| Bio::SeqIO::swissdriver(3pm) | User Contributed Perl Documentation | Bio::SeqIO::swissdriver(3pm) |
Bio::SeqIO::swissdriver - SwissProt/UniProt handler-based push parser
#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
}
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 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.
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
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.
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
bioperl-l at bioperl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq object Args : none
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
Title : seqhandler Usage : $stream->seqhandler($handler) Function: Get/Set the Bio::Seq::HandlerBaseI object Returns : Bio::Seq::HandlerBaseI Args : Bio::Seq::HandlerBaseI
| 2021-08-15 | perl v5.32.1 |