Last Change: 2018-09-07, 16:50
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Bio::Search::HSP::ModelHSP - A HSP object for model-based searches
use Bio::Search::HSP::ModelHSP;
# us it just like a Bio::Search::HSP::ModelHSP object
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 comparisons;
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
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!
noncanonical_string
Title : noncanonical_string
Usage : my $nc_seq = $hsp->noncanonical_string();
Function: Returns noncanonical string (NC) data for this HSP or undef
Returns : string of noncanonical data or undef
Args : [optional] string to set value
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.
Bio::Search::HSP::HSPI methods
Implementation of Bio::Search::HSP::HSPI methods follow
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
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.
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 : seq_str(), Bio::Seq
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
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
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
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
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
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
length
Title : length
Usage : my $len = $hsp->length( ['query'|'hit'|'total'] );
Function : Returns the length of the query or hit in the alignment
(without gaps)
or the aggregate length of the HSP (including gaps;
this may be greater than either hit or query )
Returns : integer
Args : arg 1: 'query' = length of query seq (without gaps)
'hit' = length of hit seq (without gaps)
'total' = length of alignment (with gaps)
default = 'total'
arg 2: [optional] integer length value to set for specific type
frame
Title : frame
Usage : my ($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)
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
Inherited from Bio::SeqFeature::SimilarityPair
These methods come from Bio::SeqFeature::SimilarityPair
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
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
significance
Title : significance
Usage : $evalue = $obj->significance();
$obj->significance($evalue);
Function: Get/Set the significance value
Returns : numeric
Args : [optional] new value to set
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
bits
Title : bits
Usage : my $bits = $hsp->bits();
Function: Returns the bit value for this HSP or undef
Returns : numeric
Args : none
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.
seq_inds
frac_identical
frac_conserved
matches
num_conserved
num_identical
cigar_string
generate_cigar_string
percent_identity