Bio::Search::HSP HSPI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Search::HSP::HSPI - Interface for a High Scoring Pair in a similarity search result
Package variables
No package variables defined.
Included modules
Bio::Root::RootI
Bio::SeqFeature::SimilarityPair
Carp
Inherit
Bio::Root::RootI Bio::SeqFeature::SimilarityPair
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:
Methods
algorithmDescriptionCode
pvalueDescriptionCode
evalueDescriptionCode
frac_identicalDescriptionCode
frac_conservedDescriptionCode
num_identicalDescriptionCode
num_conservedDescriptionCode
gapsDescriptionCode
query_stringDescriptionCode
hit_stringDescriptionCode
homology_stringDescriptionCode
lengthDescriptionCode
percent_identityDescriptionCode
get_alnDescriptionCode
seq_indsDescriptionCode
strandDescriptionCode
startDescriptionCode
endDescriptionCode
seqDescriptionCode
seq_strDescriptionCode
rankDescriptionCode
matchesDescriptionCode
nDescriptionCode
rangeDescriptionCode
expect
No description
Code
Methods description
algorithmcode    nextTop
 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
pvaluecodeprevnextTop
 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
evaluecodeprevnextTop
 Title   : evalue
 Usage   : my $evalue = $hsp->evalue();
 Function: Returns the e-value for this HSP
 Returns : float or exponential (2e-10)
 Args    : none
frac_identicalcodeprevnextTop
 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_conservedcodeprevnextTop
 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_identicalcodeprevnextTop
 Title   : num_identical
 Usage   : $obj->num_identical($newval)
 Function: returns the number of identical residues in the alignment
 Returns : integer
 Args    : integer (optional)
num_conservedcodeprevnextTop
 Title   : num_conserved
 Usage   : $obj->num_conserved($newval)
 Function: returns the number of conserved residues in the alignment
 Returns : inetger
 Args    : integer (optional)
gapscodeprevnextTop
 Title    : gaps
 Usage    : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
 Function : Get the number of gaps in the query, hit, or total alignment.
 Returns  : Integer, number of gaps 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_stringcodeprevnextTop
 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_stringcodeprevnextTop
 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_stringcodeprevnextTop
 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
lengthcodeprevnextTop
 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_identitycodeprevnextTop
 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_alncodeprevnextTop
 Title   : get_aln
 Usage   : my $aln = $hsp->gel_aln
 Function: Returns a Bio::SimpleAlign representing the HSP alignment
 Returns : Bio::SimpleAlign
 Args    : none
seq_indscodeprevnextTop
 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()
strandcodeprevnextTop
 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
startcodeprevnextTop
 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)
endcodeprevnextTop
 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)
seqcodeprevnextTop
 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_strcodeprevnextTop
 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()
rankcodeprevnextTop
 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.
matchescodeprevnextTop
 Usage     : $hsp->matches([seq_type], [start], [stop]);
 Purpose   : Get the total number of identical and conservative matches 
           : in the query or sbjct sequence for the given HSP. Optionally can
           : report data within a defined interval along the seq.
           : (Note: 'conservative' matches are called 'positives' in the
           : Blast report.)
 Example   : ($id,$cons) = $hsp_object->matches('hit');
           : ($id,$cons) = $hsp_object->matches('query',300,400);
 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()
ncodeprevnextTop
 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()
rangecodeprevnextTop
 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, $hsp->query->end)
Methods code
algorithmdescriptionprevnextTop
sub algorithm {
   my ($self,@args) = @_;
   $self->throw_not_implemented;
}
pvaluedescriptionprevnextTop
sub pvalue {
   my ($self) = @_;
   $self->throw_not_implemented;
}
evaluedescriptionprevnextTop
sub evalue {
   my ($self) = @_;
   $self->throw_not_implemented;
}
frac_identicaldescriptionprevnextTop
sub frac_identical {
   my ($self, $type) = @_;
   $self->throw_not_implemented;
}
frac_conserveddescriptionprevnextTop
sub frac_conserved {
    my ($self, $type) = @_;
    $self->throw_not_implemented;
}
num_identicaldescriptionprevnextTop
sub num_identical {
    shift->throw_not_implemented;
}
num_conserveddescriptionprevnextTop
sub num_conserved {
    shift->throw_not_implemented();
}
gapsdescriptionprevnextTop
sub gaps {
    my ($self, $type) = @_;
    $self->throw_not_implemented;
}
query_stringdescriptionprevnextTop
sub query_string {
   my ($self) = @_;
   $self->throw_not_implemented;
}
hit_stringdescriptionprevnextTop
sub hit_string {
   my ($self) = @_;
   $self->throw_not_implemented;
}
homology_stringdescriptionprevnextTop
sub homology_string {
   my ($self) = @_;
   $self->throw_not_implemented;
}
lengthdescriptionprevnextTop
sub length {
    shift->throw_not_implemented();
}
percent_identitydescriptionprevnextTop
sub percent_identity {
   my ($self) = @_;
   return $self->frac_identical('hsp') * 100;
}
get_alndescriptionprevnextTop
sub get_aln {
   my ($self) = @_;
   $self->throw_not_implemented;
}
seq_indsdescriptionprevnextTop
sub seq_inds {
    shift->throw_not_implemented();
}
stranddescriptionprevnextTop
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;
}
startdescriptionprevnextTop
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;
}
enddescriptionprevnextTop
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;
}
seqdescriptionprevnextTop
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; new Bio::LocatableSeq (-ID => $id, -SEQ => $str, -START => $self->start($seqType), -END => $self->end($seqType), -STRAND=> $self->strand($seqType), -DESC => "$seqType sequence ", );
}
seq_strdescriptionprevnextTop
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 '';
}
rankdescriptionprevnextTop
sub rank {
 shift->throw_not_implemented
}
matchesdescriptionprevnextTop
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 $end) { ## Get data for the whole alignment.
push @data, ($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; } elsif($end == 0) { $end = $stop; $beg = $end-$beg; } if($end >= $stop) { $end = $stop; } ##ML changed from if (end >stop)
else { $end += 1;} ##ML moved from commented position below, makes
##more sense here
# if($end > $stop) { $end = $stop; }
if($beg < $start) { $beg = $start; } # else { $end += 1;}
# my $seq = substr($self->seq_str('match'), $beg-$start, ($end-$beg));
## ML: START fix for substr out of range error ------------------
my $seq = ""; if (($self->algorithm =~ /TBLAST[NX]/) && ($seqType eq 'sbjct')) { $seq = substr($self->seq_str('match'), int(($beg-$start)/3),
int((
$end-$beg+1)/3)); } elsif (($self->algorithm =~ /T?BLASTX/) && ($seqType eq 'query')) { $seq = substr($self->seq_str('match'), int(($beg-$start)/3), int(($end-$beg+1)/3)); } else { $seq = substr($self->seq_str('match'), $beg-$start, ($end-$beg)); } ## ML: End of fix for substr out of range error -----------------
## ML: debugging code
## This is where we get our exception. Try printing out the values going
## into this:
##
# print STDERR
# qq(*------------MY EXCEPTION --------------------\nSeq: ") ,
# $self->seq_str("$seqType"), qq("\n),$self->rank,",( index:";
# print STDERR $beg-$start, ", len: ", $end-$beg," ), (HSPRealLen:",
# CORE::length $self->seq_str("$seqType");
# print STDERR ", HSPCalcLen: ", $stop - $start +1 ," ),
# ( beg: $beg, end: $end ), ( start: $start, stop: stop )\n";
## ML: END DEBUGGING CODE----------
if(!CORE::length $seq) { $self->throw("Undefined sub-sequence ($beg,$end). Valid range = $start - $stop"); } ## Get data for a substring.
# printf "Collecting HSP subsection data: beg,end = %d,%d; start,stop = %d,%d\n%s<---\n", $beg, $end, $start, $stop, $seq;
# printf "Original match seq:\n%s\n",$self->seq_str('match');
$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); # printf " HSP = %s\n id = %d; cons = %d\n", $self->rank, $len_id, $len_cons; <STDIN>;
} @data;
}
ndescriptionprevnextTop
sub n {
 shift->throw_not_implemented
}
rangedescriptionprevnextTop
sub range {
 shift->throw_not_implemented
}
expectdescriptionprevnextTop
sub expect {
 shift->evalue(@_)
}
General documentation
SEE ALSOTop
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.
FEEDBACKTop
Mailing ListsTop
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/MailList.shtml  - About the mailing lists
Reporting BugsTop
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
email or the web:
  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/
AUTHOR - Steve Chervitz, Jason StajichTop
Email sac@bioperl.org
Email jason@bioperl.org
COPYRIGHTTop
Copyright (c) 2001 Steve Chervitz, Jason Stajich. All Rights Reserved.
DISCLAIMERTop
This software is provided "as is" without warranty of any kind.
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Inherited from Bio::SeqFeature::SimilarityPairTop
These methods come from Bio::SeqFeature::SimilarityPair
queryTop
 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
hitTop
 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
significanceTop
 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)
scoreTop
 Title   : score
 Usage   : my $score = $hsp->score();
 Function: Returns the score for this HSP or undef 
 Returns : numeric           
 Args    : [optional] numeric to set value
bitsTop
 Title   : bits
 Usage   : my $bits = $hsp->bits();
 Function: Returns the bit value for this HSP or undef 
 Returns : numeric
 Args    : none