module EnsemblREST::Map

Public Instance Methods

cdna(id, region, options = {}) click to toggle source

Convert from cDNA coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the Ensembl API.

@param [String] id An Ensembl stable ID @param [String] region Query region @param [Hash] options Optional arguments for the service please goto rest.ensembl.org/documentation/info/assembly_cdna @return [JSON] genomic coordinates

# File lib/ensemblrest/map.rb, line 23
def cdna(id, region, options = {})
        return EnsemblREST.get("map/cdna/#{id}/#{region}", {format: 'json'}.merge(options))
end
cds(id, region, options = {}) click to toggle source

Convert from CDS coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the Ensembl API.

@param [String] id An Ensembl stable ID @param [String] region Query region @param [Hash] options Optional arguments for the service please goto rest.ensembl.org/documentation/info/assembly_cds @return [JSON] genomic coordinates

# File lib/ensemblrest/map.rb, line 33
def cds(id, region, options = {})
        return EnsemblREST.get("map/cds/#{id}/#{region}", {format: 'json'}.merge(options))
end
map(region, asm_one, asm_two, species = 'human', options = {}) click to toggle source

Convert the co-ordinates of one assembly to another

@param [String] region Query region @param [String] asm_one Version of the input assembly @param [String] asm_two Version of the output assembly @param [String] species Species name/alias @param [Hash] options Optional arguments for the service please goto rest.ensembl.org/documentation/info/assembly_map @return [JSON] genomic coordinates

# File lib/ensemblrest/map.rb, line 45
def map(region, asm_one, asm_two, species = 'human', options = {})
        return EnsemblREST.get("map/#{species}/#{asm_one}/#{region}/#{asm_two}", {format: 'json'}.merge(options))
end
translation(id, region, options = {}) click to toggle source

Convert from protein (translation) coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the Ensembl API.

@param [String] id An Ensembl stable ID @param [String] region Query region @param [Hash] options Optional arguments for the service please goto rest.ensembl.org/documentation/info/assembly_translation @return [JSON] genomic coordinates

# File lib/ensemblrest/map.rb, line 55
def translation(id, region, options = {})
        return EnsemblREST.get("map/translation/#{id}/#{region}", {format: 'json'}.merge(options))
end