Reference

Bio::Search::HSP::PullHSPI(3pm)

Bio::Search::HSP::HSPI interface for pull parsers.

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 [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::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 retrieve 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)

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