#-----------------------------------------------------------------
#
# BioPerl module for Bio::Search::HSP::HSPI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Steve Chervitz <sac@bioperl.org>
# and Jason Stajich <jason@bioperl.org>
#
# You may distribute this module under the same terms as perl itself
#-----------------------------------------------------------------
# POD documentation - main docs before the code
=head1 NAME
Bio::Search::HSP::HSPI - Interface for a High Scoring Pair in a similarity search result
=head1 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;
=head1 DESCRIPTION
Bio::Search::HSP::HSPI objects cannot be instantiated since this
module defines a pure interface.
Given an object that implements the L<Bio::Search::HSP::HSPI> interface,
you can do the following things with it:
=head1 SEE ALSO
This interface inherits methods from these other modules:
L<Bio::SeqFeatureI>,
L<Bio::SeqFeature::FeaturePair>
L<Bio::SeqFeature::SimilarityPair>
Please refer to these modules for documentation of the
many additional inherited methods.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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
=head1 AUTHOR - Steve Chervitz, Jason Stajich
Email sac-at-bioperl.org
Email jason-at-bioperl.org
=head1 COPYRIGHT
Copyright (c) 2001 Steve Chervitz, Jason Stajich. All Rights Reserved.
=head1 DISCLAIMER
This software is provided "as is" without warranty of any kind.
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Search::HSP::HSPI;
use strict;
use Carp;
use base qw(Bio::SeqFeature::SimilarityPair Bio::Root::RootI);
=head2 algorithm
Title : algorithm
Usage : my $r_type = $hsp->algorithm
Function: Obtain the name of the algorithm used to obtain the HSP
Returns : string (e.g., BLASTP)
Args : none
=cut
sub algorithm{
my ($self,@args) = @_;
$self->throw_not_implemented;
}
=head2 pvalue
Title : pvalue
Usage : my $pvalue = $hsp->pvalue();
Function: Returns the P-value for this HSP or undef
Returns : float or exponential (2e-10)
P-value is not defined with NCBI Blast2 reports.
Args : none
=cut
sub pvalue {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 evalue
Title : evalue
Usage : my $evalue = $hsp->evalue();
Function: Returns the e-value for this HSP
Returns : float or exponential (2e-10)
Args : none
=cut
sub evalue {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 frac_identical
Title : frac_identical
Usage : my $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] );
Function: Returns the fraction of identitical positions for this HSP
Returns : Float in range 0.0 -> 1.0
Args : 'query' = num identical / length of query seq (without gaps)
'hit' = num identical / length of hit seq (without gaps)
'total' = num identical / length of alignment (with gaps)
default = 'total'
=cut
sub frac_identical {
my ($self, $type) = @_;
$self->throw_not_implemented;
}
=head2 frac_conserved
Title : frac_conserved
Usage : my $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] );
Function : Returns the fraction of conserved positions for this HSP.
This is the fraction of symbols in the alignment with a
positive score.
Returns : Float in range 0.0 -> 1.0
Args : 'query' = num conserved / length of query seq (without gaps)
'hit' = num conserved / length of hit seq (without gaps)
'total' = num conserved / length of alignment (with gaps)
default = 'total'
=cut
sub frac_conserved {
my ($self, $type) = @_;
$self->throw_not_implemented;
}
=head2 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)
=cut
sub num_identical{
shift->throw_not_implemented;
}
=head2 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)
=cut
sub num_conserved{
shift->throw_not_implemented();
}
=head2 gaps
Title : gaps
Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
Function : Get the number of gap characters in the query, hit, or total alignment.
Returns : Integer, number of gap characters or 0 if none
Args : 'query' = num conserved / length of query seq (without gaps)
'hit' = num conserved / length of hit seq (without gaps)
'total' = num conserved / length of alignment (with gaps)
default = 'total'
=cut
sub gaps {
my ($self, $type) = @_;
$self->throw_not_implemented;
}
=head2 query_string
Title : query_string
Usage : my $qseq = $hsp->query_string;
Function: Retrieves the query sequence of this HSP as a string
Returns : string
Args : none
=cut
sub query_string{
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 hit_string
Title : hit_string
Usage : my $hseq = $hsp->hit_string;
Function: Retrieves the hit sequence of this HSP as a string
Returns : string
Args : none
=cut
sub hit_string{
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 homology_string
Title : homology_string
Usage : my $homo_string = $hsp->homology_string;
Function: Retrieves the homology sequence for this HSP as a string.
: The homology sequence is the string of symbols in between the
: query and hit sequences in the alignment indicating the degree
: of conservation (e.g., identical, similar, not similar).
Returns : string
Args : none
=cut
sub homology_string{
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 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
=cut
sub length{
shift->throw_not_implemented();
}
=head2 percent_identity
Title : percent_identity
Usage : my $percentid = $hsp->percent_identity()
Function: Returns the calculated percent identity for an HSP
Returns : floating point between 0 and 100
Args : none
=cut
sub percent_identity{
my ($self) = @_;
return $self->frac_identical('hsp') * 100;
}
=head2 get_aln
Title : get_aln
Usage : my $aln = $hsp->get_aln
Function: Returns a Bio::SimpleAlign representing the HSP alignment
Returns : Bio::SimpleAlign
Args : none
=cut
sub get_aln {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 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 : L<Bio::Search::BlastUtils::collapse_nums()|Bio::Search::BlastUtils>, L<Bio::Search::Hit::HitI::seq_inds()|Bio::Search::Hit::HitI>
=cut
sub seq_inds {
shift->throw_not_implemented();
}
=head2 Inherited from L<Bio::SeqFeature::SimilarityPair>
These methods come from L<Bio::SeqFeature::SimilarityPair>
=head2 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
=head2 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
=head2 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)
=head2 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
=head2 bits
Title : bits
Usage : my $bits = $hsp->bits();
Function: Returns the bit value for this HSP or undef
Returns : numeric
Args : none
=cut
# override
=head2 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
=cut
sub strand {
my $self = shift;
my $val = shift;
$val = 'query' unless defined $val;
$val =~ s/^\s+//;
if ( $val =~ /^q/i ) {
return $self->query->strand(@_);
}
elsif ( $val =~ /^hi|^s/i ) {
return $self->hit->strand(@_);
}
elsif ( $val =~ /^list|array/i ) {
# Do we really need to pass on additional arguments here? HL
# (formerly this was strand(shift) which is really bad coding because
# it breaks if the callee allows setting to undef)
return ( $self->query->strand(@_), $self->hit->strand(@_) );
}
else {
$self->warn("unrecognized component '$val' requested\n");
}
return 0;
}
=head2 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)
=cut
sub start {
my $self = shift;
my $val = shift;
$val = 'query' unless defined $val;
$val =~ s/^\s+//;
if( $val =~ /^q/i ) {
return $self->query->start(@_);
} elsif( $val =~ /^(hi|s)/i ) {
return $self->hit->start(@_);
} elsif ( $val =~ /^list|array/i ) {
# do we really need to pass on additional arguments here? HL
# (formerly this was strand(shift) which is really bad coding because
# it breaks if the callee allows setting to undef)
return ($self->query->start(@_),
$self->hit->start(@_) );
} else {
$self->warn("unrecognized component '$val' requested\n");
}
return 0;
}
=head2 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)
=cut
sub end {
my $self = shift;
my $val = shift;
$val = 'query' unless defined $val;
$val =~ s/^\s+//;
if( $val =~ /^q/i ) {
return $self->query->end(@_);
} elsif( $val =~ /^(hi|s)/i ) {
return $self->hit->end(@_);
} elsif ( $val =~ /^list|array/i ) {
# do we really need to pass on additional arguments here? HL
# (formerly this was strand(shift) which is really bad coding because
# it breaks if the callee allows setting to undef)
return ($self->query->end(@_),
$self->hit->end(@_) );
} else {
$self->warn("unrecognized end component '$val' requested\n");
}
return 0;
}
=head2 seq
Usage : $hsp->seq( [seq_type] );
Purpose : Get the query or sbjct sequence as a Bio::Seq.pm object.
Example : $seqObj = $hsp->seq('query');
Returns : Object reference for a Bio::Seq.pm object.
Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = 'query').
: ('sbjct' is synonymous with 'hit')
: default is 'query'
Throws : Propagates any exception that occurs during construction
: of the Bio::Seq.pm object.
Comments : The sequence is returned in an array of strings corresponding
: to the strings in the original format of the Blast alignment.
: (i.e., same spacing).
See Also : L</seq_str>, L</seq_inds>, L<Bio::Seq>
=cut
sub seq {
my($self,$seqType) = @_;
$seqType ||= 'query';
$seqType = 'sbjct' if $seqType eq 'hit';
my $str = $self->seq_str($seqType);
if( $seqType =~ /^(m|ho)/i ) {
$self->throw("cannot call seq on the homology match string, it isn't really a sequence, use get_aln to convert the HSP to a Bio::AlignIO and generate a consensus from that.");
}
require Bio::LocatableSeq;
my $id = $seqType =~ /^q/i ? $self->query->seq_id : $self->hit->seq_id;
return Bio::LocatableSeq->new( -ID => $id,
-SEQ => $str,
-START => $self->start($seqType),
-END => $self->end($seqType),
-STRAND => $self->strand($seqType),
-FORCE_NSE => $id ? 0 : 1,
-DESC => "$seqType sequence " );
}
=head2 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 : L</seq>, L</seq_inds>, C<_set_match_seq>
=cut
sub seq_str {
my $self = shift;
my $type = shift || 'query';
if( $type =~ /^q/i ) { return $self->query_string(@_) }
elsif( $type =~ /^(s)|(hi)/i ) { return $self->hit_string(@_)}
elsif ( $type =~ /^(ho)|(ma)/i ) { return $self->homology_string(@_) }
else {
$self->warn("unknown sequence type $type");
}
return '';
}
=head2 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.
=cut
sub rank { shift->throw_not_implemented }
=head2 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 : L</length>, L</gaps>, L</seq_str>, L<Bio::Search::Hit::BlastHit::_adjust_contigs()|Bio::Search::Hit::BlastHit>
=cut
#-----------
sub matches {
#-----------
my( $self, %param ) = @_;
my(@data);
my($seqType, $beg, $end) = ($param{-SEQ},
$param{-START},
$param{-STOP});
$seqType ||= 'query';
$seqType = 'sbjct' if $seqType eq 'hit';
if( (!defined $beg && !defined $end) || ! $self->seq_str('match') ) {
## Get data for the whole alignment.
push @data, ($self->num_identical, $self->num_conserved);
} else {
## Get the substring representing the desired sub-section of aln.
$beg ||= 0;
$end ||= 0;
my($start,$stop) = $self->range($seqType);
if($beg == 0) { $beg = $start; $end = $beg+$end; } # sane?
elsif($end == 0) { $end = $stop; $beg = $end-$beg; } # sane?
if($end > $stop) { $end = $stop; }
if($beg < $start) { $beg = $start; }
# now with gap handling! /maj
my $match_str = $self->seq_str('match');
if ($self->gaps) {
# strip the homology string of gap positions relative
# to the target type
$match_str = $self->seq_str('match');
my $tgt = $self->seq_str($seqType);
my $encode = $match_str ^ $tgt;
my $zap = '-'^' ';
$encode =~ s/$zap//g;
$tgt =~ s/-//g;
$match_str = $tgt ^ $encode;
}
## ML: START fix for substr out of range error ------------------
my $seq = "";
if (($self->algorithm =~ /TBLAST[NX]/) && ($seqType eq 'sbjct'))
{
$seq = substr($match_str,
int(($beg-$start)/3),
int(($end-$beg+1)/3));
} elsif (($self->algorithm =~ /T?BLASTX/) && ($seqType eq 'query')) {
$seq = substr($match_str,
int(($beg-$start)/3), int(($end-$beg+1)/3));
} else {
$seq = substr($match_str,
$beg-$start, ($end-$beg+1));
}
## ML: End of fix for substr out of range error -----------------
if(!CORE::length $seq) {
$self->throw("Undefined sub-sequence ($beg,$end). Valid range = $start - $stop");
}
$seq =~ s/ //g; # remove space (no info).
my $len_cons = CORE::length $seq;
$seq =~ s/\+//g; # remove '+' characters (conservative substitutions)
my $len_id = CORE::length $seq;
push @data, ($len_id, $len_cons);
}
@data;
}
=head2 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 : L<Bio::SeqFeature::SimilarityPair::score()|Bio::SeqFeature::SimilarityPair>
=cut
sub n { shift->throw_not_implemented }
=head2 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)
=cut
sub range { shift->throw_not_implemented }
sub expect { shift->evalue(@_) }
1;