Module: EnsemblRest::CrossReference

Defined in:
lib/bio-ensembl-rest/cross-reference.rb

Class Method Summary collapse

Class Method Details

.xrefs_id(id, opts = {}) ⇒ Object

Perform lookups of Ensembl Identifiers and retrieve their external cross references in other databases



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# File 'lib/bio-ensembl-rest/cross-reference.rb', line 7

def self.xrefs_id(id, opts = {})
  opts = EnsemblRest.parse_options opts
  path = EnsemblRest.build_path "/xrefs/id/#{id}", opts

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

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

.xrefs_name(species, name, opts = {}) ⇒ Object

Performs a lookup based upon the primary accession or display label of an external reference and returning the information we hold about the entry



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# File 'lib/bio-ensembl-rest/cross-reference.rb', line 24

def self.xrefs_name(species, name, opts = {})
  opts = EnsemblRest.parse_options opts
  path = EnsemblRest.build_path "/xrefs/name/#{species}/#{name}", opts

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

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

.xrefs_symbol(species, symbol, opts = {}) ⇒ Object

Looks up an external symbol and returns all Ensembl objects linked to it



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# File 'lib/bio-ensembl-rest/cross-reference.rb', line 40

def self.xrefs_symbol(species, symbol, opts = {})
  opts = EnsemblRest.parse_options opts
  path = EnsemblRest.build_path "/xrefs/symbol/#{species}/#{symbol}", opts

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

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