Bio::S...Result(3pm)

📦
version 1.7.3 · 2 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💖 NAME 💖

okay bestie, so this is Bio::S...Result — the perl manual page for Bio::Search::Result::HMMERResult, and it lives in the User Contributed Perl Documentation, section 3pm. it's a Result object for HMMER results, and yes it ate 💅

✨ 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 — like, it's the glow-up version 💖. there are a few extra methods it brings to the party, specifically sequence_file, hmm_name, next_models, and models. no cap.

🫶 FEEDBACK 🫶

📬 Mailing Lists

user feedback is literally 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, fr fr.

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 👑

email jason@bioperl.org — the icon behind it all 💅

📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _. iykyk.

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: (no function description given, bestie — it's just vibes)
  • Returns: value of the literature reference for the algorithm
  • Args: newvalue (optional)
🎀 and that's a wrap! this page came to you courtesy of perl v5.30.0, dated 2019-10-29, from the Bio::S...Result(3pm) manual. slay, periodt 💖✨
📦 where this page comes from