NAME¶
Bio::Search::HSP::PullHSPI - Bio::Search::HSP::HSPI interface for pull parsers.
SYNOPSIS¶
# This is an interface and cannot be instantiated
# generally we use Bio::SearchIO to build these objects
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'hmmer_pull',
-file => 'result.hmmer');
while (my $result = $in->next_result) {
while (my $hit = $result->next_hit) {
while (my $hsp = $hit->next_hsp) {
$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;
}
}
}
DESCRIPTION¶
PullHSP is for fast implementations that only do parsing work on the hsp data
when you actually request information by calling one of the HSPI methods.
Many methods of HSPI are implemented in a way suitable for inheriting classes
that use Bio::PullParserI. It only really makes sense for PullHSP modules to
be created by (and have as a -parent) PullHit modules.
In addition to the usual -chunk and -parent, -hsp_data is all you should supply
when making a PullHSP object. This will store that data and make it accessible
via _raw_hsp_data, which you can access in your subclass. It would be best to
simply provide the data as the input -chunk instead, if the raw data is large
enough.
SEE ALSO¶
This module inherits methods from these other modules:
Bio::SeqFeatureI, Bio::SeqFeature::FeaturePair Bio::SeqFeature::SimilarityPair
Please refer to these modules for documentation of the many additional inherited
methods.
FEEDBACK¶
Mailing Lists¶
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¶
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 Bugs¶
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://github.com/bioperl/bioperl-live/issues
AUTHOR - Sendu Bala¶
Email bix@sendu.me.uk
COPYRIGHT¶
Copyright (c) 2006 Sendu Bala. All Rights Reserved.
DISCLAIMER¶
This software is provided "as is" without warranty of any kind.
APPENDIX¶
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
_setup¶
Title : _setup
Usage : $self->_setup(@args)
Function: Implementers should call this to setup common fields and deal with
common arguments to new().
Returns : n/a
Args : @args received in new().
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 : none
pvalue¶
Title : pvalue
Usage : my $pvalue = $hsp->pvalue();
Function: Returns the P-value for this HSP or undef
Returns : float or exponential (2e-10)
Args : none
evalue¶
Title : evalue
Usage : my $evalue = $hsp->evalue();
Function: Returns the e-value for this HSP
Returns : float or exponential (2e-10)
Args : none
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 : 'query' = num identical / length of query seq (without gaps)
'hit' = num identical / length of hit seq (without gaps)
'total' = num identical / length of alignment (with gaps)
default = 'total'
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 : 'query' = num conserved / length of query seq (without gaps)
'hit' = num conserved / length of hit seq (without gaps)
'total' = num conserved / length of alignment (with gaps)
default = 'total'
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)
num_conserved¶
Title : num_conserved
Usage : $obj->num_conserved($newval)
Function: returns the number of conserved residues in the alignment
Returns : inetger
Args : integer (optional)
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 gap characters or 0 if none
Args : 'query', 'hit' or 'total'; default = 'total'
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 : none
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 : none
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 : none
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 : 'query' = length of query seq (without gaps)
'hit' = length of hit seq (without gaps)
'total' = length of alignment (with gaps)
default = 'total'
Args : none
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
get_aln¶
Title : get_aln
Usage : my $aln = $hsp->get_aln
Function: Returns a Bio::SimpleAlign representing the HSP alignment
Returns : Bio::SimpleAlign
Args : none
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', 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')
Note that 'conserved' includes identical unless you
use '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::BlastUtils::collapse_nums(),
Bio::Search::Hit::HitI::seq_inds()
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 (see Bio::SeqFeature::SimilarityPair)
Returns : significance value (scientific notation string)
Args : significance value (sci notation string)
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
strand¶
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)
'list' or 'array' to retreive both query and hit together
start¶
Title : start
Usage : $hsp->start('query')
Function: Retrieves the start for the HSP component requested
Returns : integer, or list of two integers (query start and subject start) in
list context
Args : 'hit' or 'subject' or 'sbjct' to retrieve the start of the subject
'query' to retrieve the query start (default)
end¶
Title : end
Usage : $hsp->end('query')
Function: Retrieves the end for the HSP component requested
Returns : integer, or list of two integers (query end and subject end) in
list context
Args : 'hit' or 'subject' or 'sbjct' to retrieve the end of the subject
'query' to retrieve the query end (default)
seq¶
Usage : $hsp->seq( [seq_type] );
Purpose : Get the query or sbjct sequence as a Bio::Seq.pm object.
Example : $seqObj = $hsp->seq('query');
Returns : Object reference for a Bio::LocatableSeq object.
Argument : seq_type = 'query' or 'hit' or 'sbjct' (default = 'query').
: ('sbjct' is synonymous with 'hit')
: default is 'query'
seq_str¶
Usage : $hsp->seq_str( seq_type );
Purpose : Get the full query, sbjct, or 'match' sequence as a string.
: The 'match' sequence is the string of symbols in between the
: query and sbjct sequences.
Example : $str = $hsp->seq_str('query');
Returns : String
Argument : seq_Type = 'query' or 'hit' or 'sbjct' or 'match'
: ('sbjct' is synonymous with 'hit')
: default is 'query'
Throws : Exception if the argument does not match an accepted seq_type.
Comments :
See Also :
seq(),
seq_inds(),
_set_match_seq()
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.
matches¶
Usage : $hsp->matches(-seq => 'hit'|'query',
-start => $start,
-stop => $stop);
Purpose : Get the total number of identical and conservative matches
: in the query or sbjct sequence for the given HSP. Optionally can
: report data within a defined interval along the seq.
Example : ($id,$cons) = $hsp_object->matches(-seq => 'hit');
: ($id,$cons) = $hsp_object->matches(-seq => 'query',
-start => 300,
-stop => 400);
Returns : 2-element array of integers
Argument : (1) seq_type = 'query' or 'hit' or 'sbjct' (default = query)
: ('sbjct' is synonymous with 'hit')
: (2) start = Starting coordinate (optional)
: (3) stop = Ending coordinate (optional)
Usage : $hsp_obj->n()
Purpose : Get the N value (num HSPs on which P/Expect is based).
Returns : Integer or null string if not defined.
Argument : n/a
Throws : n/a
Comments : The 'N' value is listed in parenthesis with P/Expect value:
: e.g., P(3) = 1.2e-30 ---> (N = 3).
: Not defined in NCBI Blast2 with gaps.
: This typically is equal to the number of HSPs but not always.
range¶
Usage : $hsp->range( [seq_type] );
Purpose : Gets the (start, end) coordinates for the query or sbjct sequence
: in the HSP alignment.
Example : ($query_beg, $query_end) = $hsp->range('query');
: ($hit_beg, $hit_end) = $hsp->range('hit');
Returns : Two-element array of integers
Argument : seq_type = string, 'query' or 'hit' or 'sbjct' (default = 'query')
: ('sbjct' is synonymous with 'hit')
Throws : n/a
Comments : This is a convenience method for constructions such as
($hsp->query->start, $hsp->query->end)