Bio::AlignIO::Handler::GenericAlignHandler(3)

NAME
Bio::AlignIO::Handler::GenericAlignHandler - Bio::HandlerI-based generic data handler class for alignment-based data

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 'Unpublished (2003)'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.

  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

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({'-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