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 listsReporting 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://bugzilla.bioperl.org/ 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/anext_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 : Noneavailable_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 : noneget_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 : noneto_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 : Nonedatabase_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 dbdatabase_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 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 stringsno_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 determining 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)