module EnsemblRest::Mapping

Public Class Methods

map(asm_one, asm_two, species, region, opts = {}) click to toggle source

Convert the co-ordinates of one assembly to another

# File lib/bio-ensembl-rest/mapping.rb, line 6
def self.map(asm_one, asm_two, species, region, opts = {})
  opts = EnsemblRest.parse_options opts
  path = EnsemblRest.build_path "/map/#{species}/#{asm_one}/#{region}/#{asm_two}", opts

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

  return EnsemblRest.fetch_data path, opts, 'mapping' 
end
map_from_cdna(id, region, opts = {}) click to toggle source

Convert from CDNA coordinates to genomic coordinates

# File lib/bio-ensembl-rest/mapping.rb, line 23
def self.map_from_cdna(id, region, opts = {})
  return _map_generic id, region, 'cdna', opts       
end
map_from_cds(id, region, opts = {}) click to toggle source

Convert from CDS coordinates to genomic coordinates

# File lib/bio-ensembl-rest/mapping.rb, line 29
def self.map_from_cds(id, region, opts = {})
  return _map_generic id, region, 'cds', opts
end
map_from_translation(id, region, opts = {}) click to toggle source

Convert from protein (translation) coordinates to genomic coordinates

# File lib/bio-ensembl-rest/mapping.rb, line 35
def self.map_from_translation(id, region, opts = {})
  return _map_generic id, region, 'translation', opts
end