#
# BioPerl module for Bio::Search::HSP::ModelHSP
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chris Fields <cjfields at bioperl dot org>
#
# Copyright Chris Fields
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Search::HSP::ModelHSP - A HSP object for model-based searches
=head1 SYNOPSIS
use Bio::Search::HSP::ModelHSP;
# us it just like a Bio::Search::HSP::ModelHSP object
=head1 DESCRIPTION
This object is a specialization of L<Bio::Search::HSP::ModelHSP> and is used
for searches which involve a query model, such as a Hidden Markov Model (HMM),
covariance model (CM), descriptor, or anything else besides a sequence. Note
that results from any HSPI class methods which rely on the query being a
sequence are unreliable and have thus been overridden with warnings indicating
they have not been implemented at this time.
=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 - Chris Fields
Email cjfields at bioperl dot org
=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::ModelHSP;
use strict;
use Bio::Seq::Meta;
use base qw(Bio::Search::HSP::GenericHSP);
=head2 new
Title : new
Usage : my $obj = Bio::Search::HSP::ModelHSP->new();
Function: Builds a new Bio::Search::HSP::ModelHSP object
Returns : Bio::Search::HSP::ModelHSP
Args :
Plus Bio::Seach::HSP::ModelHSP methods
-algorithm => algorithm used (Infernal, RNAMotif, ERPIN, 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)
-meta => optional meta data (sec structure, markup, etc)
-custom_score=> custom score data
=cut
=head2 meta
Title : meta
Usage : my $meta = $hsp->meta();
Function: Returns meta data for this HSP or undef
Returns : string of meta data or undef
Args : [optional] string to set value
Note : At some point very soon this will likely be a Bio::AnnotationI.
Don't get used to a simple string!
=cut
sub meta {
my ($self,$value) = @_;
my $previous = $self->{'META'};
if( defined $value ) {
$self->{'META'} = $value;
}
return $previous;
}
=head2 custom_score
Title : custom_score
Usage : my $data = $hsp->custom_score();
Function: Returns custom_score data for this HSP, or undef
Returns : custom_score data or undef
Args : [optional] custom_score
Note : This is a Get/Set used to deal with odd score-like data generated
from RNAMotif (and other programs) where the score section
can be customized to include non-standard data, including sequence
data, user-based scores, and other values.
=cut
sub custom_score {
my ($self,$value) = @_;
my $previous = $self->{'CUSTOMSCORE'};
if( defined $value ) {
$self->{'CUSTOMSCORE'} = $value;
}
return $previous;
}
=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
=head2 strand
Title : strand
Usage : $hsp->strand('hit')
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.
There is no strand available for 'query', as the query is a model
and not a true sequence.
=cut
# overrides HSPI::seq()
=head2 seq
Usage : $hsp->seq( [seq_type] );
Purpose : Get the query or sbjct sequence as a Bio::Seq.pm object.
Example : $seqObj = $hsp->seq('sbjct');
Returns : Object reference for a Bio::Seq.pm object.
Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = 'sbjct').
: ('sbjct' is synonymous with 'hit')
: default is 'sbjct'
: Note: if there is no sequence available (eg for a model-based
: search), this returns a LocatableSeq object w/o a sequence
Throws : Propagates any exception that occurs during construction
: of the Bio::Seq.pm object.
Comments : The sequence is returned in an array of strings corresponding
: to the strings in the original format of the Blast alignment.
: (i.e., same spacing).
See Also : L<seq_str()|seq_str>, L<Bio::Seq>
=cut
#-------
sub seq {
#-------
my($self,$seqType) = @_;
$seqType ||= 'sbjct';
$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;
$str =~ s{\*\[\s*(\d+)\s*\]\*}{'N' x $1}ge;
$str =~ s{\s+}{}g;
my $seq = Bio::LocatableSeq->new (-ID => $id,
-START => $self->start($seqType),
-END => $self->end($seqType),
-STRAND=> $self->strand($seqType),
-DESC => "$seqType sequence ",
);
$seq->seq($str) if $str;
$seq;
}
=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
=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
=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
=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
=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
=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
=head2 length
Title : length
Usage : my $len = $hsp->length( ['query'|'hit'|'total'] );
Function : Returns the length of the query or hit in the alignment
(without gaps)
or the aggregate length of the HSP (including gaps;
this may be greater than either hit or query )
Returns : integer
Args : arg 1: 'query' = length of query seq (without gaps)
'hit' = length of hit seq (without gaps)
'total' = length of alignment (with gaps)
default = 'total'
arg 2: [optional] integer length value to set for specific type
=cut
=head2 frame
Title : frame
Usage : my ($qframe, $hframe) = $hsp->frame('list',$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 subject frame if return type wants an array
or query frame if defined or subject frame if not defined
Args : 'hit' or 'subject' or 'sbjct' to retrieve the frame of the subject (default)
'query' to retrieve the query frame
'list' or 'array' to retrieve both query and hit frames together
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
=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 = Bio::SimpleAlign->new;
my %hsp = (hit => $self->hit_string,
midline => $self->homology_string,
query => $self->query_string,
meta => $self->meta);
# this takes care of infernal issues
if ($hsp{meta} && $hsp{meta} =~ m{~+}) {
$self->_postprocess_hsp(\%hsp);
}
if (!$hsp{query}) {
$self->warn("Missing query string, can't build alignment");
return;
}
my $seqonly = $hsp{query};
$seqonly =~ s/[\-\s]//g;
my ($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 = Bio::LocatableSeq->new('-seq' => $hsp{query},
'-id' => $q_nm,
'-start' => $self->query->start,
'-end' => $self->query->end,
);
$seqonly = $hsp{hit};
$seqonly =~ s/[\-\s]//g;
my $hit = Bio::LocatableSeq->new('-seq' => $hsp{hit},
'-id' => $s_nm,
'-start' => $self->hit->start,
'-end' => $self->hit->end,
);
$aln->add_seq($query);
$aln->add_seq($hit);
if ($hsp{meta}) {
my $meta_obj = Bio::Seq::Meta->new();
$meta_obj->named_meta('ss_cons', $hsp{meta});
$aln->consensus_meta($meta_obj);
}
return $aln;
}
=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
=head2 bits
Title : bits
Usage : my $bits = $hsp->bits();
Function: Returns the bit value for this HSP or undef
Returns : numeric
Args : none
=cut
=head1 ModelHSP methods overridden in ModelHSP
The following methods have been overridden due to their current reliance on
sequence-based queries. They may be implemented in future versions of this class.
=head2 seq_inds
=cut
sub seq_inds {
my $self = shift;
$self->warn('$hsp->seq_inds not implemented for Model-based searches');
return;
}
=head2 frac_identical
=cut
sub frac_identical {
my $self = shift;
$self->warn('$hsp->frac_identical not implemented for Model-based searches');
return;
}
=head2 frac_conserved
=cut
sub frac_conserved {
my $self = shift;
$self->warn('$hsp->frac_conserved not implemented for Model-based searches');
return;
}
=head2 matches
=cut
sub matches {
my $self = shift;
$self->warn('$hsp->matches not implemented for Model-based searches');
return;
}
=head2 num_conserved
=cut
sub num_conserved {
my $self = shift;
$self->warn('$hsp->num_conserved not implemented for Model-based searches');
return;
}
=head2 num_identical
=cut
sub num_identical {
my $self = shift;
$self->warn('$hsp->num_identical not implemented for Model-based searches');
return;
}
=head2 cigar_string
=cut
sub cigar_string {
my $self = shift;
$self->warn('$hsp->cigar_string not implemented for Model-based searches');
return;
}
=head2 generate_cigar_string
=cut
sub generate_cigar_string {
my $self = shift;
$self->warn('$hsp->generate_cigar_string not implemented for Model-based searches');
return;
}
=head2 percent_identity
=cut
sub percent_identity {
my $self = shift;
$self->warn('$hsp->percent_identity not implemented for Model-based searches');
return;
}
############## PRIVATE ##############
# the following method postprocesses HSP data in cases where the sequences
# aren't complete (which can trigger a validation error)
{
my $SEQ_REGEX = qr/\*\[\s*(\d+)\s*\]\*/;
my $META_REGEX = qr/(~+)/;
sub _postprocess_hsp {
my ($self, $hsp) = @_;
$self->throw('Must pass a hash ref for HSP processing') unless ref($hsp) eq 'HASH';
my @ins;
for my $type (qw(query hit meta)) {
$hsp->{$type} =~ s{\s+$}{};
my $str = $hsp->{$type};
my $regex = $type eq 'meta' ? $META_REGEX : $SEQ_REGEX;
my $ind = 0;
while ($str =~ m{$regex}g) {
$ins[$ind]->{$type} = {pos => pos($str) - length($1), str => $1};
$ind++;
}
}
for my $chunk (reverse @ins) {
my ($max, $min) = ($chunk->{hit}->{str} >= $chunk->{query}->{str}) ?
('hit', 'query') : ('query', 'hit');
my %rep;
$rep{$max} = 'N' x $chunk->{$max}->{str};
$rep{$min} = 'N' x $chunk->{$min}->{str}.
('-'x($chunk->{$max}->{str}-$chunk->{$min}->{str}));
$rep{'meta'} = '~' x $chunk->{$max}->{str};
$rep{'midline'} = ' ' x $chunk->{$max}->{str};
for my $t (qw(hit query meta midline)) {
substr($hsp->{$t}, $chunk->{meta}->{pos}, length($chunk->{meta}->{str}) , $rep{$t});
}
}
}
}
1;