Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::SeqIO::gbdriver - GenBank handler-based push parser

SYNOPSIS

         #It is probably best not to use this object directly, but
         #rather go through the SeqIO handler:

         $stream = Bio::SeqIO->new(-file => $filename,
                                   -format => 'gbdriver');

         while ( my $seq = $stream->next_seq() ) {
             # do something with $seq
         }

DESCRIPTION

       This object can transform Bio::Seq objects to and from GenBank flat file databases. The
       key difference between this parser and the tried-and-true Bio::SeqIO::genbank parser is
       this version separates the parsing and data manipulation into a 'driver' method (next_seq)
       and separate object handlers which deal with the data passed to it.

   The Driver
       The main purpose of the driver routine, in this case next_seq(), is to carve out the data
       into meaningful chunks which are passed along to relevant handlers (see below).

       Each chunk of data in the has a NAME tag attached to it, similar to that for XML parsing.
       This designates the type of data passed (annotation type or seqfeature) and the handler to
       be called for processing the data.

       For GenBank annotations, the data is divided up and passed along to handlers according to
       whether the data is tagged with a field name (i.e. LOCUS) and whether the field name
       represents 'primary' annotation (in this case, is present at the beginning of the line,
       such as REFERENCE). If the field is primary, it is assigned to the NAME tag. Field names
       which aren't primary (have at least 2 spaces before the name, like ORGANISM) are appended
       to the preceding primary field name as additional tags.

       For feature table data each new feature name signals the beginning of a new chunk of data.
       'FEATURES' is attached to NAME, the feature key ('CDS', 'gene', etc) is attached as the
       PRIMARY_ID, and the location is assigned to it's own tag name (LOCATION). Feature
       qualifiers are added as additional keys, with multiple keys included in an array.

       Once a particular event occurs (new primary tag, sequence, end of record), the data is
       passed along to be processed by a handler or (if no handler is defined) tossed away.

       Internally, the hash ref for a representative annotation (here a REFERENCE) looks like
       this:

         $VAR1 = {
                   'JOURNAL' => 'Unpublished (2003)',
                   'TITLE' => 'The DNA sequence of Homo sapiens',
                   'NAME' => 'REFERENCE',
                   'REFERENCE' => '1  (bases 1 to 10001)',
                   'AUTHORS' => 'International Human Genome Sequencing Consortium.'
                 };

       and a SeqFeature as this:

         $VAR1 = {
                   'db_xref' => [
                                  'GeneID:127086',
                                  'InterimID:127086'
                                ],
                   'LOCATION' => 'complement(3024..6641)',
                   'NAME' => 'FEATURES',
                   'FEATURE_KEY' => 'gene',
                   'gene' => 'LOC127086',
                   'note' => 'Derived by automated computational analysis using
                              gene prediction method: GNOMON.'
                 };

       Note that any driver implementation would suffice as long as it fulfilled the requirements
       above.

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 - Bioperl Project

       bioperl-l at bioperl.org

       Original author Elia Stupka, elia -at- tigem.it

CONTRIBUTORS

       Ewan Birney birney at ebi.ac.uk Jason Stajich jason at bioperl.org Chris Mungall cjm at
       fruitfly.bdgp.berkeley.edu Lincoln Stein lstein at cshl.org Heikki Lehvaslaiho, heikki at
       ebi.ac.uk Hilmar Lapp, hlapp at gmx.net Donald G. Jackson, donald.jackson at bms.com James
       Wasmuth, james.wasmuth at ed.ac.uk Brian Osborne, bosborne at alum.mit.edu

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

   next_seq
        Title   : next_seq
        Usage   : $seq = $stream->next_seq()
        Function: returns the next sequence in the stream
        Returns : Bio::Seq object
        Args    :

   write_seq
        Title   : write_seq
        Usage   : $stream->write_seq($seq)
        Function: writes the $seq object (must be seq) to the stream
        Returns : 1 for success and 0 for error
        Args    : array of 1 to n Bio::SeqI objects

   seqhandler
        Title   : seqhandler
        Usage   : $stream->seqhandler($handler)
        Function: Get/Set the Bio::Seq::HandlerBaseI object
        Returns : Bio::Seq::HandlerBaseI
        Args    : Bio::Seq::HandlerBaseI