NAME

Bio::Search::Hit::GenericHit - A generic implementation of the Bio::Search::Hit::HitI interface

SYNOPSIS

use Bio::Search::Hit::GenericHit;
my $hit = new Bio::Search::Hit::GenericHit(-algorithm => 'blastp');

# typically one gets HitI objects from a SearchIO stream via a ResultI
use Bio::SearchIO;
my $parser = new Bio::SearchIO(-format => 'blast', -file => 'result.bls');

my $result = $parser->next_result;
my $hit    = $result->next_hit;

# TODO: Describe how to configure a SearchIO stream so that it generates # GenericHit objects.

DESCRIPTION

This object handles the hit data from a Database Sequence Search such as FASTA or BLAST.

Unless you're writing a parser, you won't ever need to create a GenericHit or any other HitI-implementing object. If you use the SearchIO system, HitI objects are created automatically from a SearchIO stream which returns Bio::Search::Hit::HitI objects.

For documentation on what you can do with GenericHit (and other HitI objects), please see the API documentation in Bio::Search::Hit::HitI.

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

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 - Jason Stajich and Steve Chervitz

Email jason-at-bioperl-dot-org Email sac-at-bioperl-dot-org

CONTRIBUTORS

Sendu Bala, bix@sendu.me.uk

APPENDIX

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

new

Title   : new
Usage   : my $obj = new Bio::Search::Hit::GenericHit();
Function: Builds a new Bio::Search::Hit::GenericHit object 
Returns : Bio::Search::Hit::GenericHit
Args    : -name         => Name of Hit (required)
          -description  => Description (optional)
          -accession    => Accession number (optional)
          -length       => Length of the Hit (optional)
          -score        => Raw Score for the Hit (optional)
          -bits         => Bit Score for the Hit (optional)
          -significance => Significance value for the Hit (optional)
          -algorithm    => Algorithm used (BLASTP, FASTX, etc...)
          -hsps         => Array ref of HSPs for this Hit. 
          -found_again  => boolean, true if hit appears in a 
                           "previously found" section of a PSI-Blast report.
          -hsp_factory  => Bio::Factory::ObjectFactoryI able to create HSPI
                           objects.

add_hsp

Title   : add_hsp
Usage   : $hit->add_hsp($hsp)
Function: Add a HSP to the collection of HSPs for a Hit
Returns : number of HSPs in the Hit
Args    : Bio::Search::HSP::HSPI object, OR hash ref containing data suitable
          for creating a HSPI object (&hsp_factory must be set to get it back)

hsp_factory

Title   : hsp_factory
Usage   : $hit->hsp_factory($hsp_factory)
Function: Get/set the factory used to build HSPI objects if necessary.
Returns : Bio::Factory::ObjectFactoryI
Args    : Bio::Factory::ObjectFactoryI

Bio::Search::Hit::HitI methods

Implementation of Bio::Search::Hit::HitI methods

name

Title   : name
Usage   : $hit_name = $hit->name();
Function: returns the name of the Hit sequence
Returns : a scalar string
Args    : [optional] scalar string to set the name

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

description

Title   : description
Usage   : $desc = $hit->description();
Function: Retrieve the description for the hit
Returns : a scalar string
Args    : [optional] scalar string to set the descrition

length

Title   : length
Usage   : my $len = $hit->length
Function: Returns the length of the hit 
Returns : integer
Args    : [optional] integer to set the length

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    : [optional] scalar string to set the algorithm

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    : [optional] scalar value to set the raw score

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    : [optional] scalar value to set the significance

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 undef if bit score is not set
Argument  : n/a
Comments  : For BLAST1, the non-bit score is listed in the summary line.

next_hsp

Title    : next_hsp
Usage    : while( $hsp = $obj->next_hsp()) { ... }
Function : Returns the next available High Scoring Pair
Example  : 
Returns  : 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 Bio::Search::HSP::BlastHSP.pm 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.

num_hsps

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

rewind

Title   : rewind
Usage   : $hit->rewind;
Function: Allow one to reset the HSP iterator to the beginning
          Since this is an in-memory implementation
Returns : none
Args    : none

ambiguous_aln

Usage     : $ambig_code = $hit_object->ambiguous_aln();
Purpose   : Sets/Gets ambiguity code data member.
Example   : (see usage)
Returns   : String = 'q', 's', 'qs', '-'
          :   'q'  = query sequence contains overlapping sub-sequences 
          :          while sbjct does not.
          :   's'  = sbjct sequence contains overlapping sub-sequences 
          :          while query does not.
          :   'qs' = query and sbjct sequence contains overlapping sub-sequences
          :          relative to each other.
          :   '-'  = query and sbjct sequence do not contains multiple domains 
          :          relative to each other OR both contain the same distribution
          :          of similar domains.
Argument  : n/a
Throws    : n/a
Comment   : Note: "sbjct" is synonymous with "hit"

overlap

See documentation in Bio::Search::Hit::HitI::overlap()

n

Usage     : $hit_object->n();
Purpose   : Gets the N number for the current 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.

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.

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 Bio::Search::HSP::BlastHSP.pm 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.

logical_length

Usage     : $hit_object->logical_length( [seq_type] );
          : (mostly intended for internal use).
Purpose   : Get the logical length of the hit sequence.
          : This is necessary since the number of identical/conserved residues 
          : can be in terms of peptide sequence space, yet the query and/or hit
          : sequence are in nucleotide space.
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  :
          : In the case of BLAST flavors:
          : For TBLASTN reports, the length of the aligned portion of the 
          : nucleotide hit sequence is divided by 3; for BLASTX reports, 
          : the length of the aligned portion of the nucleotide query 
          : sequence is divided by 3. For TBLASTX reports, the length of 
          : both hit and query sequence are converted.
          :
          : 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.

length_aln

Usage     : $hit_object->length_aln( [seq_type] );
Purpose   : Get the total length of the aligned region for query or sbjct seq.
          : This number will include all HSPs
Example   : $len    = $hit_object->length_aln(); # default = query
          : $lenAln = $hit_object->length_aln('query');
Returns   : Integer 
Argument  : seq_Type = 'query' or 'hit' or 'sbjct' (Default = 'query')
            ('sbjct' is synonymous with 'hit')
Throws    : Exception if the argument is not recognized.
Comments  : This method will report the logical length of the alignment,
          : meaning that for TBLAST[NX] reports, the length is reported
          : using amino acid coordinate space (i.e., nucleotides / 3).
          : 
          : 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 length() on each (use hsps() to get all HSPs).

gaps

Usage     : $hit_object->gaps( [seq_type] );
Purpose   : Get the number of gaps in the aligned query, hit, or both sequences.
          : Data is summed across all HSPs.
Example   : $qgaps = $hit_object->gaps('query');
          : $hgaps = $hit_object->gaps('hit');
          : $tgaps = $hit_object->gaps();    # default = total (query + hit)
Returns   : scalar context: integer
          : array context without args: two-element list of integers  
          :    (queryGaps, hitGaps)
          : Array context can be forced by providing an argument of 'list' or 'array'.
          :
          : CAUTION: Calling this method within printf or sprintf is arrray context.
          : So this function may not give you what you expect. For example:
          :          printf "Total gaps: %d", $hit->gaps();
          : Actually returns a two-element array, so what gets printed 
          : is the number of gaps in the query, not the total
          :
Argument  : seq_type: 'query' | 'hit' or 'sbjct' | 'total' | 'list'  (default = 'total')
            ('sbjct' is synonymous with 'hit')
Throws    : n/a
Comments  : If you need data for each HSP, use hsps() and then interate
          : through each HSP object.
          : This method requires that all HSPs be tiled. If they have not
          : already been tiled, they will be tiled first automatically..
          : Not relying on wantarray since that will fail in situations 
          : such as printf "%d", $hit->gaps() in which you might expect to 
          : be printing the total gaps, but evaluates to array context.

matches

See documentation in Bio::Search::Hit::HitI::matches()

start

Usage     : $sbjct->start( [seq_type] );
Purpose   : Gets the start coordinate for the query, sbjct, or both sequences
          : in the BlastHit object. If there is more than one HSP, the lowest start
          : value of all HSPs is returned.
Example   : $qbeg = $sbjct->start('query');
          : $sbeg = $sbjct->start('hit');
          : ($qbeg, $sbeg) = $sbjct->start();
Returns   : scalar context: integer 
          : array context without args: list of two integers (queryStart, sbjctStart)
          : 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 there is more than one
          : HSP and they have not already been tiled, they will be tiled first automatically..
          : Remember that the start and end coordinates of all HSPs are 
          : normalized so that start < end. Strand information can be
          : obtained by calling $hit->strand().

end

Usage     : $sbjct->end( [seq_type] );
Purpose   : Gets the end coordinate for the query, sbjct, or both sequences
          : in the BlastHit object. If there is more than one HSP, 
            the largest end
          : value of all HSPs is returned.
Example   : $qend = $sbjct->end('query');
          : $send = $sbjct->end('hit');
          : ($qend, $send) = $sbjct->end();
Returns   : scalar context: integer
          : array context without args: list of two integers 
          : (queryEnd, sbjctEnd)
          : Array context can be "induced" by providing an argument 
          : of 'list' or 'array'.
Argument  : In scalar context: seq_type = 'query' or 'sbjct'
          :  (case insensitive). If not supplied, 'query' is used.
Throws    : n/a
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..
          : Remember that the start and end coordinates of all HSPs are 
          : normalized so that start < end. Strand information can be
          : obtained by calling $hit->strand().

range

Usage     : $sbjct->range( [seq_type] );
Purpose   : Gets the (start, end) coordinates for the query or sbjct sequence
          : in the HSP alignment.
Example   : ($qbeg, $qend) = $sbjct->range('query');
          : ($sbeg, $send) = $sbjct->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

frac_identical

Usage     : $hit_object->frac_identical( [seq_type] );
Purpose   : Get the overall fraction of identical positions across all HSPs.
          : The number refers to only the aligned regions and does not
          : account for unaligned regions in between the HSPs, if any.
Example   : $frac_iden = $hit_object->frac_identical('query');
Returns   : Float (2-decimal precision, e.g., 0.75).
Argument  : seq_type: 'query' | 'hit' or 'sbjct' | 'total'
          : default = 'query' (but see comments below).
          : ('sbjct' is synonymous with 'hit')
Throws    : n/a
Comments  :
          : To compute the fraction identical, the logical length of the 
          : aligned portion of the sequence is used, meaning that
          : in the case of BLAST flavors, for TBLASTN reports, the length of 
          : the aligned portion of the 
          : nucleotide hit sequence is divided by 3; for BLASTX reports, 
          : the length of the aligned portion of the nucleotide query 
          : sequence is divided by 3. For TBLASTX reports, the length of 
          : both hit and query sequence are converted.
          : This is necessary since the number of identical residues is
          : in terms of peptide sequence space.
          :
          : Different versions of Blast report different values for the total
          : length of the alignment. This is the number reported in the
          : denominators in the stats section:
          : "Identical = 34/120 Positives = 67/120".
          : NCBI BLAST uses the total length of the alignment (with gaps)
          : WU-BLAST uses the length of the query sequence (without gaps).
          :
          : Therefore, when called with an argument of 'total',
          : this method will report different values depending on the
          : version of BLAST used. Total does NOT take into account HSP
          : tiling, so it should not be used.
          :
          : To get the fraction identical among only the aligned residues,
          : ignoring the gaps, call this method without an argument or 
          : with an argument of 'query' or 'hit'.
          :
          : If you need data for each HSP, use hsps() and then iterate
          : through the HSP objects.
          : This method requires that all HSPs be tiled. If they have not
          : already been tiled, they will be tiled first automatically.

frac_conserved

Usage     : $hit_object->frac_conserved( [seq_type] );
Purpose   : Get the overall fraction of conserved positions across all HSPs.
          : The number refers to only the aligned regions and does not
          : account for unaligned regions in between the HSPs, if any.
Example   : $frac_cons = $hit_object->frac_conserved('hit');
Returns   : Float (2-decimal precision, e.g., 0.75).
Argument  : seq_type: 'query' | 'hit' or 'sbjct' | 'total'
          : default = 'query' (but see comments below).
          : ('sbjct' is synonymous with 'hit')
Throws    : n/a
Comments  :
          : To compute the fraction conserved, the logical length of the 
          : aligned portion of the sequence is used, meaning that
          : in the case of BLAST flavors, for TBLASTN reports, the length of 
          : the aligned portion of the 
          : nucleotide hit sequence is divided by 3; for BLASTX reports, 
          : the length of the aligned portion of the nucleotide query 
          : sequence is divided by 3. For TBLASTX reports, the length of 
          : both hit and query sequence are converted.
          : This is necessary since the number of conserved residues is
          : in terms of peptide sequence space.
          :
          : Different versions of Blast report different values for the total
          : length of the alignment. This is the number reported in the
          : denominators in the stats section:
          : "Positives = 34/120 Positives = 67/120".
          : NCBI BLAST uses the total length of the alignment (with gaps)
          : WU-BLAST uses the length of the query sequence (without gaps).
          :
          : Therefore, when called with an argument of 'total',
          : this method will report different values depending on the
          : version of BLAST used. Total does NOT take into account HSP
          : tiling, so it should not be used.
          :
          : To get the fraction conserved among only the aligned residues,
          : ignoring the gaps, call this method without an argument or 
          : with an argument of 'query' or 'hit'.
          :
          : If you need data for each HSP, use hsps() and then interate
          : through the HSP objects.
          : This method requires that all HSPs be tiled. If they have not
          : already been tiled, they will be tiled first automatically.

frac_aligned_query

Usage     : $hit_object->frac_aligned_query();
Purpose   : Get the fraction of the query sequence which has been aligned
          : across all HSPs (not including intervals between non-overlapping
          : HSPs).
Example   : $frac_alnq = $hit_object->frac_aligned_query();
Returns   : Float (2-decimal precision, e.g., 0.75).
Argument  : n/a
Throws    : n/a
Comments  : If you need data for each HSP, use hsps() and then interate
          : through the HSP objects.
          : This method requires that all HSPs be tiled. If they have not
          : already been tiled, they will be tiled first automatically.

frac_aligned_hit

Usage     : $hit_object->frac_aligned_hit();
Purpose   : Get the fraction of the hit (sbjct) sequence which has been aligned
          : across all HSPs (not including intervals between non-overlapping
          : HSPs).
Example   : $frac_alnq = $hit_object->frac_aligned_hit();
Returns   : Float (2-decimal precision, e.g., 0.75).
Argument  : n/a
Throws    : n/a
Comments  : If you need data for each HSP, use hsps() and then interate
          : through the HSP objects.
          : This method requires that all HSPs be tiled. If they have not
          : already been tiled, they will be tiled first automatically.

frac_aligned_sbjct

Same as frac_aligned_hit()

num_unaligned_sbjct

Same as num_unaligned_hit()

num_unaligned_hit

Usage     : $hit_object->num_unaligned_hit();
Purpose   : Get the number of the unaligned residues in the hit sequence.
          : Sums across all all HSPs.
Example   : $num_unaln = $hit_object->num_unaligned_hit();
Returns   : Integer
Argument  : n/a
Throws    : n/a
Comments  : See notes regarding logical lengths in the comments for frac_aligned_hit().
          : They apply here as well.
          : If you need data for each HSP, use hsps() and then interate
          : through the HSP objects.
          : This method requires that all HSPs be tiled. If they have not
          : already been tiled, they will be tiled first automatically..

num_unaligned_query

Usage     : $hit_object->num_unaligned_query();
Purpose   : Get the number of the unaligned residues in the query sequence.
          : Sums across all all HSPs.
Example   : $num_unaln = $hit_object->num_unaligned_query();
Returns   : Integer
Argument  : n/a
Throws    : n/a
Comments  : See notes regarding logical lengths in the comments for frac_aligned_query().
          : They apply here as well.
          : If you need data for each HSP, use hsps() and then interate
          : through the HSP objects.
          : This method requires that all HSPs be tiled. If they have not
          : already been tiled, they will be tiled first automatically..

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.

strand

See documentation in Bio::Search::Hit::HitI::strand()

frame

See documentation in Bio::Search::Hit::HitI::frame()

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)

locus

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

each_accession_number

Title   : each_accession_number
Usage   : @each_accession_number = $hit->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

See documentation in Bio::Search::SearchUtils::tile_hsps()

query_length

Title   : query_length
Usage   : $obj->query_length($newval)
Function: Get/Set the query_length
Returns : value of query_length (a scalar)
Args    : on set, new value (a scalar or undef, optional)

To install Bio::Seq, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::Seq

CPAN shell

perl -MCPAN -e shell
install Bio::Seq

For more information on module installation, please visit the detailed CPAN module installation guide.

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