Bio::SeqIO::Handler::GenericRichSeqHandler(3pm) User Contributed Perl Documentation 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 'Unpublished(2003)'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.
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://redmine.open-bio.org/projects/bioperl/
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 :
perl v5.14.2 2012-03-02 Bio::SeqIO::Handler::GenericRichSeqHandler(3pm)