Bio::SeqIO::Handler::GenericRichSeqHandler(3pm)

NAME

Bio::SeqIO::Handler::GenericRichSeqHandler - Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data

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);
  }

DESCRIPTION

This is an experimental implementation of a sequence-based HandlerBaseI parser and 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:

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.

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'
          };

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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

AUTHOR - Chris Fields

Email cjfields at bioperl dot org

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

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

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    :