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Bio::SeqIO::kegg(3)   User Contributed Perl Documentation  Bio::SeqIO::kegg(3)

NAME
       Bio::SeqIO::kegg	- KEGG sequence	input/output stream

SYNOPSIS
	 # It is probably best not to use this object directly,	but
	 # rather go through the SeqIO handler system. Go:

	 use Bio::SeqIO;

	 $stream = Bio::SeqIO->new(-file => $filename, -format => 'KEGG');

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

DESCRIPTION
       This class transforms KEGG gene records into Bio::Seq objects.

   Mapping of record properties	to object properties
       This section is supposed	to document which sections and properties of a
       KEGG databank record end	up where in the	Bioperl	object model. It is
       far from	complete and presently focuses only on those mappings which
       may be non-obvious. $seq	in the text refers to the Bio::Seq::RichSeqI
       implementing object returned by the parser for each record.

       'ENTRY'
	    $seq->primary_id

       'NAME'
	    $seq->display_id

       'DEFINITION'
	    $seq->annotation->get_Annotations('description');

       'ORTHOLOG'
	    grep {$_->database eq 'KO'}	$seq->annotation->get_Annotations('dblink')

       'CLASS'
	    grep {$_->database eq 'PATH'}
		     $seq->annotation->get_Annotations('dblink')

       'POSITION'
	   FIXME, NOT IMPLEMENTED

       'PATHWAY'
	    for	my $pathway ( $seq->annotation->get_Annotations('pathway') ) {
	       #
	    }

       'DBLINKS'
	    $seq->annotation->get_Annotations('dblink')

       'CODON_USAGE'
	   FIXME, NOT IMPLEMENTED

       'AASEQ'
	    $seq->translate->seq

       'NTSEQ'
	    $seq-E<gt>seq

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 - Allen Day
       Email allenday@ucla.edu

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::RichSeq object
	Args	:

   write_seq
	Title	: write_seq
	Note	: write_seq() is not implemented for KEGG format output.

perl v5.32.1			  2019-12-07		   Bio::SeqIO::kegg(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Allen Day | APPENDIX

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