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:
FEEDBACK
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Reporting Bugs
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AUTHOR - Steve Chervitz, Jason Stajich
Email sac-at-bioperl.org Email jason-at-bioperl.orgCOPYRIGHT
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::SimilarityPairquery
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)