SYNOPSIS
# MyHandler is a GenericAlignHandler object.
# inside a parser (driver) constructor....
$self->alignhandler($handler || MyHandler->new(-format => 'stockholm'));
# in next_aln() in driver...
$hobj = $self->alignhandler();
# 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 alignment-based HandlerBaseI parser and may change over time. It is possible that the way handler methods are set up will change over development to allow more flexibility.Standard Developer caveats:
Here thar be dragoons...
Consider yourself warned!
NOTES
As in the SeqIO Handler object (still in development), data is passed in as chunks. The Annotation and SeqFeatures are essentially the same as the SeqIO parser; the significant difference is that data hash being passed could pertain to either the alignment or to a specific sequence, so an extra tag may be needed to disambiguate between the two in some cases. Here I use the ALIGNMENT tag as a boolean flag: it must be present and set to 0 for the data to be tagged for Bio::LocatableSeq or similar (in all other cases it is assumed to be for the alignment). In some cases this will not matter (the actual sequence data, for instance) but it is highly recommmended adding this tag in to prevent possible ambiguities.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 'Unpublished (2003)'
'ALIGNMENT' => 1,
};
In the case of LocatableSeqs, one can pass them in as follows for simplicity (note the block line):
$VAR1 = {
'NAME' => 'SEQUENCE',
'BLOCK_LINE' => 0,
'NSE' => 'Q7WNI7_BORBR/113-292',
'ALPHABET' => 'protein',
'DATA' => 'VALILGVYRRL...CYVNREM..RAG....QW',
'ALIGNMENT' => 0
};
This can be done as the parser parses each block instead of parsing all the blocks and then passing them in one at a time; the handler will store the sequence data by the block line in an internal hash, concatenating them along the way. This behaviour is b/c the alignment building step requires that the sequence be checked for start/end/strand, possible meta sequence, optional accession, etc.
Similarly, a Meta sequence line can be passed in as follows:
$VAR1 = {
'NAME' => 'NAMED_META',
'BLOCK_LINE' => 0,
'NSE' => 'Q7WNI7_BORBR/113-292',
'META_KEY' => 'pAS',
'DATA' => '................................',
'ALIGNMENT' => 0
};
The meta sequence will be checked against the NSE for the block position and stored based on the meta tag. A meta sequence does not have to correspond to a real sequence. At this time, unique meta sequence tags must be used for each sequence or they will be overwritten (this may change).
An alignment consensus string:
$VAR1 = {
'NAME' => 'CONSENSUS',
'DATA' => 'VALILGVYRRL...CYVNREM..RAG....QW',
'ALIGNMENT' => 1
};
A consensus meta sequence:
$VAR1 = {
'NAME' => 'CONSENSUS_META',
'META_KEY' => 'pAS',
'DATA' => '................................',
'ALIGNMENT' => 1
};
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: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 orgAPPENDIX
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({'-seqs' => $seqs})
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
build_alignment
Title : build_alignment Usage : Function: Returns : a Bio::SimpleAlign Args : Throws : Note : This may be replaced by a Builder object at some point
annotation_collection
Title : annotation_collection Usage : Function: Returns : Args : Throws : Note :
seq_annotation_collection
Title : seq_annotation_collection Usage : Function: Returns : Args : Throws : Note :
process_seqs
Title : process_seqs
Usage : $handler->process_seqs;
Function: checks internal sequences to ensure they are converted over
to the proper Bio::AlignI-compatible sequence class
Returns : 1 if successful
Args : none