- AUTHOR - Chris Fields
- ModelHSP methods overridden in ModelHSP
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 _
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
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!
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.
Implementation of Bio::Search::HSP::HSPI methods follow
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
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.
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).
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
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
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
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
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
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
Title : length Usage : my $len = $hsp->length( ['query'|'hit'|'total'] ); Function : Returns the length of the query or hit in the alignment (without gaps) or the aggregate length of the HSP (including gaps; this may be greater than either hit or query ) Returns : integer Args : arg 1: 'query' = length of query seq (without gaps) 'hit' = length of hit seq (without gaps) 'total' = length of alignment (with gaps) default = 'total' arg 2: [optional] integer length value to set for specific type
Title : frame Usage : my ($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)
Title : get_aln Usage : my $aln = $hsp->gel_aln Function: Returns a Bio::SimpleAlign representing the HSP alignment Returns : Bio::SimpleAlign Args : none
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') : : 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 :
These methods come from Bio::SeqFeature::SimilarityPair
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
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
Title : significance Usage : $evalue = $obj->significance(); $obj->significance($evalue); Function: Get/Set the significance value Returns : numeric Args : [optional] new value to set
Title : score Usage : my $score = $hsp->score(); Function: Returns the score for this HSP or undef Returns : numeric Args : [optional] numeric to set value
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.