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Bio::Search::HSP::HSPIUser Contributed Perl DocumentaBio::Search::HSP::HSPI(3)

NAME
       Bio::Search::HSP::HSPI -	Interface for a	High Scoring Pair in a
       similarity search result

SYNOPSIS
	   # Bio::Search::HSP::HSPI objects cannot be instantiated since this
	   # module defines a pure interface.

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

	   $r_type = $hsp->algorithm;

	   $pvalue = $hsp->pvalue();

	   $evalue = $hsp->evalue();

	   $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] );

	   $frac_cons =	$hsp->frac_conserved( ['query'|'hit'|'total'] );

	   $gaps = $hsp->gaps( ['query'|'hit'|'total'] );

	   $qseq = $hsp->query_string;

	   $hseq = $hsp->hit_string;

	   $homology_string = $hsp->homology_string;

	   $len	= $hsp->length(	['query'|'hit'|'total']	);

	   $rank = $hsp->rank;

DESCRIPTION
       Bio::Search::HSP::HSPI objects cannot be	instantiated since this	module
       defines a pure interface.

       Given an	object that implements the Bio::Search::HSP::HSPI interface,
       you can do the following	things with it:

SEE ALSO
       This interface inherits methods from these other	modules:

       Bio::SeqFeatureI, Bio::SeqFeature::FeaturePair
       Bio::SeqFeature::SimilarityPair

       Please refer to these modules for documentation of the many additional
       inherited methods.

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, Jason Stajich
       Email sac-at-bioperl.org	Email jason-at-bioperl.org

COPYRIGHT
       Copyright (c) 2001 Steve	Chervitz, Jason	Stajich. 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 _

   algorithm
	Title	: algorithm
	Usage	: my $r_type = $hsp->algorithm
	Function: Obtain the name of the algorithm used	to obtain the HSP
	Returns	: string (e.g.,	BLASTP)
	Args	: none

   pvalue
	Title	: pvalue
	Usage	: my $pvalue = $hsp->pvalue();
	Function: Returns the P-value for this HSP or undef
	Returns	: float	or exponential (2e-10)
		  P-value is not defined with NCBI Blast2 reports.
	Args	: none

   evalue
	Title	: evalue
	Usage	: my $evalue = $hsp->evalue();
	Function: Returns the e-value for this HSP
	Returns	: float	or exponential (2e-10)
	Args	: none

   frac_identical
	Title	: frac_identical
	Usage	: my $frac_id =	$hsp->frac_identical( ['query'|'hit'|'total'] );
	Function: Returns the fraction of identitical positions	for this HSP
	Returns	: Float	in range 0.0 ->	1.0
	Args	: 'query' = num	identical / length of query seq	(without gaps)
		  'hit'	  = num	identical / length of hit seq (without gaps)
		  'total' = num	identical / length of alignment	(with gaps)
		  default = 'total'

   frac_conserved
	Title	 : frac_conserved
	Usage	 : my $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] );
	Function : Returns the fraction	of conserved positions for this	HSP.
		   This	is the fraction	of symbols in the alignment with a
		   positive score.
	Returns	: Float	in range 0.0 ->	1.0
	Args	: 'query' = num	conserved / length of query seq	(without gaps)
		  'hit'	  = num	conserved / length of hit seq (without gaps)
		  'total' = num	conserved / length of alignment	(with gaps)
		  default = 'total'

   num_identical
	Title	: num_identical
	Usage	: $obj->num_identical($newval)
	Function: returns the number of	identical residues in the alignment
	Returns	: integer
	Args	: integer (optional)

   num_conserved
	Title	: num_conserved
	Usage	: $obj->num_conserved($newval)
	Function: returns the number of	conserved residues in the alignment
	Returns	: inetger
	Args	: integer (optional)

   gaps
	Title	 : gaps
	Usage	 : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
	Function : Get the number of gap characters in the query, hit, or total	alignment.
	Returns	 : Integer, number of gap characters or	0 if none
	Args	 : 'query' = num conserved / length of query seq (without gaps)
		   'hit'   = num conserved / length of hit seq (without	gaps)
		   'total' = num conserved / length of alignment (with gaps)
		   default = 'total'

   query_string
	Title	: query_string
	Usage	: my $qseq = $hsp->query_string;
	Function: Retrieves the	query sequence of this HSP as a	string
	Returns	: string
	Args	: none

   hit_string
	Title	: hit_string
	Usage	: my $hseq = $hsp->hit_string;
	Function: Retrieves the	hit sequence of	this HSP as a string
	Returns	: string
	Args	: none

   homology_string
	Title	: homology_string
	Usage	: my $homo_string = $hsp->homology_string;
	Function: Retrieves the	homology sequence for this HSP as a string.
		: The homology sequence	is the string of symbols in between the
		: query	and hit	sequences in the alignment indicating the degree
		: of conservation (e.g., identical, similar, not similar).
	Returns	: string
	Args	: none

   length
	Title	 : length
	Usage	 : my $len = $hsp->length( ['query'|'hit'|'total'] );
	Function : Returns the length of the query or hit in the alignment (without gaps)
		   or the aggregate length of the HSP (including gaps;
		   this	may be greater than either hit or query	)
	Returns	 : integer
	Args	 : 'query' = length of query seq (without gaps)
		   'hit'   = length of hit seq (without	gaps)
		   'total' = length of alignment (with gaps)
		   default = 'total'
	Args	: none

   percent_identity
	Title	: percent_identity
	Usage	: my $percentid	= $hsp->percent_identity()
	Function: Returns the calculated percent identity for an HSP
	Returns	: floating point between 0 and 100
	Args	: none

   get_aln
	Title	: get_aln
	Usage	: my $aln = $hsp->get_aln
	Function: Returns a Bio::SimpleAlign representing the HSP alignment
	Returns	: Bio::SimpleAlign
	Args	: none

   seq_inds
	Title	: seq_inds
	Purpose	  : Get	a list of residue positions (indices) for all identical
		  : or conserved residues in the query or sbjct	sequence.
	Example	  : @s_ind = $hsp->seq_inds('query', 'identical');
		  : @h_ind = $hsp->seq_inds('hit', 'conserved');
		  : @h_ind = $hsp->seq_inds('hit', 'conserved',	1);
	Returns	  : List of integers
		  : May	include	ranges if collapse is true.
	Argument  : seq_type  =	'query'	or 'hit' or 'sbjct'  (default =	query)
		     ('sbjct' is synonymous with 'hit')
		    class     =	'identical' or 'conserved' or 'nomatch'	or 'gap'
				 (default = identical)
				 (can be shortened to 'id' or 'cons')

		    collapse  =	boolean, if true, 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.
	Comments  :

       See Also	  : Bio::Search::BlastUtils::collapse_nums(),
       Bio::Search::Hit::HitI::seq_inds()

   Inherited from Bio::SeqFeature::SimilarityPair
       These methods come from Bio::SeqFeature::SimilarityPair

   query
	Title	: query
	Usage	: my $query = $hsp->query
	Function: Returns a SeqFeature representing the	query in the HSP
	Returns	: Bio::SeqFeature::Similarity
	Args	: [optional] new value to set

   hit
	Title	: hit
	Usage	: my $hit = $hsp->hit
	Function: Returns a SeqFeature representing the	hit in the HSP
	Returns	: Bio::SeqFeature::Similarity
	Args	: [optional] new value to set

   significance
	Title	: significance
	Usage	: $evalue = $obj->significance();
		  $obj->significance($evalue);
	Function: Get/Set the significance value (see Bio::SeqFeature::SimilarityPair)
	Returns	: significance value (scientific notation string)
	Args	: significance value (sci notation string)

   score
	Title	: score
	Usage	: my $score = $hsp->score();
	Function: Returns the score for	this HSP or undef
	Returns	: numeric
	Args	: [optional] numeric to	set value

   bits
	Title	: bits
	Usage	: my $bits = $hsp->bits();
	Function: Returns the bit value	for this HSP or	undef
	Returns	: numeric
	Args	: none

   strand
	Title	: strand
	Usage	: $hsp->strand('query')
	Function: Retrieves the	strand for the HSP component requested
	Returns	: +1 or	-1 (0 if unknown)
	Args	: 'hit'	or 'subject' or	'sbjct'	to retrieve the	strand of the subject
		  'query' to retrieve the query	strand (default)
		  'list' or 'array' to retreive	both query and hit together

   start
	Title	: start
	Usage	: $hsp->start('query')
	Function: Retrieves the	start for the HSP component requested
	Returns	: integer
	Args	: 'hit'	or 'subject' or	'sbjct'	to retrieve the	start of the subject
		  'query' to retrieve the query	start (default)

   end
	Title	: end
	Usage	: $hsp->end('query')
	Function: Retrieves the	end for	the HSP	component requested
	Returns	: integer
	Args	: 'hit'	or 'subject' or	'sbjct'	to retrieve the	end of the subject
		  'query' to retrieve the query	end (default)

   seq
	Usage	  : $hsp->seq( [seq_type] );
	Purpose	  : Get	the query or sbjct sequence as a Bio::Seq.pm object.
	Example	  : $seqObj = $hsp->seq('query');
	Returns	  : Object reference for a Bio::Seq.pm object.
	Argument  : seq_type = 'query' or 'hit'	or 'sbjct' (default = 'query').
		  :  ('sbjct' is synonymous with 'hit')
		  : default is 'query'
	Throws	  : Propagates any exception that occurs during	construction
		  : of the Bio::Seq.pm object.
	Comments  : The	sequence is returned in	an array of strings corresponding
		  : to the strings in the original format of the Blast alignment.
		  : (i.e., same	spacing).

       See Also	  : "seq_str", "seq_inds", Bio::Seq

   seq_str
	Usage	  : $hsp->seq_str( seq_type );
	Purpose	  : Get	the full query,	sbjct, or 'match' sequence as a	string.
		  : The	'match'	sequence is the	string of symbols in between the
		  : query and sbjct sequences.
	Example	  : $str = $hsp->seq_str('query');
	Returns	  : String
	Argument  : seq_Type = 'query' or 'hit'	or 'sbjct' or 'match'
		  :  ('sbjct' is synonymous with 'hit')
		  : default is 'query'
	Throws	  : Exception if the argument does not match an	accepted seq_type.
	Comments  :

       See Also	  : "seq", "seq_inds", "_set_match_seq"

   rank
	Usage	  : $hsp->rank(	[string] );
	Purpose	  : Get	the rank of the	HSP within a given Blast hit.
	Example	  : $rank = $hsp->rank;
	Returns	  : Integer (1..n) corresponding to the	order in which the HSP
		    appears in the BLAST report.

   matches
	Usage	  : $hsp->matches(-seq	 => 'hit'|'query',
				  -start => $start,
				  -stop	 => $stop);
	Purpose	  : Get	the total number of identical and conservative matches
		  : in the query or sbjct sequence for the given HSP. Optionally can
		  : report data	within a defined interval along	the seq.
		  : (Note: 'conservative' matches are called 'positives' in the
		  : Blast report.)
	Example	  : ($id,$cons)	= $hsp_object->matches(-seq   => 'hit');
		  : ($id,$cons)	= $hsp_object->matches(-seq   => 'query',
						       -start => 300,
						       -stop  => 400);
	Returns	  : 2-element array of integers
	Argument  : (1)	seq_type = 'query' or 'hit' or 'sbjct' (default	= query)
		  :  ('sbjct' is synonymous with 'hit')
		  : (2)	start =	Starting coordinate (optional)
		  : (3)	stop  =	Ending coordinate (optional)
	Throws	  : Exception if the supplied coordinates are out of range.
	Comments  : Relies on seq_str('match') to get the string of alignment symbols
		  : between the	query and sbjct	lines which are	used for determining
		  : the	number of identical and	conservative matches.

       See Also	  : "length", "gaps", "seq_str",
       Bio::Search::Hit::BlastHit::_adjust_contigs()

   n
	Usage	  : $hsp_obj->n()
	Purpose	  : Get	the N value (num HSPs on which P/Expect	is based).
		  : This value is not defined with NCBI	Blast2 with gapping.
	Returns	  : Integer or null string if not defined.
	Argument  : n/a
	Throws	  : n/a
	Comments  : The	'N' value is listed in parenthesis with	P/Expect value:
		  : e.g., P(3) = 1.2e-30  ---> (N = 3).
		  : Not	defined	in NCBI	Blast2 with gaps.
		  : This typically is equal to the number of HSPs but not always.
		  : To obtain the number of HSPs, use Bio::Search::Hit::HitI::num_hsps().

       See Also	  : Bio::SeqFeature::SimilarityPair::score()

   range
	Usage	  : $hsp->range( [seq_type] );
	Purpose	  : Gets the (start, end) coordinates for the query or sbjct sequence
		  : in the HSP alignment.
	Example	  : ($query_beg, $query_end) = $hsp->range('query');
		  : ($hit_beg, $hit_end) = $hsp->range('hit');
	Returns	  : Two-element	array of integers
	Argument  : seq_type = string, 'query' or 'hit'	or 'sbjct'  (default = 'query')
		  :  ('sbjct' is synonymous with 'hit')
	Throws	  : n/a
	Comments  : This is a convenience method for constructions such	as
		    ($hsp->query->start, $hsp->query->end)

perl v5.24.1			  2017-07-08	     Bio::Search::HSP::HSPI(3)

NAME | SYNOPSIS | DESCRIPTION | SEE ALSO | FEEDBACK | AUTHOR - Steve Chervitz, Jason Stajich | COPYRIGHT | DISCLAIMER | APPENDIX

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