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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:

   http://bugzilla.open-bio.org/
 
 

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.