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BioPerl-1.6.920
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Search::HSP::HSPI

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://redmine.open-bio.org/projects/bioperl/

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)