Class: UniprotMapper

Inherits:
Object
  • Object
show all
Defined in:
lib/protk/uniprot_mapper.rb

Overview

Provides access to uniprot.org via its API See docs and examples here www.uniprot.org/faq/28#id_mapping_examples

Instance Method Summary collapse

Constructor Details

#initialize ⇒ UniprotMapper

Returns a new instance of UniprotMapper.



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# File 'lib/protk/uniprot_mapper.rb', line 10

def initialize
  @genv = Constants.instance
end

Instance Method Details

#map(from_id_type, from_ids, output_id) ⇒ Object 



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# File 'lib/protk/uniprot_mapper.rb', line 14

def map(from_id_type,from_ids,output_id)

  from_query = from_ids.join(" ")

  base = 'www.uniprot.org'
  tool = 'mapping'
  params = {
    'from' => from_id_type, 'to' => output_id, 'format' => 'tab',
    'query' => from_query
  }

  http = Net::HTTP.new base
  @genv.log "Mapping to #{output_id}" ,:info
  response = http.request_post '/' + tool + '/',
  params.keys.map {|key| key + '=' + params[key]}.join('&')

  loc = nil
  while response.code == '302'
    loc = response['Location']
    response = http.request_get loc
  end

  while loc
    wait = response['Retry-After'] or break
    @genv.log "Waiting (#{wait})..." , :info
    sleep wait.to_i
    response = http.request_get loc
  end

  response.value # raises http error if not 2xx
  return response.body
end