| Bio::Search::Result::HMMERResult(3pm) | User Contributed Perl Documentation | Bio::Search::Result::HMMERResult(3pm) |
Bio::Search::Result::HMMERResult - A Result object for HMMER results
use Bio::Search::Result::HMMERResult;
my $result = Bio::Search::Result::HMMERResult->new
( -hmm_name => 'pfam',
-sequence_file => 'roa1.pep',
-hits => \@hits);
# generally we use Bio::SearchIO to build these objects
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'hmmer',
-file => 'result.hmmer');
while( my $result = $in->next_result ) {
print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n";
}
This is a specialization of Bio::Search::Result::GenericResult. There are a few extra methods, specifically sequence_file, hmm_name, next_models, and models.
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
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.
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:
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Email jason@bioperl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new
Usage : my $obj = Bio::Search::Result::HMMERResult->new();
Function: Builds a new Bio::Search::Result::HMMERResult object
Returns : Bio::Search::Result::HMMERResult
Args : -hmm_name => string, name of hmm file
-sequence_file => name of the sequence file
plus Bio::Search::Result::GenericResult parameters
-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
-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)
-program_reference => literature reference string for this algorithm
Title : hmm_name Usage : $obj->hmm_name($newval) Function: Get/Set the value of hmm_name Returns : value of hmm_name Args : newvalue (optional)
Title : sequence_file Usage : $obj->sequence_file($newval) Function: Get/Set the value of sequence_file Returns : value of sequence_file Args : newvalue (optional)
Title : next_model
Usage : my $domain = $result->next_model
Function: Returns the next domain - this
is an alias for next_hit
Returns : L<Bio::Search::Hit::HitI> object
Args : none
Title : models
Usage : my @domains = $result->models;
Function: Returns the list of HMM models seen - this
is an alias for hits()
Returns : Array of L<Bio::Search::Hit::HitI> objects
Args : none
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
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 implementation
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
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
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
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
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
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
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
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 : 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 : 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_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 : 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
Title : rewind
Usage : $result->rewind;
Function: Allow one to reset the Hit iteration to the beginning
Since this is an in-memory implementation
Returns : none
Args : none
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
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
Title : num_hits Usage : my $hitcount= $result->num_hits Function: returns the number of hits for this query result Returns : integer Args : none
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
Title : program_reference Usage : $obj->program_reference($newval) Function: Returns : value of the literature reference for the algorithm Args : newvalue (optional)
| 2019-10-29 | perl v5.30.0 |