module EnsemblRest::Sequence

Public Class Methods

sequence_id(id, opts = {}) click to toggle source

Query for multiple types of Sequence by its stable identifier

# 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 = {}) click to toggle source

Query for a region of genomic sequence based on its location

# 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