Module: EnsemblREST::VEP

Defined in:
lib/ensemblrest/vep.rb

Class Method Summary collapse

Class Method Details

.hgvs_get(hgvs_notation, species = 'human', options = {}) ⇒ JSON

Fetch variant consequences based on a HGVS notation

Parameters:

  • hgvs_notation (String) —

    HGVS notation. May be genomic (g), coding © or protein (p), with reference to chromosome name, gene name, transcript ID or protein ID.

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

    Species name/alias

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

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

Returns:

  • (JSON) —

    Variants consequences



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# File 'lib/ensemblrest/vep.rb', line 45

def hgvs_get(hgvs_notation, species = 'human', options = {})
	return EnsemblREST.get("vep/#{species}/hgvs/#{hgvs_notation}", {format: 'json'}.merge(options))
end

.id_get(id, species = 'human', options = {}) ⇒ JSON

Fetch variant consequences based on a variation identifier

Parameters:

  • id (String) —

    Query ID. Supports dbSNP, COSMIC and HGMD identifiers

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

    Species name/alias

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

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

Returns:

  • (JSON) —

    Variants consequences



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# File 'lib/ensemblrest/vep.rb', line 35

def id_get(id, species = 'human', options = {})
	return EnsemblREST.get("vep/#{species}/id/#{id}", {format: 'json'}.merge(options))
end

.id_post(ids, species = 'human', options = {}) ⇒ JSON

Fetch variant consequences for multiple ids

Parameters:

  • ids (Array) —

    Query IDs. Supports dbSNP, COSMIC and HGMD identifiers

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

    Species name/alias

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

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

Returns:

  • (JSON) —

    Variants consequences



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

def id_post(ids, species = 'human', options = {})
	return EnsemblREST.post("vep/#{species}/id", {"ids" => ids}, {format: 'json'}.merge(options))
end

.region_get(allele, region, species = 'human', options = {}) ⇒ JSON

Fetch variant consequences

Parameters:

  • allele (String) —

    Variation allele, Example Values: ‘C’, ‘DUP’

  • region (String) —

    Query region. Example Values: ‘9:22125503-22125502:1’, ‘7:100318423-100321323:1’

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

    Species name/alias

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

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

Returns:

  • (JSON) —

    Variants consequences



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# File 'lib/ensemblrest/vep.rb', line 25

def region_get(allele, region, species = 'human', options = {})
	return EnsemblREST.get("vep/#{species}/region/#{region}/#{allele}", {format: 'json'}.merge(options))
end

.region_post(variants, species = 'human', options = {}) ⇒ JSON

Fetch variant consequences for multiple regions

Parameters:

  • variants (Array) —

    input lines for VEP. Example Values: [“21 26960070 rs116645811 G A . . .”, “21 26965148 rs1135638 G A . . .” ]

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

    Species name/alias

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

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

Returns:

  • (JSON) —

    Variants consequences



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# File 'lib/ensemblrest/vep.rb', line 65

def region_post(variants, species = 'human', options = {})
	return EnsemblREST.post("vep/#{species}/region", {"variants" => variants}, {format: 'json'}.merge(options))
end