Summary

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

Package variables

Included modules

Inherit

Bio::SeqIO

Synopsis

  #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
  }

Description

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

Methods

Methods description

 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : Bio::Seq::RichSeq object
 Args    :

Methods code

sub _initialize {

    my($self,@args) = @_;
    
    $self->SUPER::_initialize(@args); 
    # hash for functions for decoding keys.
    $self->{'_func_ftunit_hash'} = {}; 
    if( ! defined $self->sequence_factory ) {
	$self->sequence_factory(new Bio::Seq::SeqFactory
				(-verbose => $self->verbose(), 
				 -type => 'Bio::Seq::RichSeq'));
    }

}

sub next_seq {

  my ($self,@args) = @_;
  my $builder = $self->sequence_builder();
  my $seq;
  my %params;

  my $buffer;
  my (@acc, @features);
  my ($display_id, $annotation);
  my $species;

  # initialize; we may come here because of starting over
  @features = ();
  $annotation = undef;
  @acc = ();
  $species = undef;
  %params = (-verbose => $self->verbose); # reset hash
  local($/) = "///\n";

  $buffer = $self->_readline();

  return undef if( !defined $buffer ); # end of file
  $buffer =~ /^ENTRY/ ||
	$self->throw("KEGG stream with bad ENTRY line. Not KEGG in my book. Got '$buffer'");

  my %FIELDS;
  my @chunks = split /\n(?=\S)/, $buffer;

  foreach my $chunk (@chunks){
	my($key) = $chunk =~ /^(\S+)/;
	$FIELDS{$key} = $chunk;
  }

  my($entry_id,$entry_seqtype,$entry_species) = $FIELDS{ENTRY} =~ /^ENTRY\s+(\d+)\s+(\S+)\s+(\S+)\s*$/;

  my($name) = $FIELDS{NAME} =~ /^NAME\s+(.+)$/;

  my($definition) = $FIELDS{DEFINITION} =~ /^DEFINITION\s+(.+)$/s;
  $definition =~ s/\s+/ /gs;

  my($aa_length,$aa_seq) = $FIELDS{AASEQ} =~ /^AASEQ\s+(\d+)\n(.+)$/s;
  $aa_seq =~ s/\s+//g;
  my($nt_length,$nt_seq) = $FIELDS{NTSEQ} =~ /^NTSEQ\s+(\d+)\n(.+)$/s;
  $nt_seq =~ s/\s+//g;

  $annotation = Bio::Annotation::Collection->new();
  $annotation->add_Annotation('description',Bio::Annotation::Comment->new(-text => $definition));

  my($ortholog_db,$ortholog_id,$ortholog_desc) = $FIELDS{ORTHOLOG} =~ /^ORTHOLOG\s+(\S+):\s+(\S+)\s+(\S*)\s*$/;
  $annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new(-database => $ortholog_db,
																	-primary_id => $ortholog_id,
																	-comment => $ortholog_desc
																   )
							 );

  $FIELDS{CLASS} =~ s/^CLASS\s+//;
  while($FIELDS{CLASS} =~ /.+?\[(\S+):(\S+)\]/gs){
	$annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new(-database => $1, -primary_id => $2));
  }

  $FIELDS{DBLINKS} =~ s/^DBLINKS/       /;
  while($FIELDS{DBLINKS} =~ /\s+(\S+):\s+(\S+)\n/gs){
	$annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new(-database => $1, -primary_id => $2));
  }

  $params{'-alphabet'}         = 'dna';
  $params{'-seq'}              = $nt_seq;
  $params{'-display_id'}       = $name;
  $params{'-accession_number'} = $entry_id;
  $params{'-species'}          = Bio::Species->new(-common_name => $entry_species);
  $params{'-annotation'}       = $annotation;

  $builder->add_slot_value(%params);
  $seq = $builder->make_object();

  return $seq;

}

General documentation

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.

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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 _