Module: EnsemblRest::Variation

Defined in:
lib/bio-ensembl-rest/variation.rb

Class Method Summary collapse

Class Method Details

.vep_id(id, species, opts = {}) ⇒ Object

Fetch variant consequences based on a variation identifier



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# File 'lib/bio-ensembl-rest/variation.rb', line 6

def self.vep_id(id, species, opts = {})
  opts = EnsemblRest.parse_options opts
  path = EnsemblRest.build_path "/vep/#{species}/id/#{id}/consequences", opts

  if opts['content-type'] == 'ruby'
    plain_opts = opts.clone
    plain_opts['content-type'] = 'application/json'
    return JSON.parse vep_id id, species, plain_opts
  end

  return EnsemblRest.fetch_data path, opts, 'variation'
end

.vep_region(allele, region, species, opts = {}) ⇒ Object

Fetch variant consequences



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# File 'lib/bio-ensembl-rest/variation.rb', line 22

def self.vep_region(allele, region, species, opts = {})
  opts = EnsemblRest.parse_options opts
  path = EnsemblRest.build_path "/vep/#{species}/#{region}/#{allele}/consequences", opts

  # TODO: ruby object?
  if opts['content-type'] == 'ruby'
    plain_opts = opts.clone
    plain_opts['content-type'] = 'application/json'
    return JSON.parse vep_region allele, region, species, plain_opts
  end

  return EnsemblRest.fetch_data path, opts, 'taxonomy'
end