Bio::SeqIO::kegg - KEGG sequence input/output stream #It is probably best not to use this object directly, but #rather go through the SeqIO handler system. Go: $stream = Bio::SeqIO->new(-file => $filename, -format => 'KEGG'); while ( my $seq = $stream->next_seq() ) { # do something with $seq } 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. $seq->primary_id $seq->display_id $seq->annotation->get_Annotations('description'); grep {$_->database eq 'KO'} $seq->annotation->get_Annotations('dblink') grep {$_->database eq 'PATH'} $seq->annotation->get_Annotations('dblink') FIXME, NOT IMPLEMENTED $seq->annotation->get_Annotations('dblink') FIXME, NOT IMPLEMENTED $seq->translate->seq $seq->seq

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://www.bioperl.org/MailList.shtml - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email allenday@ucla.edu 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 :