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::GenericHSP->new();
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 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)
-query_length=> total length of the query sequence
-query_seq => query sequence portion of the HSP
-query_desc => textual description of the query
-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
-hit_seq => hit sequence portion of the HSP
-hit_desc => textual description of the hit
-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)
-hsp_group => HSP Group informat (WU-BLAST only)
-gap_symbol => symbol representing a gap (default = '-')
-hit_features=> string of features found in or near HSP hit
region (reported in some BLAST text output,
v. 2.2.13 and up)
-stranded => If the algorithm isn't known (i.e. defaults to
'generic'), setting this will indicate start/end
coordinates are to be used to determine the strand
for 'query', 'subject', 'hit', 'both', or 'none'
(default = 'none')
Bio::Search::HSP::HSPImethods
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
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
frac_identical
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 identical / length of alignment (with gaps)
synonyms: 'hsp'
default = 'total'
arg 2: [optional] frac identical value to set for the type requested
Note : for translated sequences, this adjusts the length accordingly
frac_conserved
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
gaps
Title : gaps
Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
Function : Get the number of gap characters in the query, hit, or total alignment.
Returns : Integer, number of gaps or 0 if none
Args : arg 1: 'query' = num gap characters in query seq
'hit' = num gap characters in hit seq; synonyms: 'sbjct', 'subject'
'total' = num gap characters in whole alignment; synonyms: 'hsp'
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
consensus_string
Title : consensus_string
Usage : my $cs_string = $hsp->consensus_string;
Function: Retrieves the consensus structure line for this HSP as a string (HMMER).
: If the model had any consensus structure or reference line annotation
: that it inherited from a multiple alignment (#=GC SS cons,
: #=GC RF annotation in Stockholm files), that information is shown
: as CS or RF annotation line.
Returns : string
Args : [optional] string to set for consensus structure
posterior_string
Title : posterior_string
Usage : my $pp_string = $hsp->posterior_string;
Function: Retrieves the posterior probability line for this HSP as a string (HMMer3).
: The posterior probability is the string of symbols at the bottom
: of the alignment indicating the expected accuracy of each aligned residue.
: A 0 means 0-5%, 1 means 5-15%, and so on; 9 means 85-95%,
: and a * means 95-100% posterior probability.
Returns : string
Args : [optional] string to set for posterior probability
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) (synonyms: sbjct, subject)
'total' = length of alignment (with gaps)
default = 'total'
arg 2: [optional] integer length value to set for specific type
hsp_length
Title : hsp_length
Usage : my $len = $hsp->hsp_length()
Function: shortcut length('hsp')
Returns : floating point between 0 and 100
Args : none
percent_identity
Title : percent_identity
Usage : my $percentid = $hsp->percent_identity()
Function: Returns the calculated percent identity for an HSP
Returns : floating point between 0 and 100
Args : none
frame
Title : frame
Usage : my ($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 L<Bio::SimpleAlign> object representing the HSP alignment
Returns : L<Bio::SimpleAlign>
Args : none
num_conserved
Title : num_conserved
Usage : $obj->num_conserved($newval)
Function: returns the number of conserved residues in the alignment
Returns : integer
Args : integer (optional)
num_identical
Title : num_identical
Usage : $obj->num_identical($newval)
Function: returns the number of identical residues in the alignment
Returns : integer
Args : integer (optional)
rank
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.
seq_inds
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' - identical positions
: 'conserved' - conserved positions
: 'nomatch' - mismatched residue or gap positions
: 'mismatch' - mismatched residue positions (no gaps)
: 'gap' - gap positions only
: 'frameshift'- frameshift positions only
: 'conserved-not-identical' - conserved positions w/o
: identical residues
: The name can be shortened to 'id' or 'cons' unless
: the name is . The default value is
: '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 : For HSPs partially or completely derived from translated sequences
: (TBLASTN, BLASTX, TBLASTX, or similar), some positional data
: cannot easily be attributed to a single position (i.e. the
: positional data is ambiguous). In these cases all three codon
: positions are reported. Under these conditions you can check
: ambiguous_seq_inds() to determine whether the query, subject,
: or both are ambiguous.
:
See Also : L<Bio::Search::SearchUtils::collapse_nums()|Bio::Search::SearchUtils>,
L<Bio::Search::Hit::HitI::seq_inds()|Bio::Search::Hit::HitI>
ambiguous_seq_inds
Title : ambiguous_seq_inds
Purpose : returns a string denoting whether sequence indices for query,
: subject, or both are ambiguous
Returns : String; 'query', 'subject', 'query/subject', or empty string ''
Argument : none
Comments : For HSPs partially or completely derived from translated sequences
: (TBLASTN, BLASTX, TBLASTX, or similar), some positional data
: cannot easily be attributed to a single position (i.e. the
: positional data is ambiguous). In these cases all three codon
: positions are reported when using seq_inds(). Under these
: conditions you can check ambiguous_seq_inds() to determine whether
: the query, subject, or both are ambiguous.
See Also : L<Bio::Search::Hit::HSPI::seq_inds()>
InheritedfromBio::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 : L<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 : L<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
strand
Title : strand
Usage : $hsp->strand('query')
Function: Retrieves the strand for the HSP component requested
Returns : +1 or -1
Args : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject,
'query' to retrieve the query strand (default)
score
Title : score
Usage : $score = $obj->score();
$obj->score($value);
Function: Get/Set the score value
Returns : numeric
Args : [optional] new value to set
bits
Title : bits
Usage : $bits = $obj->bits();
$obj->bits($value);
Function: Get/Set the bits value
Returns : numeric
Args : [optional] new value to set
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