Bio::Search::Hit::HitI(3) Interface for a hit in a similarity search result


# Bio::Search::Hit::HitI objects should not be instantiated since this # module defines a pure interface.

# Given an object that implements the Bio::Search::Hit::HitI interface, # you can do the following things with it:

# Get a HitI object from a SearchIO stream:
use Bio::SeachIO;
my $searchio = Bio::SearchIO->new(-format => 'blast', -file => 'result.bls');
my $result = $searchio->next_result;
my $hit = $result->next_hit;
$hit_name = $hit->name();
$desc = $hit->description();
$len = $hit->length
$alg = $hit->algorithm();
$score = $hit->raw_score();
$significance = $hit->significance();
$rank = $hit->rank(); # the Nth hit for a specific query
while( $hsp = $obj->next_hsp()) { ... } # process in iterator fashion
for my $hsp ( $obj->hsps()()) { ... } # process in list fashion


    Bio::Search::Hit::* objects are data structures that contain information
about specific hits obtained during a library search.  Some information will
be algorithm-specific, but others will be generally defined.


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AUTHOR - Aaron Mackey, Steve Chervitz

Email [email protected] (original author) Email [email protected]


Copyright (c) 1999-2001 Aaron Mackey, Steve Chervitz. All Rights Reserved.


This software is provided ``as is'' without warranty of any kind.


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : name
 Usage   : $hit_name = $hit->name();
 Function: returns the name of the Hit sequence
 Returns : a scalar string
 Args    : none

The name of a hit is unique within a Result or within an Iteration.


 Title   : description
 Usage   : $desc = $hit->description();
 Function: Retrieve the description for the hit
 Returns : a scalar string
 Args    : none


 Title   : accession
 Usage   : $acc = $hit->accession();
 Function: Retrieve the accession (if available) for the hit
 Returns : a scalar string (empty string if not set)
 Args    : none


 Title   : locus
 Usage   : $acc = $hit->locus();
 Function: Retrieve the locus(if available) for the hit
 Returns : a scalar string (empty string if not set)
 Args    : none


 Title   : length
 Usage   : my $len = $hit->length
 Function: Returns the length of the hit 
 Returns : integer
 Args    : none


 Title   : algorithm
 Usage   : $alg = $hit->algorithm();
 Function: Gets the algorithm specification that was used to obtain the hit
           For BLAST, the algorithm denotes what type of sequence was aligned 
           against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated 
           dna-prt, TBLASTN prt-translated dna, TBLASTX translated 
           dna-translated dna).
 Returns : a scalar string 
 Args    : none


 Title   : raw_score
 Usage   : $score = $hit->raw_score();
 Function: Gets the "raw score" generated by the algorithm.  What
           this score is exactly will vary from algorithm to algorithm,
           returning undef if unavailable.
 Returns : a scalar value
 Args    : none


Equivalent to raw_score()


 Title   : significance
 Usage   : $significance = $hit->significance();
 Function: Used to obtain the E or P value of a hit, i.e. the probability that
           this particular hit was obtained purely by random chance.  If
           information is not available (nor calculatable from other
           information sources), return undef.
 Returns : a scalar value or undef if unavailable
 Args    : none


 Usage     : $hit_object->bits();
 Purpose   : Gets the bit score of the best HSP for the current hit.
 Example   : $bits = $hit_object->bits();
 Returns   : Integer or double for FASTA reports
 Argument  : n/a
 Comments  : For BLAST1, the non-bit score is listed in the summary line.

See Also : score()


 Title    : next_hsp
 Usage    : while( $hsp = $obj->next_hsp()) { ... }
 Function : Returns the next available High Scoring Pair
 Example  : 
 Returns  : L<Bio::Search::HSP::HSPI> object or null if finished
 Args     : none


 Usage     : $hit_object->hsps();
 Purpose   : Get a list containing all HSP objects.
           : Get the numbers of HSPs for the current hit.
 Example   : @hsps = $hit_object->hsps();
           : $num  = $hit_object->hsps();  # alternatively, use num_hsps()
 Returns   : Array context : list of L<Bio::Search::HSP::BlastHSP> objects.
           : Scalar context: integer (number of HSPs).
           :                 (Equivalent to num_hsps()).
 Argument  : n/a. Relies on wantarray
 Throws    : Exception if the HSPs have not been collected.

See Also : hsp(), num_hsps()


 Usage     : $hit_object->num_hsps();
 Purpose   : Get the number of HSPs for the present Blast hit.
 Example   : $nhsps = $hit_object->num_hsps();
 Returns   : Integer
 Argument  : n/a
 Throws    : Exception if the HSPs have not been collected.

See Also : hsps()


 Usage     : $hit->seq_inds( seq_type, class, collapse );
 Purpose   : Get a list of residue positions (indices) across all HSPs
           : for identical or conserved residues in the query or sbjct sequence.
 Example   : @s_ind = $hit->seq_inds('query', 'identical');
           : @h_ind = $hit->seq_inds('hit', 'conserved');
           : @h_ind = $hit->seq_inds('hit', 'conserved', 1);
 Returns   : Array of integers 
           : May include ranges if collapse is non-zero.
 Argument  : [0] seq_type  = 'query' or 'hit' or 'sbjct'  (default = 'query')
           :                 ('sbjct' is synonymous with 'hit')
           : [1] class     = 'identical' or 'conserved' (default = 'identical')
           :              (can be shortened to 'id' or 'cons')
           :              (actually, anything not 'id' will evaluate to 'conserved').
           : [2] collapse  = boolean, if non-zero, 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.

See Also : Bio::Search::HSP::HSPI::seq_inds()


 Title   : rewind
 Usage   : $hit->rewind;
 Function: Allow one to reset the HSP iterator to the beginning
           if possible
 Returns : none
 Args    : none


 Usage     : $hit_object->overlap( [integer] );
 Purpose   : Gets/Sets the allowable amount overlap between different HSP sequences.
 Example   : $hit_object->overlap(5);
           : $overlap = $hit_object->overlap;
 Returns   : Integer.
 Argument  : integer.
 Throws    : n/a
 Status    : Experimental
 Comments  : Any two HSPs whose sequences overlap by less than or equal
           : to the overlap() number of resides will be considered separate HSPs
           : and will not get tiled by L<Bio::Search::BlastUtils::_adjust_contigs()>.

See Also : Bio::Search::BlastUtils::_adjust_contigs(), BUGS


 Usage     : $hit_object->n();
 Purpose   : Gets the N number for the current Blast hit.
           : This is the number of HSPs in the set which was ascribed
           : the lowest P-value (listed on the description line).
           : This number is not the same as the total number of HSPs.
           : To get the total number of HSPs, use num_hsps().
 Example   : $n = $hit_object->n();
 Returns   : Integer
 Argument  : n/a
 Throws    : Exception if HSPs have not been set (BLAST2 reports).
 Comments  : Note that the N parameter is not reported in gapped BLAST2.
           : Calling n() on such reports will result in a call to num_hsps().
           : The num_hsps() method will count the actual number of
           : HSPs in the alignment listing, which may exceed N in
           : some cases.

See Also : num_hsps()


 Usage     : $hit_object->p( [format] );
 Purpose   : Get the P-value for the best HSP of the given BLAST hit.
           : (Note that P-values are not provided with NCBI Blast2 reports).
 Example   : $p =  $sbjct->p;
           : $p =  $sbjct->p('exp');  # get exponent only.
           : ($num, $exp) =  $sbjct->p('parts');  # split sci notation into parts
 Returns   : Float or scientific notation number (the raw P-value, DEFAULT).
           : Integer if format == 'exp' (the magnitude of the base 10 exponent).
           : 2-element list (float, int) if format == 'parts' and P-value
           :                is in scientific notation (See Comments).
 Argument  : format: string of 'raw' | 'exp' | 'parts'
           :    'raw' returns value given in report. Default. (1.2e-34)
           :    'exp' returns exponent value only (34)
           :    'parts' returns the decimal and exponent as a 
           :            2-element list (1.2, -34) (See Comments).
 Throws    : Warns if no P-value is defined. Uses expect instead.
 Comments  : Using the 'parts' argument is not recommended since it will not
           : work as expected if the P-value is not in scientific notation.
           : That is, floats are not converted into sci notation before
           : splitting into parts.

See Also : expect(), signif(), Bio::Search::BlastUtils::get_exponent()


 Usage     : $hit_object->hsp( [string] );
 Purpose   : Get a single HSPI object for the present HitI object.
 Example   : $hspObj  = $hit_object->hsp;  # same as 'best'
           : $hspObj  = $hit_object->hsp('best');
           : $hspObj  = $hit_object->hsp('worst');
 Returns   : Object reference for a L<Bio::Search::HSP::HSPI> object.
 Argument  : String (or no argument).
           :   No argument (default) = highest scoring HSP (same as 'best').
           :   'best' or 'first' = highest scoring HSP.
           :   'worst' or 'last' = lowest scoring HSP.
 Throws    : Exception if the HSPs have not been collected.
           : Exception if an unrecognized argument is used.

See Also : hsps(), num_hsps()


 Usage     : $hit_object->logical_length( [seq_type] );
           : (mostly intended for internal use).
 Purpose   : Get the logical length of the hit sequence.
           : If the Blast is a TBLASTN or TBLASTX, the returned length 
           : is the length of the would-be amino acid sequence (length/3).
           : For all other BLAST flavors, this function is the same as length().
 Example   : $len    = $hit_object->logical_length();
 Returns   : Integer 
 Argument  : seq_type = 'query' or 'hit' or 'sbjct' (default = 'query')
             ('sbjct' is synonymous with 'hit')
 Throws    : n/a
 Comments  : This is important for functions like frac_aligned_query()
           : which need to operate in amino acid coordinate space when dealing
           : with [T]BLAST[NX] type reports.

See Also : length(), frac_aligned_query(), frac_aligned_hit()


 Title   : rank
 Usage   : $obj->rank($newval)
 Function: Get/Set the rank of this Hit in the Query search list
           i.e. this is the Nth hit for a specific query
 Returns : value of rank
 Args    : newvalue (optional)


 Title   : each_accession_number
 Usage   : $obj->each_accession_number
 Function: Get each accession number listed in the description of the hit.
           If there are no alternatives, then only the primary accession will 
           be given
 Returns : list of all accession numbers in the description
 Args    : none


 Usage     : $hit_object->tiled_hsps( [integer] );
 Purpose   : Gets/Sets an indicator for whether or not the HSPs in this Hit 
           : have been tiled.
           : Methods that rely on HSPs being tiled should check this
           : and then call SearchUtils::tile_hsps() if not.
 Example   : $hit_object->tiled_hsps(1);
           : if( $hit_object->tiled_hsps ) { # do something }
 Returns   : Boolean (1 or 0) 
 Argument  : integer (optional)
 Throws    : n/a


 Usage     : $sbjct->strand( [seq_type] );
 Purpose   : Gets the strand(s) for the query, sbjct, or both sequences
           : in the best HSP of the BlastHit object after HSP tiling.
           : Only valid for BLASTN, TBLASTX, BLASTX-query, TBLASTN-hit.
 Example   : $qstrand = $sbjct->strand('query');
           : $sstrand = $sbjct->strand('hit');
           : ($qstrand, $sstrand) = $sbjct->strand();
 Returns   : scalar context: integer '1', '-1', or '0'
           : array context without args: list of two strings (queryStrand, sbjctStrand)
           : Array context can be "induced" by providing an argument of 'list' or 'array'.
 Argument  : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default = 'query')
             ('sbjct' is synonymous with 'hit')
 Throws    : n/a
 Comments  : This method requires that all HSPs be tiled. If they have not
           : already been tiled, they will be tiled first automatically..
           : If you don't want the tiled data, iterate through each HSP
           : calling strand() on each (use hsps() to get all HSPs).
           : Formerly (prior to 10/21/02), this method would return the
           : string "-1/1" for hits with HSPs on both strands.
           : However, now that strand and frame is properly being accounted
           : for during HSP tiling, it makes more sense for strand()
           : to return the strand data for the best HSP after tiling.
           : If you really want to know about hits on opposite strands,
           : you should be iterating through the HSPs using methods on the
           : HSP objects.
           : A possible use case where knowing whether a hit has HSPs 
           : on both strands would be when filtering via SearchIO for hits with 
           : this property. However, in this case it would be better to have a
           : dedicated method such as $hit->hsps_on_both_strands(). Similarly
           : for frame. This could be provided if there is interest.

See Also : Bio::Search::HSP::HSPI::strand()


 Usage     : $hit_object->frame();
 Purpose   : Gets the reading frame for the best HSP after HSP tiling.
           : This is only valid for BLASTX and TBLASTN/X type reports.
 Example   : $frame = $hit_object->frame();
 Returns   : Integer (-2 .. +2)
 Argument  : n/a
 Throws    : Exception if HSPs have not been set.
 Comments  : This method requires that all HSPs be tiled. If they have not
           : already been tiled, they will be tiled first automatically..
           : If you don't want the tiled data, iterate through each HSP
           : calling frame() on each (use hsps() to get all HSPs).

See Also : hsps()


 Usage     : $hit_object->matches( [class] );
 Purpose   : Get the total number of identical or conserved matches 
           : (or both) across all HSPs.
           : (Note: 'conservative' matches are indicated as 'positives' 
           :         in BLAST reports.)
 Example   : ($id,$cons) = $hit_object->matches(); # no argument
           : $id = $hit_object->matches('id');
           : $cons = $hit_object->matches('cons'); 
 Returns   : Integer or a 2-element array of integers 
 Argument  : class = 'id' | 'cons' OR none. 
           : If no argument is provided, both identical and conservative 
           : numbers are returned in a two element list.
           : (Other terms can be used to refer to the conservative
           :  matches, e.g., 'positive'. All that is checked is whether or
           :  not the supplied string starts with 'id'. If not, the 
           : conservative matches are returned.)
 Throws    : Exception if the requested data cannot be obtained.
 Comments  : This method requires that all HSPs be tiled. If there is more than one
           : HSP and they have not already been tiled, they will be tiled first automatically..
           : If you need data for each HSP, use hsps() and then interate
           : through the HSP objects.
           : Does not rely on wantarray to return a list. Only checks for
           : the presence of an argument (no arg = return list).

See Also : Bio::Search::HSP::GenericHSP::matches(), hsps()


 Title          : sort_hsps
 Usage          : $result->sort_hsps(\&sort_function)
 Function       : Sorts the available HSP objects by a user-supplied function. Defaults to sort
                  by descending score.
 Returns        : n/a
 Args           : A coderef for the sort function.  See the documentation on the Perl sort()
                  function for guidelines on writing sort functions.  
 Note           : To access the special variables $a and $b used by the Perl sort() function 
                  the user function must access Bio::Search::Hit::HitI namespace. 
                  For example, use :
                  $hit->sort_hsps( sub{$Bio::Search::Result::HitI::a->length <=> 
                   NOT $hit->sort_hsps($a->length <=> $b->length);

_default sort_hsps

  Title : _default_sort_hsps
  Usage : Do not call directly.
  Function : Sort hsps in ascending order by evalue
  Args  : None
  Returns: 1 on success
  Note  : Used by $hit->sort_hsps()