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

_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)