hspObj  = $hit_object->hsp('best');
		  : $hspObj  = $hit_object->hsp('worst');
	Returns	  : Object reference for a L<Bio::Search::HSP::HSPI> object.
	Argument  : String (or no argument).
		  :   No argument (default) = highest scoring HSP (same	as 'best').
		  :   'best' or	'first'	= highest scoring HSP.
		  :   'worst' or 'last'	= lowest scoring HSP.
	Throws	  : Exception if the HSPs have not been	collected.
		  : Exception if an unrecognized argument is used.

       See Also	  : hsps(), num_hsps()

   logical_length
	Usage	  : $hit_object->logical_length( [seq_type] );
		  : (mostly intended for internal use).
	Purpose	  : Get	the logical length of the hit sequence.
		  : If the Blast is a TBLASTN or TBLASTX, the returned length
		  : is the length of the would-be amino	acid sequence (length/3).
		  : For	all other BLAST	flavors, this function is the same as length().
	Example	  : $len    = $hit_object->logical_length();
	Returns	  : Integer
	Argument  : seq_type = 'query' or 'hit'	or 'sbjct' (default = 'query')
		    ('sbjct' is	synonymous with	'hit')
	Throws	  : n/a
	Comments  : This is important for functions like frac_aligned_query()
		  : which need to operate in amino acid	coordinate space when dealing
		  : with [T]BLAST[NX] type reports.

       See Also	  : length(), frac_aligned_query(), frac_aligned_hit()

   rank
	Title	: rank
	Usage	: $obj->rank($newval)
	Function: Get/Set the rank of this Hit in the Query search list
		  i.e. this is the Nth hit for a specific query
	Returns	: value	of rank
	Args	: newvalue (optional)

   each_accession_number
	Title	: each_accession_number
	Usage	: $obj->each_accession_number
	Function: Get each accession number listed in the description of the hit.
		  If there are no alternatives,	then only the primary accession	will
		  be given
	Returns	: list of all accession	numbers	in the description
	Args	: none

   tiled_hsps
	Usage	  : $hit_object->tiled_hsps( [integer] );
	Purpose	  : Gets/Sets an indicator for whether or not the HSPs in this Hit
		  : have been tiled.
		  : Methods that rely on HSPs being tiled should check this
		  : and	then call SearchUtils::tile_hsps() if not.
	Example	  : $hit_object->tiled_hsps(1);
		  : if(	$hit_object->tiled_hsps	) { # do something }
	Returns	  : Boolean (1 or 0)
	Argument  : integer (optional)
	Throws	  : n/a

   strand
	Usage	  : $sbjct->strand( [seq_type] );
	Purpose	  : Gets the strand(s) for the query, sbjct, or	both sequences
		  : in the best	HSP of the BlastHit object after HSP tiling.
		  : Only valid for BLASTN, TBLASTX, BLASTX-query, TBLASTN-hit.
	Example	  : $qstrand = $sbjct->strand('query');
		  : $sstrand = $sbjct->strand('hit');
		  : ($qstrand, $sstrand) = $sbjct->strand();
	Returns	  : scalar context: integer '1', '-1', or '0'
		  : array context without args:	list of	two strings (queryStrand, sbjctStrand)
		  : Array context can be "induced" by providing	an argument of 'list' or 'array'.
	Argument  : In scalar context: seq_type	= 'query' or 'hit' or 'sbjct' (default = 'query')
		    ('sbjct' is	synonymous with	'hit')
	Throws	  : n/a
	Comments  : This method	requires that all HSPs be tiled. If they have not
		  : already been tiled,	they will be tiled first automatically..
		  : If you don't want the tiled	data, iterate through each HSP
		  : calling strand() on	each (use hsps() to get	all HSPs).
		  :
		  : Formerly (prior to 10/21/02), this method would return the
		  : string "-1/1" for hits with	HSPs on	both strands.
		  : However, now that strand and frame is properly being accounted
		  : for	during HSP tiling, it makes more sense for strand()
		  : to return the strand data for the best HSP after tiling.
		  :
		  : If you really want to know about hits on opposite strands,
		  : you	should be iterating through the	HSPs using methods on the
		  : HSP	objects.
		  :
		  : A possible use case	where knowing whether a	hit has	HSPs
		  : on both strands would be when filtering via	SearchIO for hits with
		  : this property. However, in this case it would be better to have a
		  : dedicated method such as $hit->hsps_on_both_strands(). Similarly
		  : for	frame. This could be provided if there is interest.

       See Also	  : Bio::Search::HSP::HSPI::strand()

   frame
	Usage	  : $hit_object->frame();
	Purpose	  : Gets the reading frame for the best	HSP after HSP tiling.
		  : This is only valid for BLASTX and TBLASTN/X	type reports.
	Example	  : $frame = $hit_object->frame();
	Returns	  : Integer (-2	.. +2)
	Argument  : n/a
	Throws	  : Exception if HSPs have not been set.
	Comments  : This method	requires that all HSPs be tiled. If they have not
		  : already been tiled,	they will be tiled first automatically..
		  : If you don't want the tiled	data, iterate through each HSP
		  : calling frame() on each (use hsps()	to get all HSPs).

       See Also	  : hsps()

   matches
	Usage	  : $hit_object->matches( [class] );
	Purpose	  : Get	the total number of identical or conserved matches
		  : (or	both) across all HSPs.
		  : (Note: 'conservative' matches are indicated	as 'positives'
		  :	    in BLAST reports.)
	Example	  : ($id,$cons)	= $hit_object->matches(); # no argument
		  : $id	= $hit_object->matches('id');
		  : $cons = $hit_object->matches('cons');
	Returns	  : Integer or a 2-element array of integers
	Argument  : class = 'id' | 'cons' OR none.
		  : If no argument is provided,	both identical and conservative
		  : numbers are	returned in a two element list.
		  : (Other terms can be	used to	refer to the conservative
		  :  matches, e.g., 'positive'.	All that is checked is whether or
		  :  not the supplied string starts with 'id'. If not, the
		  : conservative matches are returned.)
	Throws	  : Exception if the requested data cannot be obtained.
	Comments  : This method	requires that all HSPs be tiled. If there is more than one
		  : HSP	and they have not already been tiled, they will	be tiled first automatically..
		  :
		  : If you need	data for each HSP, use hsps() and then interate
		  : through the	HSP objects.
		  : Does not rely on wantarray to return a list. Only checks for
		  : the	presence of an argument	(no arg	= return list).

       See Also	  : Bio::Search::HSP::GenericHSP::matches(), hsps()

   sort_hits
	Title	       : sort_hsps
	Usage	       : $result->sort_hsps(\&sort_function)
	Function       : Sorts the available HSP objects by a user-supplied function. Defaults to sort
			 by descending score.
	Returns	       : n/a
	Args	       : A coderef for the sort	function.  See the documentation on the	Perl sort()
			 function for guidelines on writing sort functions.
	Note	       : To access the special variables $a and	$b used	by the Perl sort() function
			 the user function must	access Bio::Search::Hit::HitI namespace.
			 For example, use :
			 $hit->sort_hsps( sub{$Bio::Search::Result::HitI::a->length <=>
						 $Bio::Search::Result::HitI::b->length});
			  NOT $hit->sort_hsps($a->length <=> $b->length);

   _default sort_hsps
	 Title : _default_sort_hsps
	 Usage : Do not	call directly.
	 Function : Sort hsps in ascending order by evalue
	 Args  : None
	 Returns: 1 on success
	 Note  : Used by $hit->sort_hsps()

perl v5.24.1			  2017-07-08	     Bio::Search::Hit::HitI(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Aaron Mackey, Steve Chervitz | COPYRIGHT | DISCLAIMER | APPENDIX

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