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.
FEEDBACK
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Support
Please direct usage questions or support issues to the mailing list: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:
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AUTHOR - Sendu Bala
Email [email protected]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::SimilarityPairquery
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)
n
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)