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

DESCRIPTION

This object can transform Bio::Seq objects to and from UniProt flat file databases. The key difference between this parser and the tried-and-true Bio::SeqIO::swiss 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.

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:

[email protected]

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

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    : none

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 teh Bio::Seq::HandlerBaseI object
 Returns : Bio::Seq::HandlerBaseI 
 Args    : Bio::Seq::HandlerBaseI