module Entrez

Constants

VERSION

Public Class Methods

EFetch(db, params = {}) click to toggle source

E.g. Entrez.EFetch(‘snp’, id: 123, retmode: :xml)

# File lib/entrez.rb, line 18
def EFetch(db, params = {})
  perform '/efetch.fcgi', db, params
end
EInfo(db, params = {}) click to toggle source

E.g. Entrez.EInfo(‘gene’, retmode: :xml)

# File lib/entrez.rb, line 23
def EInfo(db, params = {})
  perform '/einfo.fcgi', db, params
end
ESearch(db, search_terms = {}, params = {}) click to toggle source

E.g. Entrez.ESearch(‘genomeprj’, {WORD: ‘hapmap’, SEQS: ‘inprogress’}, retmode: :xml) search_terms can also be string literal.

# File lib/entrez.rb, line 29
def ESearch(db, search_terms = {}, params = {})
  params[:term] = search_terms.is_a?(Hash) ? convert_search_term_hash(search_terms) : search_terms
  response = perform '/esearch.fcgi', db, params
  response
end
ESummary(db, params = {}) click to toggle source

E.g. Entrez.ESummary(‘snp’, id: 123, retmode: :xml)

# File lib/entrez.rb, line 36
def ESummary(db, params = {})
  perform '/esummary.fcgi', db, params
end
convert_search_term_hash(hash, operator = 'AND') click to toggle source

Take a ruby hash and convert it to an ENTREZ search term. E.g. convert_search_term_hash {WORD: ‘low coverage’, SEQS: ‘inprogress’} #=> ‘low coverage+AND+inprogress’

# File lib/entrez.rb, line 48
def convert_search_term_hash(hash, operator = 'AND')
  raise UnknownOperator.new(operator) unless ['AND', 'OR'].include?(operator)
  str = hash.map do |field, value|
    value = value.join(',') if value.is_a?(Array)
    "#{value}[#{field}]"
  end.join("+#{operator}+")
  if operator == 'OR'
    str = "(#{str})"
  end
  str
end
perform(utility_path, db, params = {}) click to toggle source 
# File lib/entrez.rb, line 40
def perform(utility_path, db, params = {})
  respect_query_limit unless ignore_query_limit?
  get utility_path, :query => {db: db}.merge(params)
end