RefSeq documentation.

  use Bio::DB::RefSeq;

  $db = new Bio::DB::RefSeq;

  # most of the time RefSeq_ID eq RefSeq acc
  $seq = $db->get_Seq_by_id('NM_006732'); # RefSeq ID
  print "accession is ", $seq->accession_number, "\n";

  # or changeing to accession number and Fasta format ...
  $db->request_format('fasta');
  $seq = $db->get_Seq_by_acc('NM_006732'); # RefSeq ACC
  print "seq is ", $seq->seq, "\n";

  # especially when using versions, you better be prepared
  # in not getting what what want
  eval {
      $seq = $db->get_Seq_by_version('NM_006732.1'); # RefSeq VERSION
  };
  print "accesion is ", $seq->accession_number, "\n" unless $@;

  # or ... best when downloading very large files, prevents
  # keeping all of the file in memory

  # also don't want features, just sequence so let's save bandwith
  # and request Fasta sequence
  $db = new Bio::DB::RefSeq(-retrievaltype => 'tempfile' ,
 			       -format => 'fasta');
  my $seqio = $db->get_Stream_by_batch(['NM_006732', 'NM_005252'] );
  while( my $seq  =  $seqio->next_seq ) {
 	print "seqid is ", $seq->id, "\n";
  }

Allows the dynamic retrieval of sequence objects Bio::Seq from the
RefSeq database using the dbfetch script at EBI:
http:EEwww.ebi.ac.ukEcgi-binEdbfetch.
In order to make changes transparent we have host type (currently only
ebi) and location (defaults to ebi) separated out. This allows later
additions of more servers in different geographical locations.
The functionality of this module is inherited from Bio::DB::DBFetch
which implements Bio::DB::WebDBSeqI.
This module retrieves entries from EBI although it
retrives database entries produced at NCBI. When read into bioperl
objects, the parser for GenBank format it used. RefSeq is a
NONSTANDARD GenBank file so be ready for surprises.

BEGIN {

    # you can add your own here theoretically.
    %HOSTS = (
	       'dbfetch' => {
		   baseurl => 'http://%s/cgi-bin/dbfetch?db=refseq&style=raw',
		   hosts   => {
		       'ebi'  => 'www.ebi.ac.uk'
		       }
	       }
	      );
    %FORMATMAP = ( 'embl'    => 'embl',
		   'genbank' => 'genbank',
		   'fasta' => 'fasta'
		   );
    $DEFAULTFORMAT = 'genbank';

}

sub new {

    my ($class, @args ) = @_;
    my $self = $class->SUPER::new(@args);

    $self->{ '_hosts' } = {};
    $self->{ '_formatmap' } = {};

    $self->hosts(\%HOSTS);
    $self->formatmap(\%FORMATMAP);
    $self->{'_default_format'} = $DEFAULTFORMAT;

    return $self;
}

1;

}

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://bio.perl.org/MailList.html             - About the mailing lists

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/

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