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

🎀 NAME 🎀

Okay bestie, welcome to Bio::SeqIO::Handler::GenericRichSeqHandler — a Bio::HandlerI-based data handler for GenBank, EMBL, UniProt and honestly whatever other sequence data you wanna throw at it 💖 (this page lives in User Contributed Perl Documentation, section 3pm, iykyk).

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✨ SYNOPSIS ✨

  # MyHandler is a GenericRichSeqHandler object.
  # inside a parser (driver) constructor....

  $self->seq_handler($handler || MyHandler->new(-format => 'genbank'));

  # in next_seq() in driver...

  $hobj = $self->seqhandler();

  # roll data up into hashref chunks, pass off into Handler for processing...

  $hobj->data_handler($data);

  # or retrieve Handler methods and pass data directly to Handler methods...

  my $hmeth = $hobj->handler_methods;

  if ($hmeth->{ $data->{NAME} }) {
      my $mth = $hmeth->{ $data->{NAME} };
      $hobj->$mth($data);
  }

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💖 DESCRIPTION 💖

So. This is an experimental implementation of a sequence-based HandlerBaseI parser, and it may change over time. It is possible (nay, likely) that the way handler methods are set up will change over development to allow more flexibility. Release pumpkins, please do not add this to a release until the API has settled. It is also likely that write_seq() will not work properly for some data. 🫠

Standard Developer caveats, babes:

Do not use for production purposes. Not responsible for destroying (your data|computer|world). Do not stare directly at GenericRichSeqHandler. If GenericRichSeqHandler glows, back slowly away and call for help. 😭

Consider yourself warned! 💀

This class acts as a demonstration on how to handle similar data chunks derived from Bio::SeqIO::gbdriver, Bio::SeqIO::embldriver, and Bio::SeqIO::swissdriver using similar (or the same) handler methods. No cap.

The modules currently pass all previous tests in t/genbank.t, t/embl.t, and t/swiss.t yet all use the same handler methods (the collected tests for handlers can be found in t/Handler.t). Some tweaking of the methods themselves is probably in order over the long run to ensure that data is consistently handled for each parser. Round-trip tests are probably in order here... 👀

Though a Bio::Seq::SeqBuilder is employed for building sequence objects no bypassing of data based on builder slots has been implemented (yet); this is planned in the near future.

As a reminder: this is the current Annotation data chunk (via Data::Dumper):

  $VAR1 = {
            'NAME' => 'REFERENCE',
            'DATA' => '1  (bases 1 to 10001)'
            'AUTHORS' => 'International Human Genome Sequencing Consortium.'
            'TITLE' => 'The DNA sequence of Homo sapiens'
            'JOURNAL' => 'Unpublished (2003)'
          };
  ...

This is the current SeqFeature data chunk (again via Data::Dumper):

  $VAR1 = {
            'mol_type' => 'genomic DNA',
            'LOCATION' => '<1..>10001',
            'NAME' => 'FEATURES',
            'FEATURE_KEY' => 'source',
            'note' => 'Accession AL451081 sequenced by The Sanger Centre',
            'db_xref' => 'taxon:9606',
            'clone' => 'RP11-302I18',
            'organism' => 'Homo sapiens'
          };

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📬 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 one of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

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👑 AUTHOR - Chris Fields 👑

Email cjfields at bioperl dot org — shoutout to the icon himself ✨

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📎 APPENDIX 📎

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ .

🆕 new

• Title: new
• Usage:
• Function:
• Returns:
• Args: -format — Sequence format to be mapped for handler methods -builder — Bio::Seq::SeqBuilder object (normally defined in SequenceStreamI object implementation constructor)
• Throws: On undefined '-format' sequence format parameter
• Note: Still under heavy development

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🧬 Bio::HandlerBaseI implementing methods 🧬

handler_methods

• Title: handler_methods
• Usage: $handler->handler_methods('GenBank') %handlers = $handler->handler_methods();
• Function: Retrieve the handler methods used for the current format() in the handler. This assumes the handler methods are already described in the HandlerI-implementing class.
• Returns: a hash reference with the data type handled and the code ref associated with it.
• Args: [optional] String representing the sequence format. If set here this will also set sequence_format()
• Throws: On unimplemented sequence format in %HANDLERS

data_handler

• Title: data_handler
• Usage: $handler->data_handler($data)
• Function: Centralized method which accepts all data chunks, then distributes to the appropriate methods for processing based on the chunk name from within the HandlerBaseI object.

One can also use

• Returns: None
• Args: an hash ref containing a data chunk.

reset_parameters

• Title: reset_parameters
• Usage: $handler->reset_parameters()
• Function: Resets the internal cache of data (normally object parameters for a builder or factory)
• Returns: None
• Args: None

format

• Title: format
• Usage: $handler->format('GenBank')
• Function: Get/Set the format for the report/record being parsed. This can be used to set handlers in classes which are capable of processing similar data chunks from multiple driver modules.
• Returns: String with the sequence format
• Args: [optional] String with the sequence format
• Note: The format may be used to set the handlers (as in the current GenericRichSeqHandler implementation)

get_params

• Title: get_params
• Usage: $handler->get_params('-species')
• Function: Convenience method used to retrieve the specified parameters from the internal parameter cache
• Returns: Hash ref containing parameters requested and data as key-value pairs. Note that some parameter values may be objects, arrays, etc.
• Args: List (array) representing the parameters requested

set_params

• Title: set_params
• Usage: $handler->set_param({'-species')
• Function: Convenience method used to set specific parameters
• Returns: None
• Args: Hash ref containing the data to be passed as key-value pairs

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🌟 Methods unique to this implementation 🌟

seqbuilder

• Title: seqbuilder
• Usage:
• Function:
• Returns:
• Args:
• Throws:
• Note:

build_sequence

• Title: build_sequence
• Usage:
• Function:
• Returns:
• Args:
• Throws:
• Note:

location_factory

• Title: location_factory
• Usage:
• Function:
• Returns:
• Args:
• Throws:
• Note:

annotation_collection

• Title: annotation_collection
• Usage:
• Function:
• Returns:
• Args:
• Throws:
• Note:

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aaaand that's the whole page bestie 💖 this one shipped with perl v5.32.1 back on 2021-08-15, so if you're reading it in a group chat from the future, that's the tea 🫶✨ periodt.