NAME¶
Bio::Search::Result::GenericResult - Generic Implementation of
Bio::Search::Result::ResultI interface applicable to most search results.
SYNOPSIS¶
# typically one gets Results from a SearchIO stream
use Bio::SearchIO;
my $io = Bio::SearchIO->new(-format => 'blast',
-file => 't/data/HUMBETGLOA.tblastx');
while( my $result = $io->next_result ) {
# process all search results within the input stream
while( my $hit = $result->next_hit ) {
# insert code here for hit processing
}
}
use Bio::Search::Result::GenericResult;
my @hits = (); # would be a list of Bio::Search::Hit::HitI objects
# typically these are created from a Bio::SearchIO stream
my $result = Bio::Search::Result::GenericResult->new
( -query_name => 'HUMBETGLOA',
-query_accession => ''
-query_description => 'Human haplotype C4 beta-globin gene, complete cds.'
-query_length => 3002
-database_name => 'ecoli.aa'
-database_letters => 4662239,
-database_entries => 400,
-parameters => { 'e' => '0.001' },
-statistics => { 'kappa' => 0.731 },
-algorithm => 'blastp',
-algorithm_version => '2.1.2',
);
my $id = $result->query_name();
my $desc = $result->query_description();
my $name = $result->database_name();
my $size = $result->database_letters();
my $num_entries = $result->database_entries();
my $gap_ext = $result->get_parameter('e');
my @params = $result->available_parameters;
my $kappa = $result->get_statistic('kappa');
my @statnames = $result->available_statistics;
# TODO: Show how to configure a SearchIO stream so that it generates #
GenericResult objects.
DESCRIPTION¶
This object is an implementation of the Bio::Search::Result::ResultI interface
and provides a generic place to store results from a sequence database search.
Unless you're writing a parser, you won't ever need to create a GenericResult or
any other ResultI-implementing object. If you use the SearchIO system, ResultI
objects are created automatically from a SearchIO stream which returns
Bio::Search::Result::ResultI objects.
For documentation on what you can do with GenericResult (and other ResultI
objects), please see the API documentation in Bio::Search::Result::ResultI.
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
Support¶
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive
experts will be able look at the problem and quickly address it. Please
include a thorough description of the problem with code and data examples if
at all possible.
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:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Jason Stajich and Steve Chervitz¶
Email jason@bioperl.org Email sac@bioperl.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 = Bio::Search::Result::GenericResult->new();
Function: Builds a new Bio::Search::Result::GenericResult object
Returns : Bio::Search::Result::GenericResult
Args : -query_name => Name of query Sequence
-query_accession => Query accession number (if available)
-query_description => Description of query sequence
-query_length => Length of query sequence
-database_name => Name of database
-database_letters => Number of residues in database
-database_entries => Number of entries in database
-hits => array ref of Bio::Search::Hit::HitI objects
-parameters => hash ref of search parameters (key => value)
-statistics => hash ref of search statistics (key => value)
-algorithm => program name (blastx)
-algorithm_version => version of the algorithm (2.1.2)
-algorithm_reference => literature reference string for this algorithm
-rid => value of the BLAST Request ID (eg. RID: ZABJ4EA7014)
-hit_factory => Bio::Factory::ObjectFactoryI capable of making
Bio::Search::Hit::HitI objects
algorithm¶
Title : algorithm
Usage : my $r_type = $hsp->algorithm
Function: Obtain the name of the algorithm used to obtain the Result
Returns : string (e.g., BLASTP)
Args : [optional] scalar string to set value
algorithm_version¶
Title : algorithm_version
Usage : my $r_version = $hsp->algorithm_version
Function: Obtain the version of the algorithm used to obtain the Result
Returns : string (e.g., 2.1.2)
Args : [optional] scalar string to set algorithm version value
Bio::Search::Result::ResultI interface methods¶
Bio::Search::Result::ResultI implementation
next_hit¶
Title : next_hit
Usage : while( $hit = $result->next_hit()) { ... }
Function: Returns the next available Hit object, representing potential
matches between the query and various entities from the database.
Returns : a Bio::Search::Hit::HitI object or undef if there are no more.
Args : none
query_name¶
Title : query_name
Usage : $id = $result->query_name();
Function: Get the string identifier of the query used by the
algorithm that performed the search.
Returns : a string.
Args : [optional] new string value for query name
query_accession¶
Title : query_accession
Usage : $id = $result->query_accession();
Function: Get the accession (if available) for the query sequence
Returns : a string
Args : [optional] new string value for accession
query_gi¶
Title : query_gi
Usage : $acc = $hit->query_gi();
Function: Retrieve the NCBI Unique ID (aka the GI #),
if available, for the query
Returns : a scalar string (empty string if not set)
Args : none
query_length¶
Title : query_length
Usage : $id = $result->query_length();
Function: Get the length of the query sequence
used in the search.
Returns : a number
Args : [optional] new integer value for query length
query_description¶
Title : query_description
Usage : $id = $result->query_description();
Function: Get the description of the query sequence
used in the search.
Returns : a string
Args : [optional] new string for the query description
database_name¶
Title : database_name
Usage : $name = $result->database_name()
Function: Used to obtain the name of the database that the query was searched
against by the algorithm.
Returns : a scalar string
Args : [optional] new string for the db name
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
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
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)
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_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
Bio::Search::Report¶
Bio::Search::Result::GenericResult specific methods
add_hit¶
Title : add_hit
Usage : $report->add_hit($hit)
Function: Adds a HitI to the stored list of hits
Returns : Number of HitI currently stored
Args : Bio::Search::Hit::HitI
hit_factory¶
Title : hit_factory
Usage : $hit->hit_factory($hit_factory)
Function: Get/set the factory used to build HitI objects if necessary.
Returns : Bio::Factory::ObjectFactoryI
Args : Bio::Factory::ObjectFactoryI
rewind¶
Title : rewind
Usage : $result->rewind;
Function: Allow one to reset the Hit iterator to the beginning
Since this is an in-memory implementation
Returns : none
Args : none
_nexthitindex¶
Title : _nexthitindex
Usage : private
add_parameter¶
Title : add_parameter
Usage : $report->add_parameter('gapext', 11);
Function: Adds a parameter
Returns : none
Args : key - key value name for this parama
value - value for this parameter
add_statistic¶
Title : add_statistic
Usage : $report->add_statistic('lambda', 2.3);
Function: Adds a parameter
Returns : none
Args : key - key value name for this parama
value - value for this parameter
num_hits¶
Title : num_hits
Usage : my $hitcount= $result->num_hits
Function: returns the number of hits for this query result
Returns : integer
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
algorithm_reference¶
Title : algorithm_reference
Usage : $obj->algorithm_reference($newval)
Function:
Returns : string containing literature reference for the algorithm
Args : newvalue string (optional)
Comments: Formerly named program_reference(), which is still supported
for backwards compatibility.
program_reference¶
Title : program_reference
Usage : $obj->program_reference()
Function:
Returns : string containing literature reference for the algorithm
Args :
Comments: Deprecated - use algorithm_reference() instead.
rid¶
Title : rid
Usage : $obj->rid($newval)
Function:
Returns : value of the BLAST Request ID (eg. RID: ZABJ4EA7014)
Args : newvalue (optional)
Comments: The default implementation in ResultI returns an empty string
rather than throwing a NotImplemented exception, since
the RID may not always be available and is not critical.
See: (1) http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/BLAST/rid.html
(2) http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node63.html
no_hits_found¶
See documentation in
Bio::Search::Result::ResultI::no_hits_found()
set_no_hits_found¶
See documentation in
Bio::Search::Result::ResultI::set_no_hits_found()
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:
[GenericResult] <analysis_method> query=<name> <description> db=<database
e.g.:
[GenericResult] BLASTP query=YEL060C vacuolar protease B, db=PDBUNIQ
Args : None