Module: EnsemblREST::Map

Defined in:
lib/ensemblrest/map.rb

Class Method Summary collapse

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:

Returns:

  • (JSON) —

    genomic coordinates



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# 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:

Returns:

  • (JSON) —

    genomic coordinates



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# 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:

  • region (String) —

    Query region

  • asm_one (String) —

    Version of the input assembly

  • asm_two (String) —

    Version of the output assembly

  • species (String) (defaults to: 'human') —

    Species name/alias

  • options (Hash) (defaults to: {}) —

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

Returns:

  • (JSON) —

    genomic coordinates



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# 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:

Returns:

  • (JSON) —

    genomic coordinates



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# File 'lib/ensemblrest/map.rb', line 55

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