#
# BioPerl module for Bio::Search::HSP::PullHSPI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Search::HSP::PullHSPI - Bio::Search::HSP::HSPI interface for pull parsers.
=head1 SYNOPSIS
# This is an interface and cannot be instantiated
# generally we use Bio::SearchIO to build these objects
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'hmmer_pull',
-file => 'result.hmmer');
while (my $result = $in->next_result) {
while (my $hit = $result->next_hit) {
while (my $hsp = $hit->next_hsp) {
$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
PullHSP is for fast implementations that only do parsing work on the hsp
data when you actually request information by calling one of the HSPI
methods.
Many methods of HSPI are implemented in a way suitable for inheriting classes
that use Bio::PullParserI. It only really makes sense for PullHSP modules to be
created by (and have as a -parent) PullHit modules.
In addition to the usual -chunk and -parent, -hsp_data is all you should supply
when making a PullHSP object. This will store that data and make it accessible
via _raw_hsp_data, which you can access in your subclass. It would be best to
simply provide the data as the input -chunk instead, if the raw data is large
enough.
=head1 SEE ALSO
This module 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://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Sendu Bala
Email bix@sendu.me.uk
=head1 COPYRIGHT
Copyright (c) 2006 Sendu Bala. 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::PullHSPI;
use strict;
use base qw(Bio::Search::HSP::HSPI Bio::PullParserI);
=head2 _setup
Title : _setup
Usage : $self->_setup(@args)
Function: Implementers should call this to setup common fields and deal with
common arguments to new().
Returns : n/a
Args : @args received in new().
=cut
sub _setup {
my ($self, @args) = @_;
# fields most subclasses probably will want
$self->_fields( { ( hsp_length => undef,
identical => undef,
percent_identity => undef,
conserved => undef,
hsp_gaps => undef,
query_gaps => undef,
hit_gaps => undef,
evalue => undef,
pvalue => undef,
score => undef,
query_start => undef,
query_end => undef,
query_string => undef,
hit_start => undef,
hit_end => undef,
hit_string => undef,
homology_string => undef,
rank => undef,
seq_inds => undef,
hit_identical_inds => undef,
hit_conserved_inds => undef,
hit_nomatch_inds => undef,
hit_gap_inds => undef,
query_identical_inds => undef,
query_conserved_inds => undef,
query_nomatch_inds => undef,
query_gap_inds => undef ) } );
my ($parent, $chunk, $hsp_data) = $self->_rearrange([qw(PARENT
CHUNK
HSP_DATA)], @args);
$self->throw("Need -parent or -chunk to be defined") unless defined $parent || $chunk;
$self->parent($parent) if $parent;
if ($chunk) {
my ($io, $start, $end) = (undef, 0, undef);
if (ref($chunk) eq 'ARRAY') {
($io, $start, $end) = @{$chunk};
}
else {
$io = $chunk;
}
$self->chunk($io, -start => $start, -end => $end);
}
$self->_raw_hsp_data($hsp_data) if $hsp_data;
return $self;
}
sub _raw_hsp_data {
my $self = shift;
if (@_) {
$self->{_raw_hsp_data} = shift;
}
return $self->{_raw_hsp_data};
}
#
# Some of these methods are written explitely to avoid HSPI throwing not
# implemented or the wrong ancestor class being used to answer the method;
# if it didn't do that then PullParserI AUTOLOAD would have cought them.
#
=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 {
return shift->get_field('algorithm');
}
=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)
Args : none
=cut
sub pvalue {
return shift->get_field('pvalue');
}
=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 {
return shift->get_field('evalue');
}
*expect = \&evalue;
=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) = @_;
$type = lc $type if defined $type;
$type = 'hit' if (defined $type && $type =~ /subject|sbjct/);
$type = 'total' if (! defined $type || $type eq 'hsp' || $type !~ /query|hit|subject|sbjct|total/);
my $ratio = $self->num_identical($type) / $self->length($type);
return sprintf( "%.4f", $ratio);
}
=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) = @_;
$type = lc $type if defined $type;
$type = 'hit' if (defined $type && $type =~ /subject|sbjct/);
$type = 'total' if (! defined $type || $type eq 'hsp' || $type !~ /query|hit|subject|sbjct|total/);
my $ratio = $self->num_conserved($type) / $self->length($type);
return sprintf( "%.4f", $ratio);
}
=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 $self = shift;
return scalar($self->seq_inds('hit', 'identical'));
}
=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 $self = shift;
return scalar($self->seq_inds('hit', 'conserved-not-identical'));
}
=head2 gaps
Title : gaps
Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
Function : Get the number of gap characters in the query, hit, or total alignment.
Returns : Integer, number of gap characters or 0 if none
Args : 'query', 'hit' or 'total'; default = 'total'
=cut
sub gaps {
my ($self, $type) = @_;
$type = lc $type if defined $type;
$type = 'total' if (! defined $type || $type eq 'hsp' || $type !~ /query|hit|subject|sbjct|total/);
$type = 'hit' if $type =~ /sbjct|subject/;
if ($type eq 'total') {
return scalar($self->seq_inds('hit', 'gap')) + scalar($self->seq_inds('query', 'gap'));
}
return scalar($self->seq_inds($type, 'gap'));
}
=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 {
return shift->get_field('query_string');
}
=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 {
return shift->get_field('hit_string');
}
=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 {
return shift->get_field('homology_string');
}
=head2 length
Title : length
Usage : my $len = $hsp->length( ['query'|'hit'|'total'] );
Function : Returns the length of the query or hit in the alignment (without gaps)
or the aggregate length of the HSP (including gaps;
this may be greater than either hit or query )
Returns : integer
Args : 'query' = length of query seq (without gaps)
'hit' = length of hit seq (without gaps)
'total' = length of alignment (with gaps)
default = 'total'
Args : none
=cut
sub length {
my ($self, $type) = @_;
$type = 'total' unless defined $type;
$type = lc $type;
if ($type =~ /^q/i) {
return $self->query->length;
}
elsif ($type =~ /^(hit|subject|sbjct)/) {
return $self->hit->length;
}
else {
return $self->hit->length + $self->gaps('hit');
}
}
=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('total');
}
=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 = shift;
require Bio::LocatableSeq;
require Bio::SimpleAlign;
my $aln = Bio::SimpleAlign->new();
my $hs = $self->seq('hit');
my $qs = $self->seq('query');
if ($hs && $qs) {
$aln->add_seq($hs);
$aln->add_seq($qs);
return $aln;
}
return;
}
=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 = $hsp->seq_inds('hit', 'conserved', 1);
Returns : List of integers
: May include ranges if collapse is true.
Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = query)
('sbjct' is synonymous with 'hit')
class = 'identical' or 'conserved' or 'nomatch' or 'gap'
(default = identical)
(can be shortened to 'id' or 'cons')
Note that 'conserved' includes identical unless you
use 'conserved-not-identical'
collapse = boolean, if true, consecutive positions are merged
using a range notation, e.g., "1 2 3 4 5 7 9 10 11"
collapses to "1-5 7 9-11". This is useful for
consolidating long lists. Default = no collapse.
Throws : n/a.
Comments :
See Also : L<Bio::Search::BlastUtils::collapse_nums()|Bio::Search::BlastUtils>, L<Bio::Search::Hit::HitI::seq_inds()|Bio::Search::Hit::HitI>
=cut
sub seq_inds {
my ($self, $seqType, $class, $collapse) = @_;
$seqType ||= 'query';
$class ||= 'identical';
$collapse ||= 0;
$seqType = lc($seqType);
$class = lc($class);
$seqType = 'hit' if $seqType eq 'sbjct';
my $t = substr($seqType,0,1);
if ($t eq 'q') {
$seqType = 'query';
}
elsif ($t eq 's' || $t eq 'h') {
$seqType = 'hit';
}
else {
$self->warn("unknown seqtype $seqType using 'query'");
$seqType = 'query';
}
$t = substr($class,0,1);
if ($t eq 'c') {
if ($class eq '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';
}
$seqType .= '_';
$class .= '_inds';
my @ary;
if ($class eq 'conservedall_inds') {
my %tmp = map { $_, 1 } @{$self->get_field($seqType.'conserved_inds')},
@{$self->get_field($seqType.'identical_inds')};
@ary = sort {$a <=> $b} keys %tmp;
}
else {
@ary = @{$self->get_field($seqType.$class)};
}
return $collapse ? &Bio::Search::SearchUtils::collapse_nums(@ary) : @ary;
}
=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)
=cut
sub significance {
return shift->get_field('evalue');
}
=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
sub score {
return shift->get_field('score');
}
=head2 bits
Title : bits
Usage : my $bits = $hsp->bits();
Function: Returns the bit value for this HSP or undef
Returns : numeric
Args : none
=cut
sub bits {
return shift->get_field('bits');
}
# 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) {
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, or list of two integers (query start and subject start) in
list context
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 = (wantarray ? 'list' : '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) {
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, or list of two integers (query end and subject end) in
list context
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 = (wantarray ? 'list' : '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) {
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 = $hsp->seq('query');
Returns : Object reference for a Bio::LocatableSeq object.
Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = 'query').
: ('sbjct' is synonymous with 'hit')
: default is 'query'
=cut
sub seq {
my ($self, $seqType) = @_;
$seqType ||= 'query';
$seqType = 'hit' if $seqType eq 'sbjct';
if ($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.");
}
my $str = $self->seq_str($seqType) || return;
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()|seq>, L<seq_inds()|seq_inds>, B<_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 {
return shift->get_field('rank');
}
=head2 matches
Usage : $hsp->matches(-seq => 'hit'|'query',
-start => $start,
-stop => $stop);
Purpose : Get the total number of identical and conservative matches
: in the query or sbjct sequence for the given HSP. Optionally can
: report data within a defined interval along the seq.
Example : ($id,$cons) = $hsp_object->matches(-seq => 'hit');
: ($id,$cons) = $hsp_object->matches(-seq => 'query',
-start => 300,
-stop => 400);
Returns : 2-element array of integers
Argument : (1) seq_type = 'query' or 'hit' or 'sbjct' (default = query)
: ('sbjct' is synonymous with 'hit')
: (2) start = Starting coordinate (optional)
: (3) stop = Ending coordinate (optional)
=cut
sub matches {
my ($self, @args) = @_;
my($seqType, $beg, $end) = $self->_rearrange([qw(SEQ START STOP)], @args);
$seqType ||= 'query';
$seqType = 'hit' if $seqType eq 'sbjct';
my @data;
if ((!defined $beg && !defined $end) || ! $self->seq_str('match')) {
push @data, ($self->num_identical, $self->num_conserved);
}
else {
$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;
}
else {
$end += 1;
}
if ($beg < $start) {
$beg = $start;
}
my $seq = substr($self->seq_str('homology'), $beg-$start, ($end-$beg));
if (!CORE::length $seq) {
$self->throw("Undefined sub-sequence ($beg,$end). Valid range = $start - $stop");
}
## Get data for a substring.
$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);
}
return @data;
}
=head2 n
Usage : $hsp_obj->n()
Purpose : Get the N value (num HSPs on which P/Expect is based).
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.
=cut
sub n {
return shift->get_field('num_hsps');
}
=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, $hsp->query->end)
=cut
sub range {
my ($self, $seqType) = @_;
$seqType ||= 'query';
my ($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);
}
#*** would want cigar stuff from GenericHSP - move to HSPI?
1;