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Man Pages


Manual Reference Pages  -  BIO::SEQIO::KEGG (3)

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NAME

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

CONTENTS

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.



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perl v5.20.3 BIO::SEQIO::KEGG (3) 2016-04-05

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