Raw content of Bio::Search::HSP::GenericHSP
<![CDATA[# $Id: GenericHSP.pm,v 1.40.2.3 2003/03/24 20:44:45 jason Exp $
#
# BioPerl module for Bio::Search::HSP::GenericHSP
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Search::HSP::GenericHSP - A "Generic" implementation of a High Scoring Pair
=head1 SYNOPSIS
my $hsp = new Bio::Search::HSP::GenericHSP( -algorithm => 'blastp',
-evalue => '1e-30',
);
$r_type = $hsp->algorithm
$pvalue = $hsp->p();
$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;
$homo_string = $hsp->homology_string;
$len = $hsp->length( ['query'|'hit'|'total'] );
$len = $hsp->length( ['query'|'hit'|'total'] );
$rank = $hsp->rank;
=head1 DESCRIPTION
This implementation is "Generic", meaning it is is suitable for
holding information about High Scoring pairs from most Search reports
such as BLAST and FastA. Specialized objects can be derived from
this.
=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/MailList.shtml - About the mailing lists
=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
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Jason Stajich and Steve Chervitz
Email jason@bioperl.org
Email sac@bioperl.org
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails here
=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::GenericHSP;
use vars qw(@ISA $GAP_SYMBOL);
use strict;
use Bio::Root::Root;
use Bio::SeqFeature::Similarity;
use Bio::Search::HSP::HSPI;
@ISA = qw(Bio::Search::HSP::HSPI Bio::Root::Root );
BEGIN {
$GAP_SYMBOL = '-';
}
=head2 new
Title : new
Usage : my $obj = new Bio::Search::HSP::GenericHSP();
Function: Builds a new Bio::Search::HSP::GenericHSP object
Returns : Bio::Search::HSP::GenericHSP
Args : -algorithm => algorithm used (BLASTP, TBLASTX, FASTX, etc)
-evalue => evalue
-pvalue => pvalue
-bits => bit value for HSP
-score => score value for HSP (typically z-score but depends on
analysis)
-hsp_length=> Length of the HSP (including gaps)
-identical => # of residues that that matched identically
-conserved => # of residues that matched conservatively
(only protein comparisions;
conserved == identical in nucleotide comparisons)
-hsp_gaps => # of gaps in the HSP
-query_gaps => # of gaps in the query in the alignment
-hit_gaps => # of gaps in the subject in the alignment
-query_name => HSP Query sequence name (if available)
-query_start => HSP Query start (in original query sequence coords)
-query_end => HSP Query end (in original query sequence coords)
-hit_name => HSP Hit sequence name (if available)
-hit_start => HSP Hit start (in original hit sequence coords)
-hit_end => HSP Hit end (in original hit sequence coords)
-hit_length => total length of the hit sequence
-query_length=> total length of the query sequence
-query_seq => query sequence portion of the HSP
-hit_seq => hit sequence portion of the HSP
-homology_seq=> homology sequence for the HSP
-hit_frame => hit frame (only if hit is translated protein)
-query_frame => query frame (only if query is translated protein)
-rank => HSP rank
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($algo, $evalue, $pvalue, $identical, $conserved,
$gaps, $query_gaps, $hit_gaps,
$hit_seq, $query_seq, $homology_seq,
$hsp_len, $query_len,$hit_len,
$hit_name,$query_name,$bits,$score,
$hs,$he,$qs,$qe,
$qframe,$hframe,
$rank) = $self->_rearrange([qw(ALGORITHM
EVALUE
PVALUE
IDENTICAL
CONSERVED
HSP_GAPS
QUERY_GAPS
HIT_GAPS
HIT_SEQ
QUERY_SEQ
HOMOLOGY_SEQ
HSP_LENGTH
QUERY_LENGTH
HIT_LENGTH
HIT_NAME
QUERY_NAME
BITS
SCORE
HIT_START
HIT_END
QUERY_START
QUERY_END
QUERY_FRAME
HIT_FRAME
RANK
)], @args);
$algo = 'GENERIC' unless defined $algo;
$self->algorithm($algo);
# defined $evalue && $self->evalue($evalue)
# $hsp->significance is initialized by the
# the SimilarityPair object - let's only keep one
# value, don't need 2 slots.
defined $pvalue && $self->pvalue($pvalue);
defined $bits && $self->bits($bits);
defined $score && $self->score($score);
my ($queryfactor, $hitfactor) = (0,0);
if( $algo =~ /^(PSI)?T(BLAST|FAST)[NY]/oi ) {
$hitfactor = 1;
} elsif ($algo =~ /^(FAST|BLAST)(X|Y|XY)/oi ) {
$queryfactor = 1;
} elsif ($algo =~ /^T(BLAST|FAST)(X|Y|XY)/oi ||
$algo =~ /^(BLAST|FAST)N/oi ||
$algo eq 'WABA' ||
$algo eq 'EXONERATE' || $algo eq 'MEGABLAST' ||
$algo eq 'SMITH-WATERMAN' ){
$hitfactor = 1;
$queryfactor = 1;
} elsif( $algo eq 'RPSBLAST' ) {
$queryfactor = $hitfactor = 0;
$qframe = $hframe = 0;
}
# Store the aligned query as sequence feature
my $strand;
unless( defined $qe && defined $qs ) { $self->throw("Did not specify a Query End or Query Begin @args ($qs,$qe)"); }
unless( defined $he && defined $hs ) { $self->throw("Did not specify a Hit End or Hit Begin"); }
if ($qe > $qs) { # normal query: start < end
if ($queryfactor) { $strand = 1; } else { $strand = undef; }
} else { # reverse query (i dont know if this is possible,
# but feel free to correct)
if ($queryfactor) { $strand = -1; } else { $strand = undef; }
($qs,$qe) = ($qe,$qs);
}
$self->query( new Bio::SeqFeature::Similarity
('-primary' => $self->primary_tag,
'-start' => $qs,
'-expect' => $evalue,
'-bits' => $bits,
'-end' => $qe,
'-strand' => $strand,
'-seq_id' => $query_name,
'-seqlength'=> $query_len,
'-source' => $algo,
) );
# to determine frame from something like FASTXY which doesn't
# report the frame
if( defined $strand && ! defined $qframe && $queryfactor ) {
$qframe = ( $self->query->start % 3 ) * $strand;
} elsif( ! defined $strand ) {
$qframe = 0;
}
# store the aligned subject as sequence feature
if ($he > $hs) { # normal subject
if ($hitfactor) { $strand = 1; } else { $strand = undef; }
} else {
if ($hitfactor) { $strand = -1; } else { $strand = undef; }
($hs,$he) = ( $he,$hs); # reverse subject: start bigger than end
}
$self->hit( Bio::SeqFeature::Similarity->new
('-start' => $hs,
'-end' => $he,
'-strand' => $strand,
'-expect' => $evalue,
'-bits' => $bits,
'-source' => $algo,
'-seq_id' => $hit_name,
'-seqlength' => $hit_len,
'-primary' => $self->primary_tag ));
if( defined $strand && ! defined $hframe && $hitfactor ) {
$hframe = ( $hs % 3 ) * $strand;
} elsif( ! defined $strand ) {
$hframe = 0;
}
$self->frame($qframe,$hframe);
if( ! defined $query_len || ! defined $hit_len ) {
$self->throw("Must defined hit and query length");
}
if( ! defined $identical ) {
$self->warn("Did not defined the number of identical matches in the HSP assuming 0");
$identical = 0;
}
if( ! defined $conserved ) {
$self->warn("Did not defined the number of conserved matches in the HSP assuming conserved == identical ($identical)")
if( $algo !~ /^((FAST|BLAST)N)|Exonerate/oi);
$conserved = $identical;
}
# protect for divide by zero if user does not specify
# hsp_len, query_len, or hit_len
$self->num_identical($identical);
$self->num_conserved($conserved);
if( $hsp_len ) {
$self->length('total', $hsp_len);
$self->frac_identical( 'total', $identical / $self->length('total'));
$self->frac_conserved( 'total', $conserved / $self->length('total'));
}
if( $hit_len ) {
# $self->length('hit', $self->hit->length);
$self->frac_identical( 'hit', $identical / $self->length('hit'));
$self->frac_conserved( 'hit', $conserved / $self->length('hit'));
}
if( $query_len ) {
# $self->length('query', $self->query->length);
$self->frac_identical( 'query', $identical / $self->length('query')) ;
$self->frac_conserved( 'query', $conserved / $self->length('query'));
}
$self->query_string($query_seq);
$self->hit_string($hit_seq);
$self->homology_string($homology_seq);
if( defined $query_gaps ) {
$self->gaps('query', $query_gaps);
} elsif( defined $query_seq ) {
$self->gaps('query', scalar ( $query_seq =~ tr/\-//));
}
if( defined $hit_gaps ) {
$self->gaps('hit', $hit_gaps);
} elsif( defined $hit_seq ) {
$self->gaps('hit', scalar ( $hit_seq =~ tr/\-//));
}
if( ! defined $gaps ) {
$gaps = $self->gaps("query") + $self->gaps("hit");
}
$self->gaps('total', $gaps);
$self->percent_identity($identical / $hsp_len ) if( $hsp_len > 0 );
$rank && $self->rank($rank);
return $self;
}
=head2 Bio::Search::HSP::HSPI methods
Implementation of Bio::Search::HSP::HSPI methods follow
=head2 algorithm
Title : algorithm
Usage : my $r_type = $hsp->algorithm
Function: Obtain the name of the algorithm used to obtain the HSP
Returns : string (e.g., BLASTP)
Args : [optional] scalar string to set value
=cut
sub algorithm{
my ($self,$value) = @_;
my $previous = $self->{'_algorithm'};
if( defined $value || ! defined $previous ) {
$value = $previous = '' unless defined $value;
$self->{'_algorithm'} = $value;
}
return $previous;
}
=head2 pvalue
Title : pvalue
Usage : my $pvalue = $hsp->pvalue();
Function: Returns the P-value for this HSP or undef
Returns : float or exponential (2e-10)
P-value is not defined with NCBI Blast2 reports.
Args : [optional] numeric to set value
=cut
sub pvalue {
my ($self,$value) = @_;
my $previous = $self->{'_pvalue'};
if( defined $value ) {
$self->{'_pvalue'} = $value;
}
return $previous;
}
=head2 evalue
Title : evalue
Usage : my $evalue = $hsp->evalue();
Function: Returns the e-value for this HSP
Returns : float or exponential (2e-10)
Args : [optional] numeric to set value
=cut
sub evalue { shift->significance(@_) }
=head2 frac_identical
Title : frac_identical
Usage : my $frac_id = $hsp->frac_identical( ['query'|'hit'|'total'] );
Function: Returns the fraction of identitical positions for this HSP
Returns : Float in range 0.0 -> 1.0
Args : arg 1: 'query' = num identical / length of query seq (without gaps)
'hit' = num identical / length of hit seq (without gaps)
'total' = num identical / length of alignment (with gaps)
default = 'total'
arg 2: [optional] frac identical value to set for the type requested
=cut
sub frac_identical {
my ($self, $type,$value) = @_;
$type = lc $type if defined $type;
$type = 'total' if( ! defined $type ||
$type !~ /query|hit|total/);
my $previous = $self->{'_frac_identical'}->{$type};
if( defined $value || ! defined $previous ) {
$value = $previous = '' unless defined $value;
if( $type eq 'hit' || $type eq 'query' ) {
$self->$type()->frac_identical( $value);
}
$self->{'_frac_identical'}->{$type} = $value;
}
return $previous;
}
=head2 frac_conserved
Title : frac_conserved
Usage : my $frac_cons = $hsp->frac_conserved( ['query'|'hit'|'total'] );
Function : Returns the fraction of conserved positions for this HSP.
This is the fraction of symbols in the alignment with a
positive score.
Returns : Float in range 0.0 -> 1.0
Args : arg 1: 'query' = num conserved / length of query seq (without gaps)
'hit' = num conserved / length of hit seq (without gaps)
'total' = num conserved / length of alignment (with gaps)
default = 'total'
arg 2: [optional] frac conserved value to set for the type requested
=cut
sub frac_conserved {
my ($self, $type,$value) = @_;
$type = lc $type if defined $type;
$type = 'total' if( ! defined $type ||
$type !~ /query|hit|total/);
my $previous = $self->{'_frac_conserved'}->{$type};
if( defined $value || ! defined $previous ) {
$value = $previous = '' unless defined $value;
$self->{'_frac_conserved'}->{$type} = $value;
}
return $previous;
}
=head2 gaps
Title : gaps
Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
Function : Get the number of gaps in the query, hit, or total alignment.
Returns : Integer, number of gaps or 0 if none
Args : arg 1: 'query' = num gaps in query seq
'hit' = num gaps in hit seq
'total' = num gaps in whole alignment
default = 'total'
arg 2: [optional] integer gap value to set for the type requested
=cut
sub gaps {
my ($self, $type,$value) = @_;
$type = lc $type if defined $type;
$type = 'total' if( ! defined $type ||
$type !~ /query|hit|subject|sbjct|total/);
$type = 'hit' if $type =~ /sbjct|subject/;
my $previous = $self->{'_gaps'}->{$type};
if( defined $value || ! defined $previous ) {
$value = $previous = '' unless defined $value;
$self->{'_gaps'}->{$type} = $value;
}
return $previous || 0;
}
=head2 query_string
Title : query_string
Usage : my $qseq = $hsp->query_string;
Function: Retrieves the query sequence of this HSP as a string
Returns : string
Args : [optional] string to set for query sequence
=cut
sub query_string{
my ($self,$value) = @_;
my $previous = $self->{'_query_string'};
if( defined $value || ! defined $previous ) {
$value = $previous = '' unless defined $value;
$self->{'_query_string'} = $value;
# do some housekeeping so we know when to
# re-run _calculate_seq_positions
$self->{'_sequenceschanged'} = 1;
}
return $previous;
}
=head2 hit_string
Title : hit_string
Usage : my $hseq = $hsp->hit_string;
Function: Retrieves the hit sequence of this HSP as a string
Returns : string
Args : [optional] string to set for hit sequence
=cut
sub hit_string{
my ($self,$value) = @_;
my $previous = $self->{'_hit_string'};
if( defined $value || ! defined $previous ) {
$value = $previous = '' unless defined $value;
$self->{'_hit_string'} = $value;
# do some housekeeping so we know when to
# re-run _calculate_seq_positions
$self->{'_sequenceschanged'} = 1;
}
return $previous;
}
=head2 homology_string
Title : homology_string
Usage : my $homo_string = $hsp->homology_string;
Function: Retrieves the homology sequence for this HSP as a string.
: The homology sequence is the string of symbols in between the
: query and hit sequences in the alignment indicating the degree
: of conservation (e.g., identical, similar, not similar).
Returns : string
Args : [optional] string to set for homology sequence
=cut
sub homology_string{
my ($self,$value) = @_;
my $previous = $self->{'_homology_string'};
if( defined $value || ! defined $previous ) {
$value = $previous = '' unless defined $value;
$self->{'_homology_string'} = $value;
# do some housekeeping so we know when to
# re-run _calculate_seq_positions
$self->{'_sequenceschanged'} = 1;
}
return $previous;
}
=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 : arg 1: 'query' = length of query seq (without gaps)
'hit' = length of hit seq (without gaps)
'total' = length of alignment (with gaps)
default = 'total'
arg 2: [optional] integer length value to set for specific type
=cut
sub length {
my $self = shift;
my $type = shift;
$type = 'total' unless defined $type;
$type = lc $type;
if( $type =~ /^q/i ) {
return $self->query()->length(shift);
} elsif( $type =~ /^(hit|subject|sbjct)/ ) {
return $self->hit()->length(shift);
} else {
my $v = shift;
if( defined $v ) {
$self->{'_hsplength'} = $v;
}
return $self->{'_hsplength'};
}
return 0; # should never get here
}
=head2 hsp_length
Title : hsp_length
Usage : my $len = $hsp->hsp_length()
Function: shortcut length('hsp')
Returns : floating point between 0 and 100
Args : none
=cut
sub hsp_length { return shift->length('hsp', shift); }
=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
=head2 frame
Title : frame
Usage : $hsp->frame($queryframe,$subjectframe)
Function: Set the Frame for both query and subject and insure that
they agree.
This overrides the frame() method implementation in
FeaturePair.
Returns : array of query and subjects if return type wants an array
or query frame if defined or subject frame
Args : none
Note : Frames are stored in the GFF way (0-2) not 1-3
as they are in BLAST (negative frames are deduced by checking
the strand of the query or hit)
=cut
sub frame {
my ($self, $qframe, $sframe) = @_;
if( defined $qframe ) {
if( $qframe == 0 ) {
$qframe = 0;
} elsif( $qframe !~ /^([+-])?([1-3])/ ) {
$self->warn("Specifying an invalid query frame ($qframe)");
$qframe = undef;
} else {
my $dir = $1;
$dir = '+' unless defined $dir;
if( ($dir eq '-' && $self->query->strand >= 0) ||
($dir eq '+' && $self->query->strand <= 0) ) {
$self->warn("Query frame ($qframe) did not match strand of query (". $self->query->strand() . ")");
}
# Set frame to GFF [0-2] -
# what if someone tries to put in a GFF frame!
$qframe = $2 - 1;
}
$self->query->frame($qframe);
}
if( defined $sframe ) {
if( $sframe == 0 ) {
$sframe = 0;
} elsif( $sframe !~ /^([+-])?([1-3])/ ) {
$self->warn("Specifying an invalid subject frame ($sframe)");
$sframe = undef;
} else {
my $dir = $1;
$dir = '+' unless defined $dir;
if( ($dir eq '-' && $self->hit->strand >= 0) ||
($dir eq '+' && $self->hit->strand <= 0) )
{
$self->warn("Subject frame ($sframe) did not match strand of subject (". $self->hit->strand() . ")");
}
# Set frame to GFF [0-2]
$sframe = $2 - 1;
}
$self->hit->frame($sframe);
}
if (wantarray() && $self->algorithm =~ /^T(BLAST|FAST)(X|Y|XY)/oi)
{
return ($self->query->frame(), $self->hit->frame());
} elsif (wantarray()) {
($self->query->frame() &&
return ($self->query->frame(), undef)) ||
($self->hit->frame() &&
return (undef, $self->hit->frame()));
} else {
($self->query->frame() &&
return $self->query->frame()) ||
($self->hit->frame() &&
return $self->hit->frame());
}
}
=head2 get_aln
Title : get_aln
Usage : my $aln = $hsp->gel_aln
Function: Returns a Bio::SimpleAlign representing the HSP alignment
Returns : Bio::SimpleAlign
Args : none
=cut
sub get_aln {
my ($self) = @_;
require Bio::LocatableSeq;
require Bio::SimpleAlign;
my $aln = new Bio::SimpleAlign;
my $hs = $self->hit_string();
my $qs = $self->query_string();
# FASTA specific stuff moved to the FastaHSP object
my $seqonly = $qs;
$seqonly =~ s/[\-\s]//g;
my ($q_nm,$s_nm) = ($self->query->seq_id(),
$self->hit->seq_id());
unless( defined $q_nm && CORE::length ($q_nm) ) {
$q_nm = 'query';
}
unless( defined $s_nm && CORE::length ($s_nm) ) {
$s_nm = 'hit';
}
my $query = new Bio::LocatableSeq('-seq' => $qs,
'-id' => $q_nm,
'-start' => 1,
'-end' => CORE::length($seqonly),
);
$seqonly = $hs;
$seqonly =~ s/[\-\s]//g;
my $hit = new Bio::LocatableSeq('-seq' => $hs,
'-id' => $s_nm,
'-start' => 1,
'-end' => CORE::length($seqonly),
);
$aln->add_seq($query);
$aln->add_seq($hit);
return $aln;
}
=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{
my ($self,$value) = @_;
if( defined $value) {
$self->{'num_conserved'} = $value;
}
return $self->{'num_conserved'};
}
=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{
my ($self,$value) = @_;
if( defined $value) {
$self->{'_num_identical'} = $value;
}
return $self->{'_num_identical'};
}
=head2 rank
Usage : $hsp->rank( [string] );
Purpose : Get the rank of the HSP within a given Blast hit.
Example : $rank = $hsp->rank;
Returns : Integer (1..n) corresponding to the order in which the HSP
appears in the BLAST report.
=cut
sub rank {
my ($self,$value) = @_;
if( defined $value) {
$self->{'_rank'} = $value;
}
return $self->{'_rank'};
}
=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-not-identical');
: @h_ind = $hsp->seq_inds('hit', 'conserved', 1);
Returns : List of integers
: May include ranges if collapse is true.
Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = query)
: ('sbjct' is synonymous with 'hit')
: class = 'identical' or 'conserved' or 'nomatch' or 'gap'
: (default = identical)
: (can be shortened to 'id' or 'cons')
: or 'conserved-not-identical'
: collapse = boolean, if true, consecutive positions are merged
: using a range notation, e.g., "1 2 3 4 5 7 9 10 11"
: collapses to "1-5 7 9-11". This is useful for
: consolidating long lists. Default = no collapse.
Throws : n/a.
Comments :
See Also : L<Bio::Search::SearchUtils::collapse_nums()|Bio::Search::SearchUtils>,
L<Bio::Search::Hit::HitI::seq_inds()|Bio::Search::Hit::HitI>
=cut
sub seq_inds{
my ($self, $seqType, $class, $collapse) = @_;
# prepare the internal structures - this is cached so
# if the strings have not changed we're okay
$self->_calculate_seq_positions();
$seqType ||= 'query';
$class ||= 'identical';
$collapse ||= 0;
$seqType = 'sbjct' if $seqType eq 'hit';
my $t = lc(substr($seqType,0,1));
if( $t eq 'q' ) {
$seqType = 'query';
} elsif ( $t eq 's' || $t eq 'h' ) {
$seqType = 'sbjct';
} else {
$self->warn("unknown seqtype $seqType using 'query'");
$seqType = 'query';
}
$t = lc(substr($class,0,1));
if( $t eq 'c' ) {
if( $class =~ /conserved\-not\-identical/ ) {
$class = 'conserved';
} else {
$class = 'conservedall';
}
} elsif( $t eq 'i' ) {
$class = 'identical';
} elsif( $t eq 'n' ) {
$class = 'nomatch';
} elsif( $t eq 'g' ) {
$class = 'gap';
} else {
$self->warn("unknown sequence class $class using 'identical'");
$class = 'identical';
}
## Sensitive to member name changes.
$seqType = "_\L$seqType\E";
$class = "_\L$class\E";
my @ary;
if( $class eq '_gap' ) {
# this means that we are remapping the gap length that is stored
# in the hash (for example $self->{'_gapRes_query'} )
# so we'll return an array which has the values of the position of the
# of the gap (the key in the hash) + the gap length (value in the
# hash for this key - 1.
@ary = map { $_ > 1 ?
$_..($_ + $self->{"${class}Res$seqType"}->{$_} - 1) :
$_ }
sort { $a <=> $b } keys %{ $self->{"${class}Res$seqType"}};
} elsif( $class eq '_conservedall' ) {
@ary = sort { $a <=> $b }
keys %{ $self->{"_conservedRes$seqType"}},
keys %{ $self->{"_identicalRes$seqType"}},
} else {
@ary = sort { $a <=> $b } keys %{ $self->{"${class}Res$seqType"}};
}
require Bio::Search::BlastUtils if $collapse;
return $collapse ? &Bio::Search::SearchUtils::collapse_nums(@ary) : @ary;
}
=head2 Inherited from Bio::SeqFeature::SimilarityPair
These methods come from 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
Returns : numeric
Args : [optional] new value to set
=head2 score
Title : score
Usage : my $score = $hsp->score();
Function: Returns the score for this HSP or undef
Returns : numeric
Args : [optional] numeric to set value
=cut
# overriding
sub score {
my ($self,$value) = @_;
my $previous = $self->{'_score'};
if( defined $value ) {
$self->{'_score'} = $value;
}
return $previous;
}
=head2 bits
Title : bits
Usage : my $bits = $hsp->bits();
Function: Returns the bit value for this HSP or undef
Returns : numeric
Args : none
=cut
# overriding
sub bits {
my ($self,$value) = @_;
my $previous = $self->{'_bits'};
if( defined $value ) {
$self->{'_bits'} = $value;
}
return $previous;
}
=head2 strand
Title : strand
Usage : $hsp->strand('quer')
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)
=cut
=head1 Private methods
=cut
=head2 _calculate_seq_positions
Title : _calculate_seq_positions
Usage : $self->_calculate_seq_positions
Function: Internal function
Returns :
Args :
=cut
sub _calculate_seq_positions {
my ($self,@args) = @_;
return unless ( $self->{'_sequenceschanged'} );
$self->{'_sequenceschanged'} = 0;
my ($mchar, $schar, $qchar);
my ($seqString, $qseq,$sseq) = ( $self->homology_string(),
$self->query_string(),
$self->hit_string() );
# Using hashes to avoid saving duplicate residue numbers.
my %identicalList_query = ();
my %identicalList_sbjct = ();
my %conservedList_query = ();
my %conservedList_sbjct = ();
my %gapList_query = ();
my %gapList_sbjct = ();
my %nomatchList_query = ();
my %nomatchList_sbjct = ();
my $qdir = $self->query->strand || 1;
my $sdir = $self->hit->strand || 1;
my $resCount_query = ($qdir >=0) ? $self->query->end : $self->query->start;
my $resCount_sbjct = ($sdir >=0) ? $self->hit->end : $self->hit->start;
my $prog = $self->algorithm;
if( $prog =~ /FAST/i ) {
# fasta reports some extra 'regional' sequence information
# we need to clear out first
# this seemed a bit insane to me at first, but it appears to
# work --jason
# we infer the end of the regional sequence where the first
# non space is in the homology string
# then we use the HSP->length to tell us how far to read
# to cut off the end of the sequence
# one possible problem is the sequence which
my ($start) = (0);
if( $seqString =~ /^(\s+)/ ) {
$start = CORE::length($1);
}
$seqString = substr($seqString, $start,$self->length('total'));
$qseq = substr($qseq, $start,$self->length('total'));
$sseq = substr($sseq, $start,$self->length('total'));
$qseq =~ s![\\\/]!!g;
$sseq =~ s![\\\/]!!g;
}
if($prog =~ /^(PSI)?T(BLAST|FAST)N/oi ) {
$resCount_sbjct = int($resCount_sbjct / 3);
} elsif($prog =~ /^(BLAST|FAST)(X|Y|XY)/oi ) {
$resCount_query = int($resCount_query / 3);
} elsif($prog =~ /^T(BLAST|FAST)(X|Y|XY)/oi ) {
$resCount_query = int($resCount_query / 3);
$resCount_sbjct = int($resCount_sbjct / 3);
}
while( $mchar = chop($seqString) ) {
($qchar, $schar) = (chop($qseq), chop($sseq));
if( $mchar eq '+' || $mchar eq '.' || $mchar eq ':' ) {
$conservedList_query{ $resCount_query } = 1;
$conservedList_sbjct{ $resCount_sbjct } = 1;
} elsif( $mchar ne ' ' ) {
$identicalList_query{ $resCount_query } = 1;
$identicalList_sbjct{ $resCount_sbjct } = 1;
} elsif( $mchar eq ' ') {
$nomatchList_query{ $resCount_query } = 1;
$nomatchList_sbjct{ $resCount_sbjct } = 1;
}
if( $qchar eq $GAP_SYMBOL ) {
$gapList_query{ $resCount_query } ++;
} else {
$resCount_query -= $qdir;
}
if( $schar eq $GAP_SYMBOL ) {
$gapList_sbjct{ $resCount_query } ++;
} else {
$resCount_sbjct -=$sdir;
}
}
$self->{'_identicalRes_query'} = \%identicalList_query;
$self->{'_conservedRes_query'} = \%conservedList_query;
$self->{'_nomatchRes_query'} = \%nomatchList_query;
$self->{'_gapRes_query'} = \%gapList_query;
$self->{'_identicalRes_sbjct'} = \%identicalList_sbjct;
$self->{'_conservedRes_sbjct'} = \%conservedList_sbjct;
$self->{'_nomatchRes_sbjct'} = \%nomatchList_sbjct;
$self->{'_gapRes_sbjct'} = \%gapList_sbjct;
return 1;
}
=head2 n
See documentation in L<Bio::Search::HSP::HSPI::n()|Bio::Search::HSP::HSPI>
=cut
#-----
sub n {
my $self = shift;
if(@_) { $self->{'_n'} = shift; }
defined $self->{'_n'} ? $self->{'_n'} : '';
}
=head2 range
See documentation in L<Bio::Search::HSP::HSPI::range()|Bio::Search::HSP::HSPI>
=cut
#----------
sub range {
#----------
my ($self, $seqType) = @_;
$seqType ||= 'query';
$seqType = 'sbjct' if $seqType eq 'hit';
my ($start, $end);
if( $seqType eq 'query' ) {
$start = $self->query->start;
$end = $self->query->end;
}
else {
$start = $self->hit->start;
$end = $self->hit->end;
}
return ($start, $end);
}
1;
]]>