Bio::Search::HSP::GenericHSP - A "Generic" implementation of a High Scoring Pair
my $hsp = new Bio::Search::HSP::GenericHSP( -algorithm => 'blastp',
-evalue => '1e-30',
);
$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;
# TODO: Describe how to configure a SearchIO stream so that it generates # GenericHSP objects.
This implementation is "Generic", meaning it is is suitable for holding information about High Scoring pairs from most Search reports such as BLAST and FastA. Specialized objects can be derived from this.
Unless you're writing a parser, you won't ever need to create a GenericHSP or any other HSPI-implementing object. If you use the SearchIO system, HSPI objects are created automatically from a SearchIO stream which returns Bio::Search::Result::ResultI objects and you get the HSPI objects via the ResultI API.
For documentation on what you can do with GenericHSP (and other HSPI objects), please see the API documentation in Bio::Search::HSP::HSPI.
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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 = new Bio::Search::HSP::GenericHSP();
Function: Builds a new Bio::Search::HSP::GenericHSP object
Returns : Bio::Search::HSP::GenericHSP
Args : -algorithm => algorithm used (BLASTP, TBLASTX, FASTX, 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
-percent_identity => (optional) percent identity
-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)
-rank => HSP rank
-links => HSP links information (WU-BLAST only)
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 : 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 : 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 : arg 1: 'query' = num identical / length of query seq (without gaps)
'hit' = num identical / length of hit seq (without gaps)
synonyms: 'sbjct', 'subject'
'total' = num conserved / length of alignment (with gaps)
synonyms: 'hsp'
default = 'total'
arg 2: [optional] frac identical value to set for the type requested
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 : arg 1: 'query' = num conserved / length of query seq (without gaps)
'hit' = num conserved / length of hit seq (without gaps)
synonyms: 'sbjct', 'subject'
'total' = num conserved / length of alignment (with gaps)
synonyms: 'hsp'
default = 'total'
arg 2: [optional] frac conserved value to set for the type requested
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; synonyms: 'sbjct', 'subject'
'total' = num gaps in whole alignment; synonyms: 'hsp'
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) (synonyms: sbjct, subject)
'total' = length of alignment (with gaps)
default = 'total'
arg 2: [optional] integer length value to set for specific type
Title : hsp_length
Usage : my $len = $hsp->hsp_length()
Function: shortcut length('hsp')
Returns : floating point between 0 and 100
Args : none
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
Title : frame
Usage : $hsp->frame($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 subjects if return type wants an array
or query frame if defined or subject frame
Args : none
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 L<Bio::SimpleAlign> object representing the HSP alignment Returns : L<Bio::SimpleAlign> Args : none
Title : num_conserved Usage : $obj->num_conserved($newval) Function: returns the number of conserved residues in the alignment Returns : inetger Args : integer (optional)
Title : num_identical Usage : $obj->num_identical($newval) Function: returns the number of identical residues in the alignment Returns : integer Args : integer (optional)
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.
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-not-identical');
: @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')
: or '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 : Bio::Search::SearchUtils::collapse_nums(), Bio::Search::Hit::HitI::seq_inds()
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 : L<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 : L<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 : bits
Usage : $bits = $obj->bits();
$obj->bits($value);
Function: Get/Set the bits value
Returns : numeric
Args : [optional] new value to set
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)
Title : _calculate_seq_positions Usage : $self->_calculate_seq_positions Function: Internal function Returns : Args :
See documentation in Bio::Search::HSP::HSPI::n()
See documentation in Bio::Search::HSP::HSPI::range()
Title : links
Usage : $obj->links($newval)
Function: Get/Set the Links value (from WU-BLAST)
Indicates the placement of the alignment in the group of HSPs
Returns : Value of links
Args : On set, new value (a scalar or undef, optional)
NOTE: the concept is originally from EnsEMBL docs at http://www.ensembl.org/Docs/wiki/html/EnsemblDocs/CigarFormat.html. Please append to these docs if you have a better definition.
Sequence alignment hits can be stored in a database as ungapped alignments. This imposes 2 major constraints on alignments:
a) alignments for a single hit record require multiple rows in the database, and b) it is not possible to accurately retrieve the exact original alignment.
Alternatively, sequence alignments can be stored as gapped alignments using the CIGAR line format (where CIGAR stands for Concise Idiosyncratic Gapped Alignment Report).
In the cigar line format alignments are stored as follows:
M: Match D: Deletion I: Insertion
An example of an alignment for a hypthetical protein match is shown below:
Query: 42 PGPAGLP----GSVGLQGPRGLRGPLP-GPLGPPL...
PG P G GP R PLGP
Sbjct: 1672 PGTP*TPLVPLGPWVPLGPSSPR--LPSGPLGPTD...
protein_align_feature table as the following cigar line:
7M4D12M2I2MD7M
Name: cigar_string Usage: $cigar_string = $hsp->cigar_string Function: Generate and return cigar string for this HSP alignment Args: No input needed Return: a cigar string
Name: generate_cigar_string Usage: my $cigar_string = Bio::Search::HSP::GenericHSP::generate_cigar_string ($qstr, $hstr); Function: generate cigar string from a simple sequence of alignment. Args: the string of query and subject Return: cigar string
