bio::seqio::kegg(3pm) [debian man page]

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

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://redmine.open-bio.org/projects/bioperl/

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 v5.14.2							    2012-03-02						     Bio::SeqIO::kegg(3pm)