Bio::Search::HSP ModelHSP
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Summary
Bio::Search::HSP::ModelHSP - A HSP object for model-based searches
Package variables
Privates (from "my" definitions)
$SEQ_REGEX = qr/\*\[\s*(\d+)\s*\]\*/
$META_REGEX = qr/(~+)/
Included modules
Bio::Seq::Meta
Inherit
Bio::Search::HSP::GenericHSP
Synopsis
    use Bio::Search::HSP::ModelHSP;
# us it just like a Bio::Search::HSP::ModelHSP object
Description
This object is a specialization of 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.
Methods
metaDescriptionCode
custom_scoreDescriptionCode
seqDescriptionCode
get_alnDescriptionCode
seq_indsDescriptionCode
frac_identicalDescriptionCode
frac_conservedDescriptionCode
matchesDescriptionCode
num_conservedDescriptionCode
num_identicalDescriptionCode
cigar_stringDescriptionCode
generate_cigar_stringDescriptionCode
percent_identityDescriptionCode
_postprocess_hsp
No description
Code
Methods description
metacode    nextTop
 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!
custom_scorecodeprevnextTop
 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.
seqcodeprevnextTop
 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 : seq_str(), Bio::Seq
get_alncodeprevnextTop
 Title   : get_aln
Usage : my $aln = $hsp->gel_aln
Function: Returns a Bio::SimpleAlign representing the HSP alignment
Returns : Bio::SimpleAlign
Args : none
seq_indscodeprevnextTop
frac_identicalcodeprevnextTop
frac_conservedcodeprevnextTop
matchescodeprevnextTop
num_conservedcodeprevnextTop
num_identicalcodeprevnextTop
cigar_stringcodeprevnextTop
generate_cigar_stringcodeprevnextTop
percent_identitycodeprevnextTop
Methods code
metadescriptionprevnextTop
sub meta {
    my ($self,$value) = @_;
    my $previous = $self->{'META'};
    if( defined $value  ) {
        $self->{'META'} = $value;
    }
    return $previous;
}
custom_scoredescriptionprevnextTop
sub custom_score {
    my ($self,$value) = @_;
    my $previous = $self->{'CUSTOMSCORE'};
    if( defined $value  ) {
        $self->{'CUSTOMSCORE'} = $value;
    }
    return $previous;
}
seqdescriptionprevnextTop
sub seq {
#-------
my($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; $seq;
}
get_alndescriptionprevnextTop
sub get_aln {
    my ($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;
}
seq_indsdescriptionprevnextTop
sub seq_inds {
    my $self = shift;
    $self->warn('$hsp->seq_inds not implemented for Model-based searches');
    return;
}
frac_identicaldescriptionprevnextTop
sub frac_identical {
    my $self = shift;
    $self->warn('$hsp->frac_identical not implemented for Model-based searches');
    return;
}
frac_conserveddescriptionprevnextTop
sub frac_conserved {
    my $self = shift;
    $self->warn('$hsp->frac_conserved not implemented for Model-based searches');
    return;
}
matchesdescriptionprevnextTop
sub matches {
    my $self = shift;
    $self->warn('$hsp->matches not implemented for Model-based searches');
    return;
}
num_conserveddescriptionprevnextTop
sub num_conserved {
    my $self = shift;
    $self->warn('$hsp->num_conserved not implemented for Model-based searches');
    return;
}
num_identicaldescriptionprevnextTop
sub num_identical {
    my $self = shift;
    $self->warn('$hsp->num_identical not implemented for Model-based searches');
    return;
}
cigar_stringdescriptionprevnextTop
sub cigar_string {
    my $self = shift;
    $self->warn('$hsp->cigar_string not implemented for Model-based searches');
    return;
}
generate_cigar_stringdescriptionprevnextTop
sub generate_cigar_string {
    my $self = shift;
    $self->warn('$hsp->generate_cigar_string not implemented for Model-based searches');
    return;
}
percent_identitydescriptionprevnextTop
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 $META_REGEX = qr/(~+)/;
}
_postprocess_hspdescriptionprevnextTop
sub _postprocess_hsp {
	my ($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;
}
General documentation
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/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
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.
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 the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chris FieldsTop
Email cjfields at bioperl dot org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 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
Bio::Search::HSP::HSPI methodsTop
Implementation of Bio::Search::HSP::HSPI methods follow
algorithmTop
 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
strandTop
 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.
pvalueTop
 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
evalueTop
 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
gapsTop
 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
query_stringTop
 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
hit_stringTop
 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
homology_stringTop
 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
lengthTop
 Title    : length
Usage : my $len = $hsp->length( ['query'|'hit'|'total'] );
Function : Returns the length of the query or hit in the alignment
(without gaps)
or the aggregate length of the HSP (including gaps;
this may be greater than either hit or query )
Returns : integer
Args : arg 1: 'query' = length of query seq (without gaps)
'hit' = length of hit seq (without gaps)
'total' = length of alignment (with gaps)
default = 'total'
arg 2: [optional] integer length value to set for specific type
frameTop
 Title   : frame
Usage : my ($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)
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
Returns : numeric
Args : [optional] new value to set
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
ModelHSP methods overridden in ModelHSPTop
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.