Bio::Search::Hit::HitI.3pm

Langue: en

Version: 2008-06-24 (ubuntu - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Search::Hit::HitI - Interface for a hit in a similarity search result

SYNOPSIS

# 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 = new Bio::SearchIO(-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
 
 

DESCRIPTION

     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.
 
 

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 one of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the web:

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

AUTHOR - Aaron Mackey, Steve Chervitz

Email amackey@virginia.edu (original author) Email sac@bioperl.org Copyright (c) 1999-2001 Aaron Mackey, Steve Chervitz. 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 _

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()