NAME

Bio::DB::RefSeq - Database object interface for RefSeq retrieval

SYNOPSIS

  use Bio::DB::RefSeq;
  $db = Bio::DB::RefSeq->new();
  # 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 bandwidth
  # and request Fasta sequence
  $db = Bio::DB::RefSeq->new(-retrievaltype => 'tempfile' ,
                               -format => 'fasta');
  my $seqio = $db->get_Stream_by_id(['NM_006732', 'NM_005252'] );
  while( my $seq  =  $seqio->next_seq ) {
        print "seqid is ", $seq->id, "\n";
  }

DESCRIPTION

Allows the dynamic retrieval of sequence objects Bio::Seq from the RefSeq nucleotide database using the dbfetch script at EBI:

http://www.ebi.ac.uk/Tools/dbfetch/dbfetch

At this time the module specifically retrieves nucleotide sequences only.

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 retrieves 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.

FEEDBACK

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Heikki Lehvaslaiho

Email Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _