Bio::Search::Result::HMMERResult.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Search::Result::HMMERResult - A Result object for HMMER results

SYNOPSIS

     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";
     }
 
 

DESCRIPTION

This is a specialization of Bio::Search::Result::GenericResult. There are a few extra methods, specifically sequence_file, hmm_name, next_models, and models.

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:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason@bioperl.org

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::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
 
 

hmm_name

  Title   : hmm_name
  Usage   : $obj->hmm_name($newval)
  Function: Get/Set the value of hmm_name
  Returns : value of hmm_name
  Args    : newvalue (optional)
 
 

sequence_file

  Title   : sequence_file
  Usage   : $obj->sequence_file($newval)
  Function: Get/Set the value of sequence_file
  Returns : value of sequence_file
  Args    : newvalue (optional)
 
 

next_model

  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
 
 

models

  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
 
 

Bio::Search::Result::GenericResult inherited methods

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_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::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
 
 

rewind

  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
 
 

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
 
 

program_reference

  Title   : program_reference
  Usage   : $obj->program_reference($newval)
  Function: 
  Returns : value of the literature reference for the algorithm
  Args    : newvalue (optional)