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 'Unpublished (2003)',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.

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

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