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Bio::Search::HSP::PullHSPI.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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)
 
 

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)