Method: Bio::NCBI::REST#efetch

Defined in:

lib/bio/io/ncbirest.rb

#efetch(ids, hash = {}, step = 100) ⇒ Object

Retrieve database entries by given IDs and using E-Utils (efetch) service.

For information on the possible arguments, see

• eutils.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html

Usage

ncbi = Bio::NCBI::REST.new
ncbi.efetch("185041", {"db"=>"nucleotide", "rettype"=>"gb", "retmode" => "xml"})
ncbi.efetch("J00231", {"db"=>"nuccore", "rettype"=>"gb", "retmode"=>"xml"})
ncbi.efetch("AAA52805", {"db"=>"protein", "rettype"=>"gb"})

Bio::NCBI::REST.efetch("185041", {"db"=>"nucleotide", "rettype"=>"gb", "retmode" => "xml"})
Bio::NCBI::REST.efetch("J00231", {"db"=>"nuccore", "rettype"=>"gb"})
Bio::NCBI::REST.efetch("AAA52805", {"db"=>"protein", "rettype"=>"gb"})

---

Arguments:

• ids: list of NCBI entry IDs (required)

• hash: hash of E-Utils option => “nuccore”, “rettype” => “gb”

  • db: “sequences”, “nucleotide”, “protein”, “pubmed”, “omim”, …

  • retmode: “text”, “xml”, “html”, …

  • rettype: “gb”, “gbc”, “medline”, “count”,…

• step: maximum number of entries retrieved at a time

Returns

String

# File 'lib/bio/io/ncbirest.rb', line 205

def efetch(ids, hash = {}, step = 100)
  serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
  opts = {
    "tool"     => "bioruby",
    "retmode"  => "text",
  }
  opts.update(hash)

  case ids
  when Array
    list = ids
  else
    list = ids.to_s.split(/\s*,\s*/)
  end

  result = ""
  0.step(list.size, step) do |i|
    opts["id"] = list[i, step].join(',')
    unless opts["id"].empty?
      ncbi_access_wait
      response = Bio::Command.post_form(serv, opts)
      result += response.body
    end
  end
  return result.strip
  #return result.strip.split(/\n\n+/)
end