ensemblrest 1.1.0 → 1.1.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/ensemblrest/archive.rb

@@ -15,8 +15,8 @@ module EnsemblREST
 		module_function
 		# Uses the given identifier to return the archived sequence
 		# 
-		# @param [String] An Ensembl stable ID
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/archive_id_get
+		# @param [String] id An Ensembl stable ID
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/archive_id_get
 		# @return [JSON] Variants consequences
 		def id_get(id, options = {})
 			return EnsemblREST.get("archive/id/#{id}", {format: 'json'}.merge(options))
@@ -24,8 +24,8 @@ module EnsemblREST
 		
 		# Retrieve the archived sequence for a set of identifiers
 		# 
-		# @param [Array] Ensembl stable IDs
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/archive_id_post
+		# @param [Array] ids Ensembl stable IDs
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/archive_id_post
 		# @return [JSON] Requested response
 		def id_post(ids, options = {})
 			return EnsemblREST.post("archive/id", {"id" => ids}, {format: 'json'}.merge(options))

data/lib/ensemblrest/comparativegenomics.rb

@@ -17,8 +17,8 @@ module EnsemblREST
 		
 		# Retrieves a gene tree dump for a gene tree stable identifier
 		# 
-		# @param [String] An Ensembl genetree ID
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree
+		# @param [String] id An Ensembl genetree ID
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree
 		# @return [JSON] a gene tree
 		def genetree(id, options = {})
 			return EnsemblREST.get("genetree/id/#{id}", {format: 'json'}.merge(options))
@@ -26,8 +26,8 @@ module EnsemblREST
 		
 		# Retrieves a gene tree that contains the stable identifier
 		# 
-		# @param [String] An Ensembl stable ID
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree_member_id
+		# @param [String] id An Ensembl stable ID
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree_member_id
 		# @return [JSON] gene trees
 		def genetree_member_id(id, options = {})
 			return EnsemblREST.get("genetree/member/id/#{id}", {format: 'json'}.merge(options))
@@ -35,9 +35,9 @@ module EnsemblREST
 		
 		# Retrieves a gene tree containing the gene identified by a symbol
 		# 
-		# @param [String] Symbol or display name of a gene
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree_member_symbol
+		# @param [String] symbol Symbol or display name of a gene
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree_member_symbol
 		# @return [JSON] gene trees
 		def genetree_member_symbol(symbol, species = 'human', options = {})
 			return EnsemblREST.get("genetree/member/symbol/#{species}/#{symbol}", {format: 'json'}.merge(options))
@@ -45,9 +45,9 @@ module EnsemblREST
 		
 		# Retrieves genomic alignments as separate blocks based on a region and species
 		# 
-		# @param [String] Query region. A maximum of 10Mb is allowed to be requested at any one time
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genomic_alignment_region
+		# @param [String] region Query region. A maximum of 10Mb is allowed to be requested at any one time
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genomic_alignment_region
 		# @return [JSON] an alignment
 		def genomic_alignment_region(region, species = 'human', options = {})
 			return EnsemblREST.get("alignment/region/#{species}/#{region}", {format: 'json'}.merge(options))
@@ -55,8 +55,8 @@ module EnsemblREST
 		
 		# Retrieves homology information (orthologs) by Ensembl gene id
 		# 
-		# @param [String] An Ensembl stable ID
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/homology_ensemblgene
+		# @param [String] id An Ensembl stable ID
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/homology_ensemblgene
 		# @return [JSON] a homology information
 		def homology_ensemblgene(id, options = {})
 			return EnsemblREST.get("homology/id/#{id}", {format: 'json'}.merge(options))
@@ -64,9 +64,9 @@ module EnsemblREST
 		
 		# Retrieves homology information (orthologs) by symbol
 		# 
-		# @param [String] Symbol or display name of a gene
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/homology_symbol
+		# @param [String] symbol Symbol or display name of a gene
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/homology_symbol
 		# @return [JSON] gene trees
 		def homology_symbol(symbol, species = 'human', options = {})
 			return EnsemblREST.get("homology/symbol/#{species}/#{symbol}", {format: 'json'}.merge(options))

data/lib/ensemblrest/connect.rb

@@ -40,7 +40,7 @@ module EnsemblREST
 	
 	# Connect to Ensembl REST Service
 	# 
-	# @param [String] Base Ensembl REST Service URL
+	# @param [String] server Base Ensembl REST Service URL
 	def connect(server)
 		@@url = URI.parse(server)
 		@@http_connect = Net::HTTP.new(@@url.host, @@url.port)

data/lib/ensemblrest/info.rb

@@ -16,8 +16,8 @@ module EnsemblREST
 		
 		# List the names of analyses involved in generating Ensembl data.
 		# 
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/analysis
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/analysis
 		# @return [JSON] List the names of analyses
 		def analysis(species = 'human', options = {})
 			return EnsemblREST.get("info/analysis/#{species}", {format: 'json'}.merge(options))
@@ -25,8 +25,8 @@ module EnsemblREST
 		
 		# List the currently available assemblies for a species.
 		# 
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_info
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_info
 		# @return [JSON] List the currently available assemblies
 		def assembly_info(species = 'human', options = {})
 			return EnsemblREST.get("info/assembly/#{species}", {format: 'json'}.merge(options))
@@ -34,9 +34,9 @@ module EnsemblREST
 		
 		# Returns information about the specified toplevel sequence region for the given species.
 		# 
-		# @param [String] The (top level) sequence region name.
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_stats
+		# @param [String] region_name The (top level) sequence region name.
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_stats
 		# @return [JSON] Returns information about the specified toplevel sequence region
 		def assembly_stats(region_name, species = 'human', options = {})
 			return EnsemblREST.get("info/assembly/#{species}/#{region_name}", {format: 'json'}.merge(options))
@@ -45,8 +45,8 @@ module EnsemblREST
 		# List the functional classifications of gene models that Ensembl associates with a particular species. 
 		# Useful for restricting the type of genes/transcripts retrieved by other endpoints.
 		# 
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/biotypes
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/biotypes
 		# @return [JSON] List the currently available assemblies
 		def biotypes(species = 'human', options = {})
 			return EnsemblREST.get("info/biotypes/#{species}", {format: 'json'}.merge(options))
@@ -54,7 +54,7 @@ module EnsemblREST
 		
 		# List all compara analyses available (an analysis defines the type of comparative data).
 		# 
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/compara_methods
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/compara_methods
 		# @return [JSON] List all compara analyses
 		def compara_methods(options = {})
 			return EnsemblREST.get("info/compara/methods", {format: 'json'}.merge(options))
@@ -62,8 +62,8 @@ module EnsemblREST
 		
 		# List all collections of species analysed with the specified compara method.
 		# 
-		# @param [String] Filter by compara method. Use one the methods returned by /info/compara/methods endpoint.
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/compara_species_sets
+		# @param [String] method Filter by compara method. Use one the methods returned by /info/compara/methods endpoint.
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/compara_species_sets
 		# @return [JSON] List the currently available assemblies
 		def compara_species_sets(method, options = {})
 			return EnsemblREST.get("info/compara/species_sets/#{method}", {format: 'json'}.merge(options))
@@ -71,7 +71,7 @@ module EnsemblREST
 		
 		# Lists all available comparative genomics databases and their data release.
 		# 
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/comparas
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/comparas
 		# @return [JSON] List all compara analyses
 		def comparas(options = {})
 			return EnsemblREST.get("info/comparas", {format: 'json'}.merge(options))
@@ -79,7 +79,7 @@ module EnsemblREST
 		
 		# Shows the data releases available on this REST server. May return more than one release (unfrequent non-standard Ensembl configuration).
 		# 
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/data
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/data
 		# @return [JSON] Shows the data releases available on this REST server
 		def data(options = {})
 			return EnsemblREST.get("info/data", {format: 'json'}.merge(options))
@@ -87,8 +87,8 @@ module EnsemblREST
 		
 		# Lists all available external sources for a species.
 		# 
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/external_dbs
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/external_dbs
 		# @return [JSON] Lists all available external sources
 		def external_dbs(species = 'human', options = {})
 			return EnsemblREST.get("info/external_dbs/#{species}", {format: 'json'}.merge(options))
@@ -96,7 +96,7 @@ module EnsemblREST
 		
 		# Checks if the service is alive.
 		# 
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ping
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ping
 		# @return [Boolean] True/False
 		def ping(options = {})
 			begin
@@ -109,7 +109,7 @@ module EnsemblREST
 		
 		# Shows the current version of the Ensembl REST API.
 		# 
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/rest
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/rest
 		# @return [String] version of this REST server
 		def rest(options = {})
 			return EnsemblREST.get("info/rest", {format: 'json'}.merge(options))["release"]
@@ -117,7 +117,7 @@ module EnsemblREST
 		
 		# Shows the current version of the Ensembl API used by the REST server.
 		# 
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/software
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/software
 		# @return [String] the current version of the Ensembl API
 		def software(options = {})
 			return EnsemblREST.get("info/software", {format: 'json'}.merge(options))["release"]
@@ -125,7 +125,7 @@ module EnsemblREST
 		
 		# Lists all available species, their aliases, available adaptor groups and data release.
 		# 
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/species
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/species
 		# @return [String] Lists all available species
 		def species(options = {})
 			return EnsemblREST.get("info/species", {format: 'json'}.merge(options))

data/lib/ensemblrest/lookup.rb

@@ -15,9 +15,9 @@ module EnsemblREST
 		
 		# Find the species and database for a symbol in a linked external database
 		# 
-		# @param [String] A name or symbol from an annotation source has been linked to a genetic feature
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/symbol_lookup
+		# @param [String] symbol A name or symbol from an annotation source has been linked to a genetic feature
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/symbol_lookup
 		# @return [JSON] Cross references
 		def symbol(symbol, species = 'human', options = {})
 			return EnsemblREST.get("lookup/symbol/#{species}/#{symbol}", {format: 'json'}.merge(options))
@@ -25,8 +25,8 @@ module EnsemblREST
 		
 		# Find the species and database for a single identifier
 		# 
-		# @param [String] An Ensembl Stable ID
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/lookup
+		# @param [String] id An Ensembl Stable ID
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/lookup
 		# @return [JSON] Cross references
 		def id(id, options = {})
 			return EnsemblREST.get("lookup/id/#{id}", {format: 'json'}.merge(options))
@@ -34,9 +34,9 @@ module EnsemblREST
 		
 		# Find the species and database for a set of symbols in a linked external database. Unknown symbols are omitted from the response.
 		# 
-		# @param [String] An array of names or symbols from an annotation source has been linked to a genetic feature
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/symbol_post
+		# @param [String] symbols An array of names or symbols from an annotation source has been linked to a genetic feature
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/symbol_post
 		# @return [JSON] Cross references
 		def symbol_post(symbols, species = 'human', options = {})
 			return EnsemblREST.post("lookup/symbol/#{species}", {'symbols' => symbols}, {format: 'json'}.merge(options))
@@ -44,8 +44,8 @@ module EnsemblREST
 		
 		# Find the species and database for several identifiers. IDs that are not found are returned with no data.
 		# 
-		# @param [String] Ensembl Stable IDs
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/lookup_post
+		# @param [String] ids Ensembl Stable IDs
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/lookup_post
 		# @return [JSON] Cross references
 		def id_post(ids, options = {})
 			return EnsemblREST.post("lookup/id", {'ids' => ids}, {format: 'json'}.merge(options))

data/lib/ensemblrest/map.rb

@@ -16,9 +16,9 @@ module EnsemblREST
 		
 		# Convert from cDNA coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the Ensembl API.
 		# 
-		# @param [String] An Ensembl stable ID
-		# @param [String] Query region
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_cdna
+		# @param [String] id An Ensembl stable ID
+		# @param [String] region Query region
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_cdna
 		# @return [JSON] genomic coordinates
 		def cdna(id, region, options = {})
 			return EnsemblREST.get("map/cdna/#{id}/#{region}", {format: 'json'}.merge(options))
@@ -26,9 +26,9 @@ module EnsemblREST
 		
 		# Convert from CDS coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the Ensembl API.
 		# 
-		# @param [String] An Ensembl stable ID
-		# @param [String] Query region
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_cds
+		# @param [String] id An Ensembl stable ID
+		# @param [String] region Query region
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_cds
 		# @return [JSON] genomic coordinates
 		def cds(id, region, options = {})
 			return EnsemblREST.get("map/cds/#{id}/#{region}", {format: 'json'}.merge(options))
@@ -36,11 +36,11 @@ module EnsemblREST
 		
 		# Convert the co-ordinates of one assembly to another
 		# 
-		# @param [String] Query region
-		# @param [String] Version of the input assembly
-		# @param [String] Version of the output assembly
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_map
+		# @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 http://rest.ensembl.org/documentation/info/assembly_map
 		# @return [JSON] genomic coordinates
 		def map(region, asm_one, asm_two, species = 'human', options = {})
 			return EnsemblREST.get("map/#{species}/#{asm_one}/#{region}/#{asm_two}", {format: 'json'}.merge(options))
@@ -48,9 +48,9 @@ module EnsemblREST
 		
 		# Convert from protein (translation) coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the Ensembl API.
 		# 
-		# @param [String] An Ensembl stable ID
-		# @param [String] Query region
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_translation
+		# @param [String] id An Ensembl stable ID
+		# @param [String] region Query region
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_translation
 		# @return [JSON] genomic coordinates
 		def translation(id, region, options = {})
 			return EnsemblREST.get("map/translation/#{id}/#{region}", {format: 'json'}.merge(options))

data/lib/ensemblrest/ontoandtaxo.rb

@@ -17,8 +17,8 @@ module EnsemblREST
 		
 		# Reconstruct the entire ancestry of a term from is_a and part_of relationships
 		# 
-		# @param [String] An ontology term identifier
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_ancestors
+		# @param [String] id An ontology term identifier
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_ancestors
 		# @return [JSON] the entire ancestry of a term
 		def ancestors(id, options = {})
 			return EnsemblREST.get("ontology/ancestors/#{id}", {format: 'json'}.merge(options))
@@ -26,8 +26,8 @@ module EnsemblREST
 		
 		# Reconstruct the entire ancestry of a term from is_a and part_of relationships.
 		# 
-		# @param [String] An ontology term identifier
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_ancestors_chart
+		# @param [String] id An ontology term identifier
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_ancestors_chart
 		# @return [JSON] the entire ancestry of a term
 		def ancestors_chart(id, options = {})
 			return EnsemblREST.get("ontology/ancestors/chart/#{id}", {format: 'json'}.merge(options))
@@ -35,8 +35,8 @@ module EnsemblREST
 		
 		# Find all the terms descended from a given term. By default searches are conducted within the namespace of the given identifier
 		# 
-		# @param [String] An ontology term identifier
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_descendants
+		# @param [String] id An ontology term identifier
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_descendants
 		# @return [JSON] the terms descended from a given term
 		def descendants(id, options = {})
 			return EnsemblREST.get("ontology/descendants/#{id}", {format: 'json'}.merge(options))
@@ -44,8 +44,8 @@ module EnsemblREST
 		
 		# Search for an ontological term by its namespaced identifier
 		# 
-		# @param [String] An ontology term identifier
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_id
+		# @param [String] name An ontology term identifier
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_id
 		# @return [JSON] an ontological term
 		def id(name, options = {})
 			return EnsemblREST.get("ontology/id/#{name}", {format: 'json'}.merge(options))
@@ -53,8 +53,8 @@ module EnsemblREST
 		
 		# Search for a list of ontological terms by their name
 		# 
-		# @param [String] An ontology name. SQL wildcards are supported
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_name
+		# @param [String] name An ontology name. SQL wildcards are supported
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_name
 		# @return [JSON] a list of ontological terms
 		def name(name, options = {})
 			return EnsemblREST.get("ontology/name/#{URI.escape(name)}", {format: 'json'}.merge(options))
@@ -67,8 +67,8 @@ module EnsemblREST
 	
 		# Return the taxonomic classification of a taxon node
 		# 
-		# @param [String] A taxon identifier. Can be a NCBI taxon id or a name
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/taxonomy_classification
+		# @param [String] id A taxon identifier. Can be a NCBI taxon id or a name
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/taxonomy_classification
 		# @return [JSON] the taxonomic classification
 		def classification(id, options = {})
 			return EnsemblREST.get("taxonomy/classification/#{id}", {format: 'json'}.merge(options))
@@ -76,8 +76,8 @@ module EnsemblREST
 		
 		# Search for a taxonomic term by its identifier or name
 		# 
-		# @param [String] A taxon identifier. Can be a NCBI taxon id or a name
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/taxonomy_id
+		# @param [String] id A taxon identifier. Can be a NCBI taxon id or a name
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/taxonomy_id
 		# @return [JSON] the taxonomic classification
 		def id(id, options = {})
 			return EnsemblREST.get("taxonomy/id/#{id}", {format: 'json'}.merge(options))
@@ -85,8 +85,8 @@ module EnsemblREST
 		
 		# Search for a taxonomic id by a non-scientific name
 		# 
-		# @param [String] A non-scientific species name. Can include SQL wildcards
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/taxonomy_name
+		# @param [String] name A non-scientific species name. Can include SQL wildcards
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/taxonomy_name
 		# @return [JSON] the taxonomic classification
 		def name(name, options = {})
 			return EnsemblREST.get("taxonomy/name/#{URI.escape(name)}", {format: 'json'}.merge(options))

data/lib/ensemblrest/overlap.rb

@@ -14,11 +14,11 @@ module EnsemblREST
 		
 		# Request multiple types of sequence by a list of regions.
 		# 
-		# @param [Array] Query regions. A maximum of 10Mb is allowed to be requested at any one time
-		# @param [Array] The type of feature to retrieve. Multiple values are accepted. Array of gene, transcript, cds, exon, repeat, simple, misc, variation, somatic_variation, 
+		# @param [Array] region Query regions. A maximum of 10Mb is allowed to be requested at any one time
+		# @param [Array] features The type of feature to retrieve. Multiple values are accepted. Array of gene, transcript, cds, exon, repeat, simple, misc, variation, somatic_variation, 
 		# structural_variation, somatic_structural_variation, constrained, regulatory, segmentation, motif, chipseq, array_probe
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/overlap_region
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/overlap_region
 		# @return [JSON] Requested response
 		def region(region, features = [], species = 'human', options = {})
 			return EnsemblREST.get("overlap/region/#{species}/#{region}", {format: 'json', feature: features}.merge(options))
@@ -26,10 +26,10 @@ module EnsemblREST
 		
 		# Retrieves features (e.g. genes, transcripts, variations etc.) that overlap a region defined by the given identifier.
 		# 
-		# @param [String] An Ensembl stable ID
-		# @param [Array] The type of feature to retrieve. Multiple values are accepted. Array of gene, transcript, cds, exon, repeat, simple, misc, variation, somatic_variation, 
+		# @param [String] id An Ensembl stable ID
+		# @param [Array] features The type of feature to retrieve. Multiple values are accepted. Array of gene, transcript, cds, exon, repeat, simple, misc, variation, somatic_variation, 
 		# structural_variation, somatic_structural_variation, constrained, regulatory, segmentation, motif, chipseq, array_probe
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/overlap_id
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/overlap_id
 		# @return [JSON] Requested response
 		def id(id, features = [], options = {})
 			return EnsemblREST.get("overlap/id/#{id}", {format: 'json', feature: features}.merge(options))
@@ -37,8 +37,8 @@ module EnsemblREST
 		
 		# Retrieve features related to a specific Translation as described by its stable ID (e.g. domains, variations).
 		# 
-		# @param [String] An Ensembl stable ID
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/overlap_translation
+		# @param [String] id An Ensembl stable ID
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/overlap_translation
 		# @return [JSON] Requested response
 		def translation(id, options = {})
 			return EnsemblREST.get("overlap/translation/#{id}", {format: 'json'}.merge(options))

data/lib/ensemblrest/regulation.rb

@@ -16,9 +16,9 @@ module EnsemblREST
 		
 		# Returns a RegulatoryFeature given its stable ID (e.g. ENSR00001348195)
 		# 
-		# @param [String] RegulatoryFeature stable ID
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/regulatory_id
+		# @param [String] id RegulatoryFeature stable ID
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/regulatory_id
 		# @return [JSON] the entire ancestry of a term
 		def id(id, species = 'human', options = {})
 			return EnsemblREST.get("regulatory/#{species}/#{id}", {format: 'json'}.merge(options))

data/lib/ensemblrest/sequence.rb

@@ -16,8 +16,8 @@ module EnsemblREST
 		
 		# Request multiple types of sequence by stable identifier.
 		# 
-		# @param [String] An Ensembl stable ID
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_id
+		# @param [String] id An Ensembl stable ID
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_id
 		# @return [FastaFormat] requested sequence
 		def id(id, options = {})
 			return EnsemblREST.get("sequence/id/#{id}", {format: 'fasta'}.merge(options))
@@ -25,9 +25,9 @@ module EnsemblREST
 		
 		# Returns the genomic sequence of the specified region of the given species.
 		# 
-		# @param [String] Query region. A maximum of 10Mb is allowed to be requested at any one time
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_region
+		# @param [String] regionQuery region. A maximum of 10Mb is allowed to be requested at any one time
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_region
 		# @return [FastaFormat] requested sequence
 		def region(region, species = 'human', options = {})
 			return EnsemblREST.get("sequence/region/#{species}/#{region}", {format: 'fasta'}.merge(options))
@@ -35,8 +35,8 @@ module EnsemblREST
 		
 		# Request multiple types of sequence by a stable identifier list.
 		# 
-		# @param [Array] Ensembl stable IDs
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_id_post
+		# @param [Array] ids Ensembl stable IDs
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_id_post
 		# @return [JSON] Requested response
 		def id_post(ids, options = {})
 			return EnsemblREST.post("sequence/id", {"ids" => ids}, {format: 'json'}.merge(options))
@@ -44,9 +44,9 @@ module EnsemblREST
 		
 		# Request multiple types of sequence by a list of regions.
 		# 
-		# @param [Array] Query regions. A maximum of 10Mb is allowed to be requested at any one time
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_region_post
+		# @param [Array] regions Query regions. A maximum of 10Mb is allowed to be requested at any one time
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_region_post
 		# @return [JSON] Requested response
 		def region_post(regions, species = 'human', options = {})
 			return EnsemblREST.post("sequence/region/#{species}", {"regions" => regions}, {format: 'json'}.merge(options))

data/lib/ensemblrest/variation.rb

@@ -16,9 +16,9 @@ module EnsemblREST
 		
 		# Uses a variation identifier (e.g. rsID) to return the variation features
 		# 
-		# @param [String] RegulatoryFeature stable ID
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/variation_id
+		# @param [String] id RegulatoryFeature stable ID
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/variation_id
 		# @return [JSON] the variation features
 		def id(id, species = 'human', options = {})
 			return EnsemblREST.get("variation/#{species}/#{id}", {format: 'json'}.merge(options))
@@ -26,8 +26,9 @@ module EnsemblREST
 		
 		# Uses a list of variation identifiers (e.g. rsID) to return the variation features
 		# 
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/variation_post
+		# @param [Array] ids RegulatoryFeature stable IDs
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/variation_post
 		# @return [JSON] the variation features
 		def post(ids, species = 'human', options = {})
 			return EnsemblREST.post("variation/#{species}", {"ids" => ids}, {format: 'json'}.merge(options))

data/lib/ensemblrest/variationga4gh.rb

@@ -16,7 +16,7 @@ module EnsemblREST
 		
 		# Return a list of sets of genotype calls for specific samples in GA4GH format
 		# 
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gacallSet
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gacallSet
 		# @return [JSON] a list of sets of genotype calls for specific samples
 		def gacallSet(options = {})
 			return EnsemblREST.post("ga4gh/callsets/search", {}, {format: 'json'}.merge(options))
@@ -24,11 +24,11 @@ module EnsemblREST
 		
 		# Return variant call information in GA4GH format for a region on a reference sequence
 		#
-		# @param [Integer] Start position of region (zero-based, inclusive)
-		# @param [Integer] End position of region (zero-based, exclusive)
-		# @param [String] Reference sequence name
-		# @param [String] Return variant data for specific variantSets
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gavariants
+		# @param [Integer] start Start position of region (zero-based, inclusive)
+		# @param [Integer] stop End position of region (zero-based, exclusive)
+		# @param [String] referenceName Reference sequence name
+		# @param [Array] variantSetIds Return variant data for specific variantSets
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gavariants
 		# @return [JSON] variant call information in GA4GH format
 		def gavariants(start, stop, referenceName, variantSetIds, options = {})
 			return EnsemblREST.post("ga4gh/variants/search", {"variantSetIds" => variantSetIds, "referenceName" => referenceName,"start" => start ,"end" => stop}, {format: 'json'}.merge(options))
@@ -36,7 +36,7 @@ module EnsemblREST
 		
 		# Return a list of variant sets in GA4GH format
 		# 
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gavariantset
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gavariantset
 		# @return [JSON] a list of variant sets in GA4GH format
 		def gavariantset(options = {})
 			return EnsemblREST.post("ga4gh/variantsets/search", {}, {format: 'json'}.merge(options))

data/lib/ensemblrest/vep.rb

@@ -17,10 +17,10 @@ module EnsemblREST
 		
 		# Fetch variant consequences
 		# 
-		# @param [String] Variation allele, Example Values: 'C', 'DUP'
-		# @param [String] Query region. Example Values: '9:22125503-22125502:1', '7:100318423-100321323:1'
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_region_get
+		# @param [String] allele Variation allele, Example Values: 'C', 'DUP'
+		# @param [String] region Query region. Example Values: '9:22125503-22125502:1', '7:100318423-100321323:1'
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_region_get
 		# @return [JSON] Variants consequences
 		def region_get(allele, region, species = 'human', options = {})
 			return EnsemblREST.get("vep/#{species}/region/#{region}/#{allele}", {format: 'json'}.merge(options))
@@ -28,9 +28,9 @@ module EnsemblREST
 		
 		# Fetch variant consequences based on a variation identifier
 		# 
-		# @param [String] Query ID. Supports dbSNP, COSMIC and HGMD identifiers
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_region_get
+		# @param [String] id Query ID. Supports dbSNP, COSMIC and HGMD identifiers
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_region_get
 		# @return [JSON] Variants consequences
 		def id_get(id, species = 'human', options = {})
 			return EnsemblREST.get("vep/#{species}/id/#{id}", {format: 'json'}.merge(options))
@@ -38,9 +38,9 @@ module EnsemblREST
 		
 		# Fetch variant consequences based on a HGVS notation
 		# 
-		# @param [String] HGVS notation. May be genomic (g), coding (c) or protein (p), with reference to chromosome name, gene name, transcript ID or protein ID.
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_hgvs_get
+		# @param [String] hgvs_notation HGVS notation. May be genomic (g), coding (c) or protein (p), with reference to chromosome name, gene name, transcript ID or protein ID.
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_hgvs_get
 		# @return [JSON] Variants consequences
 		def hgvs_get(hgvs_notation, species = 'human', options = {})
 			return EnsemblREST.get("vep/#{species}/hgvs/#{hgvs_notation}", {format: 'json'}.merge(options))
@@ -48,9 +48,9 @@ module EnsemblREST
 		
 		# Fetch variant consequences for multiple ids
 		# 
-		# @param [Array] Query IDs. Supports dbSNP, COSMIC and HGMD identifiers
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_id_post
+		# @param [Array] ids Query IDs. Supports dbSNP, COSMIC and HGMD identifiers
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_id_post
 		# @return [JSON] Variants consequences
 		def id_post(ids, species = 'human', options = {})
 			return EnsemblREST.post("vep/#{species}/id", {"ids" => ids}, {format: 'json'}.merge(options))
@@ -58,9 +58,9 @@ module EnsemblREST
 		
 		# Fetch variant consequences for multiple regions
 		# 
-		# @param [Array] input lines for VEP. Example Values: ["21 26960070 rs116645811 G A . . .", "21 26965148 rs1135638 G A . . ." ]
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_region_get
+		# @param [Array] variants input lines for VEP. Example Values: ["21 26960070 rs116645811 G A . . .", "21 26965148 rs1135638 G A . . ." ]
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_region_get
 		# @return [JSON] Variants consequences
 		def region_post(variants, species = 'human', options = {})
 			return EnsemblREST.post("vep/#{species}/region", {"variants" => variants}, {format: 'json'}.merge(options))

data/lib/ensemblrest/version.rb

@@ -11,5 +11,5 @@
 
 
 module EnsemblREST
-	VERSION = "1.1.0"
+	VERSION = "1.1.1"
 end

data/lib/ensemblrest/xref.rb

@@ -18,9 +18,9 @@ module EnsemblREST
 		# This can be a display name for a gene/transcript/translation, a synonym or an externally linked reference. 
 		# If a gene's transcript is linked to the supplied symbol the service will return both gene and transcript (it supports transient links).
 		# 
-		# @param [String] Symbol or display name of a gene
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/xref_external
+		# @param [String] symbol Symbol or display name of a gene
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/xref_external
 		# @return [JSON] Cross references
 		def external(symbol, species = 'human', options = {})
 			return EnsemblREST.get("xrefs/symbol/#{species}/#{symbol}", {format: 'json'}.merge(options))
@@ -28,8 +28,8 @@ module EnsemblREST
 		
 		# Perform lookups of Ensembl Identifiers and retrieve their external references in other databases
 		# 
-		# @param [String] An Ensembl Stable ID
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/xref_id
+		# @param [String] id An Ensembl Stable ID
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/xref_id
 		# @return [JSON] Cross references
 		def id(id, options = {})
 			return EnsemblREST.get("xrefs/id/#{id}", {format: 'json'}.merge(options))
@@ -38,9 +38,9 @@ module EnsemblREST
 		# Performs a lookup based upon the primary accession or display label of 
 		# an external reference and returning the information we hold about the entry
 		# 
-		# @param [String] Symbol or display name of a gene
-		# @param [String] Species name/alias
-		# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/xref_name
+		# @param [String] name Symbol or display name of a gene
+		# @param [String] species Species name/alias
+		# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/xref_name
 		# @return [JSON] Cross references
 		def name(name, species = 'human', options = {})
 			return EnsemblREST.get("xrefs/name/#{species}/#{name}", {format: 'json'}.merge(options))

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ensemblrest
 version: !ruby/object:Gem::Version
-  version: 1.1.0
+  version: 1.1.1
 platform: ruby
 authors:
 - Natapol Pornputtapong