Module: EnsemblREST::Map

Defined in:

lib/ensemblrest/map.rb

Class Method Summary

• .cdna(id, region, options = {}) ⇒ JSON

  Convert from cDNA coordinates to genomic coordinates.

• .cds(id, region, options = {}) ⇒ JSON

  Convert from CDS coordinates to genomic coordinates.

• .map(region, asm_one, asm_two, species = 'human', options = {}) ⇒ JSON

  Convert the co-ordinates of one assembly to another.

• .translation(id, region, options = {}) ⇒ JSON

  Convert from protein (translation) coordinates to genomic coordinates.

Class Method Details

.cdna(id, region, options = {}) ⇒ JSON

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

Parameters:

• An Ensembl stable ID

• Query region

• (defaults to: {})

  Optional arguments for the service please goto rest.ensembl.org/documentation/info/assembly_cdna

Returns:

• 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 = {}) ⇒ JSON

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

Parameters:

• An Ensembl stable ID

• Query region

• (defaults to: {})

  Optional arguments for the service please goto rest.ensembl.org/documentation/info/assembly_cds

Returns:

• 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 = {}) ⇒ JSON

Convert the co-ordinates of one assembly to another

Parameters:

• Query region

• Version of the input assembly

• Version of the output assembly

• (defaults to: 'human')

  Species name/alias

• (defaults to: {})

  Optional arguments for the service please goto rest.ensembl.org/documentation/info/assembly_map

Returns:

• 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 = {}) ⇒ JSON

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

Parameters:

• An Ensembl stable ID

• Query region

• (defaults to: {})

  Optional arguments for the service please goto rest.ensembl.org/documentation/info/assembly_translation

Returns:

• 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