The rest of the documentation details each of the object methods. Internal methods are usually preceded
with a _
name
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.
description
Title : description
Usage : $desc = $hit->description();
Function: Retrieve the description for the hit
Returns : a scalar string
Args : none
accession
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
locus
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
length
Title : length
Usage : my $len = $hit->length
Function: Returns the length of the hit
Returns : integer
Args : none
algorithm
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
raw_score
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
score
Equivalent to raw_score()significance
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
bits
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()next_hsp
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
hsps
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()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()seq_inds
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()rewind
Title : rewind
Usage : $hit->rewind;
Function: Allow one to reset the HSP iterator to the beginning
if possible
Returns : none
Args : none
overlap
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
n
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()p
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()hsp
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()
logical_length
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()rank
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)
each_accession_number
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
tiled_hsps
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
strand
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()
frame
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()matches
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()sort_hits
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 <=>
$Bio::Search::Result::HitI::b->length});
NOT $hit->sort_hsps($a->length <=> $b->length);
_defaultsort_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()
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