Module: EnsemblRest::Sequence

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

Class Method Summary collapse

Class Method Details

.sequence_id(id, opts = {}) ⇒ Object

Query for multiple types of Sequence by its stable identifier



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

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

  # FIXME: if multiseq is true Bio::Sequence can't parse text/plain right
  if opts['content-type'] == 'ruby'
    plain_opts = opts.clone
    plain_opts['content-type'] = 'text/plain'
    return Bio::Sequence.auto(sequence_id(id, plain_opts))
  end

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

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

Query for a region of genomic sequence based on its location



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# File 'lib/bio-ensembl-rest/sequence.rb', line 23

def self.sequence_region(species, region, opts = {})
  opts = EnsemblRest.parse_options opts
  path = EnsemblRest.build_path "/sequence/region/#{species}/#{region}", opts

  if opts['content-type'] == 'ruby'
    plain_opts = opts.clone
    plain_opts['content-type'] = 'text/plain'
    return Bio::Sequence.auto sequence_region(species, region, plain_opts)
  end

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