NAME¶
Bio::SeqIO::swissdriver - SwissProt/UniProt 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 => '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.
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://redmine.open-bio.org/projects/bioperl/
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