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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:

	 http://bugzilla.open-bio.org/

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 v5.14.1			  2011-07-22	     Bio::Search::HSP::HSPI(3)
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