SYNOPSIS
# MyHandler is a Bio::HandlerBaseI-derived class for dealing with GenBank
# sequence data, derived from a GenBank event-driven parser
# inside a parser (driver) constructor
$self->seqhandler($handler || MyHandler->new(-format => 'genbank'));
# in the driver parsing method ( such as next_seq() ) ...
$handler = $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} }; # code ref
$hobj->$mth($data);
}
DESCRIPTION
This interface describes simple class methods used for processing data from an event-based parser (a driver). This is similar in theme to an XML SAX-based driver but differs in that one can optionally pass related data semi-intelligently as chunks (defined in a hash reference) vs. passing as single data elements in a stream. For instance, any reference-related and species-related data as well as individual sequence features could be passed as chunks of data to be processed in part or as a whole (from Data::Dumper output):Annotation Data (References):
$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 'Unpublished (2003)'
};
Sequence features (source seqfeature):
$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'
};
These would be 'handled' accordingly by methods specified in a HandlerI-based class. The data in a chunk is intentionally left vague here since this may vary from implementation to implementation and can be somewhat open to interpretation. A data chunk in a sequence record, for instance, will be different than a data chunk in a BLAST report. This also allows one the flexibility to pass data as more XML-like small bits, as huge chunks, or even as indexed locations in a file (such as when using a ``pull'' parser, like a Bio::PullParserI).
For an sequence-based implementation see Bio::SeqIO::RichSeq::GenericRichSeqHandler, which handles any GenBank, UniProt, and EMBL data from their respective driver modules (Bio::SeqIO::gbdriver, Bio::SeqIO::swissdriver, and Bio::SeqIO::embldriver).
FEEDBACK
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Reporting Bugs
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https://github.com/bioperl/bioperl-live/issues
AUTHOR - Chris Fields
Email cjfields at bioperl dot orgAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _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.
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
format
Title : format
Usage : $handler->format('GenBank')
$handler->format('BLAST')
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_params({
'-species' => $species,
'-accession_number' => $acc
});
Function: Convenience method used to set specific parameters
Returns : None
Args : Hash ref containing the data to be passed as key-value pairs
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