Bio::Search::Result::BlastResult - A top-level BLAST Report object
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.
This module supports BLAST versions 1.x and 2.x, gapped and ungapped, and PSI-BLAST.
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:
Encapsulates a single a single BLAST hit.
Provides an interface to a blast database metadata.
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
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/
Steve Chervitz <sac@bioperl.org>
See the FEEDBACK section for where to send bug reports and comments.
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 (c) 2001 Steve Chervitz. All Rights Reserved.
This software is provided "as is" without warranty of any kind.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
See Bio::Search::Result::ResultI::next_hit() for documentation
See Bio::Search::Result::ResultI::query_name() for documentation
See Bio::Search::Result::ResultI::query_length() for documentation
See Bio::Search::Result::ResultI::query_description() for documentation
See Bio::AnalysisResultI::analysis_method() for documentation
This implementation ensures that the name matches /blast/i.
See Bio::AnalysisResultI::analysis_method_version() for documentation
See Bio::AnalysisResultI::analysis_query() for documentation
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
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
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
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)
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)
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
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
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
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
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().
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.
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').
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
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.
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)
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)
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)
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.