Ewan Birney

NAME

Bio::Search::Result::BlastResult - A top-level BLAST Report object

SYNOPSIS

The construction of BlastResult objects is performed by by the Bio::SearchIO::psiblast parser. Therefore, you do not need to use Bio::Search::Result::BlastResult) directly. If you need to construct BlastHits directly, see the new() function for details.

For Bio::SearchIO BLAST parsing usage examples, see the examples/search-blast directory of the Bioperl distribution.

DESCRIPTION

This module supports BLAST versions 1.x and 2.x, gapped and ungapped, and PSI-BLAST.

DEPENDENCIES

Bio::Search::Result::BlastResult.pm is a concrete class that inherits from Bio::Root::Root and Bio::Search::Result::ResultI. It relies on two other modules:

Bio::Search::Hit::BlastHit

Encapsulates a single a single BLAST hit.

Bio::Search::GenericDatabase

Provides an interface to a blast database metadata.

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://bio.perl.org/MailList.html  - 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 email or the web:

    bioperl-bugs@bio.perl.org                   
    http://bio.perl.org/bioperl-bugs/           

AUTHOR

Steve Chervitz <sac@bioperl.org>

See the FEEDBACK section for where to send bug reports and comments.

ACKNOWLEDGEMENTS

This software was originally developed in the Department of Genetics at Stanford University. I would also like to acknowledge my colleagues at Affymetrix for useful feedback.

COPYRIGHT

Copyright (c) 2001 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 _

next_hit

See Bio::Search::Result::ResultI::next_hit() for documentation

query_name

See Bio::Search::Result::ResultI::query_name() for documentation

query_length

See Bio::Search::Result::ResultI::query_length() for documentation

query_description

See Bio::Search::Result::ResultI::query_description() for documentation

analysis_method

See Bio::AnalysisResultI::analysis_method() for documentation

This implementation ensures that the name matches /blast/i.

analysis_method_version

See Bio::AnalysisResultI::analysis_method_version() for documentation

analysis_query

See Bio::AnalysisResultI::analysis_query() for documentation

analysis_subject

 Usage     : $blastdb = $result->analyis_subject();
 Purpose   : Get a Bio::Search::DatabaseI object containing
             information about the database used in the BLAST analysis.
 Returns   : Bio::Search::DatabaseI object.
 Argument  : n/a

next_feature

 Title   : next_feature
 Usage   : while( my $feat = $blast_result->next_feature ) { # do something }
 Function: Returns the next feature available in the analysis result, or
           undef if there are no more features.
 Example :
 Returns : A Bio::SeqFeatureI compliant object, in this case, 
           each Bio::Search::HSP::BlastHSP object within each BlastHit.
 Args    : None

to_string

 Title   : to_string
 Usage   : print $blast->to_string;
 Function: Returns a string representation for the Blast result. 
           Primarily intended for debugging purposes.
 Example : see usage
 Returns : A string of the form:
           [BlastResult] <analysis_method> query=<name> <description> db=<database
           e.g.:
           [BlastResult] BLASTP query=YEL060C vacuolar protease B, db=PDBUNIQ 
 Args    : None

hits

 Title   : hits
 Usage   : my @hits = $result->hits
 Function: Returns the available hits for this Result
 Returns : Array of L<Bio::Search::Hit::HitI> objects
 Args    : none

add_hit

 Usage     : $blast->add_hit( $hit );
 Purpose   : Adds a hit object to the collection of hits in this BLAST result.
 Returns   : n/a
 Argument  : A Bio::Search::Hit::HitI object
 Comments  : For PSI-BLAST, hits from all iterations are lumped together.
             For any given hit, you can determine the iteration in which it was
             found by checking $hit->iteration().

is_signif

 Usage     : $blast->is_signif();
 Purpose   : Determine if the BLAST report contains significant hits.
 Returns   : Boolean
 Argument  : n/a
 Comments  : BLAST reports without significant hits but with defined
           : significance criteria will throw exceptions during construction.
           : This obviates the need to check significant() for
           : such objects.

matrix

 Usage     : $blast_object->matrix();
 Purpose   : Get the name of the scoring matrix used.
           : This is extracted from the report.
 Argument  : n/a
 Returns   : string or undef if not defined
 Comments  : TODO: Deprecate this and implement get_parameter('matrix').

raw_statistics

 Usage     : @stats = $blast_result->raw_statistics();
 Purpose   : Get the raw, unparsed statistical parameter section of the Blast report.
             This is the section at the end after the last HSP alignment.
 Argument  : n/a
 Returns   : Array of strings

no_hits_found

 Usage     : $nohits = $blast->no_hits_found( [iteration_number] ); 
 Purpose   : Get boolean indicator indicating whether or not any hits
             were present in the report.

             This is NOT the same as deteriming the number of hits via
             the hits() method, which will return zero hits if there were no
             hits in the report or if all hits were filtered out during the parse.

             Thus, this method can be used to distinguish these possibilities
             for hitless reports generated when filtering.

 Returns   : Boolean
 Argument  : (optional) integer indicating the iteration number (PSI-BLAST)
             If iteration number is not specified and this is a PSI-BLAST result,
             then this method will return true only if all iterations had
             no hits found.

set_no_hits_found

 Usage     : $blast->set_no_hits_found( [iteration_number] ); 
 Purpose   : Set boolean indicator indicating whether or not any hits
             were present in the report.
 Returns   : n/a
 Argument  : (optional) integer indicating the iteration number (PSI-BLAST)

iterations

 Usage     : $num_iterations = $blast->iterations;  (get)
             $blast->iterations($num_iterations);   (set)
 Purpose   : Set/get the number of iterations in the Blast Report (PSI-BLAST).
 Returns   : Total number of iterations in the report
 Argument  : integer  (when setting)

psiblast

 Usage     : if( $blast->psiblast ) { ... }
 Purpose   : Set/get a boolean indicator whether or not the report 
             is a PSI-BLAST report.
 Returns   : 1 if PSI-BLAST, undef if not.
 Argument  : 1 (when setting)

database_entries

 Title   : database_entries
 Usage   : $num_entries = $result->database_entries()
 Function: Used to obtain the number of entries contained in the database.
 Returns : a scalar integer representing the number of entities in the database
           or undef if the information was not available.
 Args    : [optional] new integer for the number of sequence entries in the db

database_letters

 Title   : database_letters
 Usage   : $size = $result->database_letters()
 Function: Used to obtain the size of database that was searched against.
 Returns : a scalar integer (units specific to algorithm, but probably the
           total number of residues in the database, if available) or undef if
           the information was not available to the Processor object.
 Args    : [optional] new scalar integer for number of letters in db 

available_parameters

 Title   : available_parameters
 Usage   : my @params = $report->available_paramters
 Function: Returns the names of the available parameters
 Returns : Return list of available parameters used for this report
 Args    : none

get_parameter

 Title   : get_parameter
 Usage   : my $gap_ext = $report->get_parameter('gapext')
 Function: Returns the value for a specific parameter used
           when running this report
 Returns : string
 Args    : name of parameter (string)

get_statistic

 Title   : get_statistic
 Usage   : my $gap_ext = $report->get_statistic('kappa')
 Function: Returns the value for a specific statistic available 
           from this report
 Returns : string
 Args    : name of statistic (string)

available_statistics

 Title   : available_statistics
 Usage   : my @statnames = $report->available_statistics
 Function: Returns the names of the available statistics
 Returns : Return list of available statistics used for this report
 Args    : none