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Bio::SeqIO::swissdriveUser Contributed Perl DocumentBio::SeqIO::swissdriver(3)

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://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 the Bio::Seq::HandlerBaseI object
	Returns	: Bio::Seq::HandlerBaseI
	Args	: Bio::Seq::HandlerBaseI

perl v5.24.1			  2017-07-08	    Bio::SeqIO::swissdriver(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Bioperl Project | APPENDIX

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