ensemblrest 1.1.0 → 1.1.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
1
1
  ---
2
2
  SHA1:
3
- metadata.gz: 61c74f74f07aaedc9f7f77b799d7965ab583f306
4
- data.tar.gz: 4138d77a8d0fe8c1ee791500c55fca7b6b0d0b15
3
+ metadata.gz: 7a5efeea2ea4a92716b931614be8456de09ee9df
4
+ data.tar.gz: 73c7fb0a3ab39f3560672d555ec1d99bf4256901
5
5
  SHA512:
6
- metadata.gz: 98a42e9f686cce15bb8d0c376957df4420d2e75620bfdf29fa1d165671a9743ea0b28960f1bac049d1863d4d34d664eb037df7b6bcc6a658385f8d1749a0ff74
7
- data.tar.gz: d62c2fc1e5b6feaa29a553a4b7e976d6e26588c90c70e49373e047acfa0ed5c95d78e80186991e613e732c0f574d199464c2d888926d66acfeae27329277a31b
6
+ metadata.gz: 874dfb83b62b9be675d43253d1328699eb38e5a0729762f42a8381474ed5a439585b834d24a4c04beb54459e1537e29cfc5744af885c51ef3e1b640360fcbe83
7
+ data.tar.gz: 6b4f7c42b9f91ed52b15d70a861476ed29df3066c82e128284e93a9aad8b32a14c2336cccd1603be7613ccdf060bf908c234e6df0491772709c363ea808881ef
@@ -15,8 +15,8 @@ module EnsemblREST
15
15
  module_function
16
16
  # Uses the given identifier to return the archived sequence
17
17
  #
18
- # @param [String] An Ensembl stable ID
19
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/archive_id_get
18
+ # @param [String] id An Ensembl stable ID
19
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/archive_id_get
20
20
  # @return [JSON] Variants consequences
21
21
  def id_get(id, options = {})
22
22
  return EnsemblREST.get("archive/id/#{id}", {format: 'json'}.merge(options))
@@ -24,8 +24,8 @@ module EnsemblREST
24
24
 
25
25
  # Retrieve the archived sequence for a set of identifiers
26
26
  #
27
- # @param [Array] Ensembl stable IDs
28
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/archive_id_post
27
+ # @param [Array] ids Ensembl stable IDs
28
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/archive_id_post
29
29
  # @return [JSON] Requested response
30
30
  def id_post(ids, options = {})
31
31
  return EnsemblREST.post("archive/id", {"id" => ids}, {format: 'json'}.merge(options))
@@ -17,8 +17,8 @@ module EnsemblREST
17
17
 
18
18
  # Retrieves a gene tree dump for a gene tree stable identifier
19
19
  #
20
- # @param [String] An Ensembl genetree ID
21
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree
20
+ # @param [String] id An Ensembl genetree ID
21
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree
22
22
  # @return [JSON] a gene tree
23
23
  def genetree(id, options = {})
24
24
  return EnsemblREST.get("genetree/id/#{id}", {format: 'json'}.merge(options))
@@ -26,8 +26,8 @@ module EnsemblREST
26
26
 
27
27
  # Retrieves a gene tree that contains the stable identifier
28
28
  #
29
- # @param [String] An Ensembl stable ID
30
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree_member_id
29
+ # @param [String] id An Ensembl stable ID
30
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree_member_id
31
31
  # @return [JSON] gene trees
32
32
  def genetree_member_id(id, options = {})
33
33
  return EnsemblREST.get("genetree/member/id/#{id}", {format: 'json'}.merge(options))
@@ -35,9 +35,9 @@ module EnsemblREST
35
35
 
36
36
  # Retrieves a gene tree containing the gene identified by a symbol
37
37
  #
38
- # @param [String] Symbol or display name of a gene
39
- # @param [String] Species name/alias
40
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree_member_symbol
38
+ # @param [String] symbol Symbol or display name of a gene
39
+ # @param [String] species Species name/alias
40
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree_member_symbol
41
41
  # @return [JSON] gene trees
42
42
  def genetree_member_symbol(symbol, species = 'human', options = {})
43
43
  return EnsemblREST.get("genetree/member/symbol/#{species}/#{symbol}", {format: 'json'}.merge(options))
@@ -45,9 +45,9 @@ module EnsemblREST
45
45
 
46
46
  # Retrieves genomic alignments as separate blocks based on a region and species
47
47
  #
48
- # @param [String] Query region. A maximum of 10Mb is allowed to be requested at any one time
49
- # @param [String] Species name/alias
50
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genomic_alignment_region
48
+ # @param [String] region Query region. A maximum of 10Mb is allowed to be requested at any one time
49
+ # @param [String] species Species name/alias
50
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genomic_alignment_region
51
51
  # @return [JSON] an alignment
52
52
  def genomic_alignment_region(region, species = 'human', options = {})
53
53
  return EnsemblREST.get("alignment/region/#{species}/#{region}", {format: 'json'}.merge(options))
@@ -55,8 +55,8 @@ module EnsemblREST
55
55
 
56
56
  # Retrieves homology information (orthologs) by Ensembl gene id
57
57
  #
58
- # @param [String] An Ensembl stable ID
59
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/homology_ensemblgene
58
+ # @param [String] id An Ensembl stable ID
59
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/homology_ensemblgene
60
60
  # @return [JSON] a homology information
61
61
  def homology_ensemblgene(id, options = {})
62
62
  return EnsemblREST.get("homology/id/#{id}", {format: 'json'}.merge(options))
@@ -64,9 +64,9 @@ module EnsemblREST
64
64
 
65
65
  # Retrieves homology information (orthologs) by symbol
66
66
  #
67
- # @param [String] Symbol or display name of a gene
68
- # @param [String] Species name/alias
69
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/homology_symbol
67
+ # @param [String] symbol Symbol or display name of a gene
68
+ # @param [String] species Species name/alias
69
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/homology_symbol
70
70
  # @return [JSON] gene trees
71
71
  def homology_symbol(symbol, species = 'human', options = {})
72
72
  return EnsemblREST.get("homology/symbol/#{species}/#{symbol}", {format: 'json'}.merge(options))
@@ -40,7 +40,7 @@ module EnsemblREST
40
40
 
41
41
  # Connect to Ensembl REST Service
42
42
  #
43
- # @param [String] Base Ensembl REST Service URL
43
+ # @param [String] server Base Ensembl REST Service URL
44
44
  def connect(server)
45
45
  @@url = URI.parse(server)
46
46
  @@http_connect = Net::HTTP.new(@@url.host, @@url.port)
@@ -16,8 +16,8 @@ module EnsemblREST
16
16
 
17
17
  # List the names of analyses involved in generating Ensembl data.
18
18
  #
19
- # @param [String] Species name/alias
20
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/analysis
19
+ # @param [String] species Species name/alias
20
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/analysis
21
21
  # @return [JSON] List the names of analyses
22
22
  def analysis(species = 'human', options = {})
23
23
  return EnsemblREST.get("info/analysis/#{species}", {format: 'json'}.merge(options))
@@ -25,8 +25,8 @@ module EnsemblREST
25
25
 
26
26
  # List the currently available assemblies for a species.
27
27
  #
28
- # @param [String] Species name/alias
29
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_info
28
+ # @param [String] species Species name/alias
29
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_info
30
30
  # @return [JSON] List the currently available assemblies
31
31
  def assembly_info(species = 'human', options = {})
32
32
  return EnsemblREST.get("info/assembly/#{species}", {format: 'json'}.merge(options))
@@ -34,9 +34,9 @@ module EnsemblREST
34
34
 
35
35
  # Returns information about the specified toplevel sequence region for the given species.
36
36
  #
37
- # @param [String] The (top level) sequence region name.
38
- # @param [String] Species name/alias
39
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_stats
37
+ # @param [String] region_name The (top level) sequence region name.
38
+ # @param [String] species Species name/alias
39
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_stats
40
40
  # @return [JSON] Returns information about the specified toplevel sequence region
41
41
  def assembly_stats(region_name, species = 'human', options = {})
42
42
  return EnsemblREST.get("info/assembly/#{species}/#{region_name}", {format: 'json'}.merge(options))
@@ -45,8 +45,8 @@ module EnsemblREST
45
45
  # List the functional classifications of gene models that Ensembl associates with a particular species.
46
46
  # Useful for restricting the type of genes/transcripts retrieved by other endpoints.
47
47
  #
48
- # @param [String] Species name/alias
49
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/biotypes
48
+ # @param [String] species Species name/alias
49
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/biotypes
50
50
  # @return [JSON] List the currently available assemblies
51
51
  def biotypes(species = 'human', options = {})
52
52
  return EnsemblREST.get("info/biotypes/#{species}", {format: 'json'}.merge(options))
@@ -54,7 +54,7 @@ module EnsemblREST
54
54
 
55
55
  # List all compara analyses available (an analysis defines the type of comparative data).
56
56
  #
57
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/compara_methods
57
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/compara_methods
58
58
  # @return [JSON] List all compara analyses
59
59
  def compara_methods(options = {})
60
60
  return EnsemblREST.get("info/compara/methods", {format: 'json'}.merge(options))
@@ -62,8 +62,8 @@ module EnsemblREST
62
62
 
63
63
  # List all collections of species analysed with the specified compara method.
64
64
  #
65
- # @param [String] Filter by compara method. Use one the methods returned by /info/compara/methods endpoint.
66
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/compara_species_sets
65
+ # @param [String] method Filter by compara method. Use one the methods returned by /info/compara/methods endpoint.
66
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/compara_species_sets
67
67
  # @return [JSON] List the currently available assemblies
68
68
  def compara_species_sets(method, options = {})
69
69
  return EnsemblREST.get("info/compara/species_sets/#{method}", {format: 'json'}.merge(options))
@@ -71,7 +71,7 @@ module EnsemblREST
71
71
 
72
72
  # Lists all available comparative genomics databases and their data release.
73
73
  #
74
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/comparas
74
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/comparas
75
75
  # @return [JSON] List all compara analyses
76
76
  def comparas(options = {})
77
77
  return EnsemblREST.get("info/comparas", {format: 'json'}.merge(options))
@@ -79,7 +79,7 @@ module EnsemblREST
79
79
 
80
80
  # Shows the data releases available on this REST server. May return more than one release (unfrequent non-standard Ensembl configuration).
81
81
  #
82
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/data
82
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/data
83
83
  # @return [JSON] Shows the data releases available on this REST server
84
84
  def data(options = {})
85
85
  return EnsemblREST.get("info/data", {format: 'json'}.merge(options))
@@ -87,8 +87,8 @@ module EnsemblREST
87
87
 
88
88
  # Lists all available external sources for a species.
89
89
  #
90
- # @param [String] Species name/alias
91
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/external_dbs
90
+ # @param [String] species Species name/alias
91
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/external_dbs
92
92
  # @return [JSON] Lists all available external sources
93
93
  def external_dbs(species = 'human', options = {})
94
94
  return EnsemblREST.get("info/external_dbs/#{species}", {format: 'json'}.merge(options))
@@ -96,7 +96,7 @@ module EnsemblREST
96
96
 
97
97
  # Checks if the service is alive.
98
98
  #
99
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ping
99
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ping
100
100
  # @return [Boolean] True/False
101
101
  def ping(options = {})
102
102
  begin
@@ -109,7 +109,7 @@ module EnsemblREST
109
109
 
110
110
  # Shows the current version of the Ensembl REST API.
111
111
  #
112
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/rest
112
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/rest
113
113
  # @return [String] version of this REST server
114
114
  def rest(options = {})
115
115
  return EnsemblREST.get("info/rest", {format: 'json'}.merge(options))["release"]
@@ -117,7 +117,7 @@ module EnsemblREST
117
117
 
118
118
  # Shows the current version of the Ensembl API used by the REST server.
119
119
  #
120
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/software
120
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/software
121
121
  # @return [String] the current version of the Ensembl API
122
122
  def software(options = {})
123
123
  return EnsemblREST.get("info/software", {format: 'json'}.merge(options))["release"]
@@ -125,7 +125,7 @@ module EnsemblREST
125
125
 
126
126
  # Lists all available species, their aliases, available adaptor groups and data release.
127
127
  #
128
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/species
128
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/species
129
129
  # @return [String] Lists all available species
130
130
  def species(options = {})
131
131
  return EnsemblREST.get("info/species", {format: 'json'}.merge(options))
@@ -15,9 +15,9 @@ module EnsemblREST
15
15
 
16
16
  # Find the species and database for a symbol in a linked external database
17
17
  #
18
- # @param [String] A name or symbol from an annotation source has been linked to a genetic feature
19
- # @param [String] Species name/alias
20
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/symbol_lookup
18
+ # @param [String] symbol A name or symbol from an annotation source has been linked to a genetic feature
19
+ # @param [String] species Species name/alias
20
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/symbol_lookup
21
21
  # @return [JSON] Cross references
22
22
  def symbol(symbol, species = 'human', options = {})
23
23
  return EnsemblREST.get("lookup/symbol/#{species}/#{symbol}", {format: 'json'}.merge(options))
@@ -25,8 +25,8 @@ module EnsemblREST
25
25
 
26
26
  # Find the species and database for a single identifier
27
27
  #
28
- # @param [String] An Ensembl Stable ID
29
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/lookup
28
+ # @param [String] id An Ensembl Stable ID
29
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/lookup
30
30
  # @return [JSON] Cross references
31
31
  def id(id, options = {})
32
32
  return EnsemblREST.get("lookup/id/#{id}", {format: 'json'}.merge(options))
@@ -34,9 +34,9 @@ module EnsemblREST
34
34
 
35
35
  # Find the species and database for a set of symbols in a linked external database. Unknown symbols are omitted from the response.
36
36
  #
37
- # @param [String] An array of names or symbols from an annotation source has been linked to a genetic feature
38
- # @param [String] Species name/alias
39
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/symbol_post
37
+ # @param [String] symbols An array of names or symbols from an annotation source has been linked to a genetic feature
38
+ # @param [String] species Species name/alias
39
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/symbol_post
40
40
  # @return [JSON] Cross references
41
41
  def symbol_post(symbols, species = 'human', options = {})
42
42
  return EnsemblREST.post("lookup/symbol/#{species}", {'symbols' => symbols}, {format: 'json'}.merge(options))
@@ -44,8 +44,8 @@ module EnsemblREST
44
44
 
45
45
  # Find the species and database for several identifiers. IDs that are not found are returned with no data.
46
46
  #
47
- # @param [String] Ensembl Stable IDs
48
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/lookup_post
47
+ # @param [String] ids Ensembl Stable IDs
48
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/lookup_post
49
49
  # @return [JSON] Cross references
50
50
  def id_post(ids, options = {})
51
51
  return EnsemblREST.post("lookup/id", {'ids' => ids}, {format: 'json'}.merge(options))
@@ -16,9 +16,9 @@ module EnsemblREST
16
16
 
17
17
  # Convert from cDNA coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the Ensembl API.
18
18
  #
19
- # @param [String] An Ensembl stable ID
20
- # @param [String] Query region
21
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_cdna
19
+ # @param [String] id An Ensembl stable ID
20
+ # @param [String] region Query region
21
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_cdna
22
22
  # @return [JSON] genomic coordinates
23
23
  def cdna(id, region, options = {})
24
24
  return EnsemblREST.get("map/cdna/#{id}/#{region}", {format: 'json'}.merge(options))
@@ -26,9 +26,9 @@ module EnsemblREST
26
26
 
27
27
  # Convert from CDS coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the Ensembl API.
28
28
  #
29
- # @param [String] An Ensembl stable ID
30
- # @param [String] Query region
31
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_cds
29
+ # @param [String] id An Ensembl stable ID
30
+ # @param [String] region Query region
31
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_cds
32
32
  # @return [JSON] genomic coordinates
33
33
  def cds(id, region, options = {})
34
34
  return EnsemblREST.get("map/cds/#{id}/#{region}", {format: 'json'}.merge(options))
@@ -36,11 +36,11 @@ module EnsemblREST
36
36
 
37
37
  # Convert the co-ordinates of one assembly to another
38
38
  #
39
- # @param [String] Query region
40
- # @param [String] Version of the input assembly
41
- # @param [String] Version of the output assembly
42
- # @param [String] Species name/alias
43
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_map
39
+ # @param [String] region Query region
40
+ # @param [String] asm_one Version of the input assembly
41
+ # @param [String] asm_two Version of the output assembly
42
+ # @param [String] species Species name/alias
43
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_map
44
44
  # @return [JSON] genomic coordinates
45
45
  def map(region, asm_one, asm_two, species = 'human', options = {})
46
46
  return EnsemblREST.get("map/#{species}/#{asm_one}/#{region}/#{asm_two}", {format: 'json'}.merge(options))
@@ -48,9 +48,9 @@ module EnsemblREST
48
48
 
49
49
  # Convert from protein (translation) coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the Ensembl API.
50
50
  #
51
- # @param [String] An Ensembl stable ID
52
- # @param [String] Query region
53
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_translation
51
+ # @param [String] id An Ensembl stable ID
52
+ # @param [String] region Query region
53
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_translation
54
54
  # @return [JSON] genomic coordinates
55
55
  def translation(id, region, options = {})
56
56
  return EnsemblREST.get("map/translation/#{id}/#{region}", {format: 'json'}.merge(options))
@@ -17,8 +17,8 @@ module EnsemblREST
17
17
 
18
18
  # Reconstruct the entire ancestry of a term from is_a and part_of relationships
19
19
  #
20
- # @param [String] An ontology term identifier
21
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_ancestors
20
+ # @param [String] id An ontology term identifier
21
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_ancestors
22
22
  # @return [JSON] the entire ancestry of a term
23
23
  def ancestors(id, options = {})
24
24
  return EnsemblREST.get("ontology/ancestors/#{id}", {format: 'json'}.merge(options))
@@ -26,8 +26,8 @@ module EnsemblREST
26
26
 
27
27
  # Reconstruct the entire ancestry of a term from is_a and part_of relationships.
28
28
  #
29
- # @param [String] An ontology term identifier
30
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_ancestors_chart
29
+ # @param [String] id An ontology term identifier
30
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_ancestors_chart
31
31
  # @return [JSON] the entire ancestry of a term
32
32
  def ancestors_chart(id, options = {})
33
33
  return EnsemblREST.get("ontology/ancestors/chart/#{id}", {format: 'json'}.merge(options))
@@ -35,8 +35,8 @@ module EnsemblREST
35
35
 
36
36
  # Find all the terms descended from a given term. By default searches are conducted within the namespace of the given identifier
37
37
  #
38
- # @param [String] An ontology term identifier
39
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_descendants
38
+ # @param [String] id An ontology term identifier
39
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_descendants
40
40
  # @return [JSON] the terms descended from a given term
41
41
  def descendants(id, options = {})
42
42
  return EnsemblREST.get("ontology/descendants/#{id}", {format: 'json'}.merge(options))
@@ -44,8 +44,8 @@ module EnsemblREST
44
44
 
45
45
  # Search for an ontological term by its namespaced identifier
46
46
  #
47
- # @param [String] An ontology term identifier
48
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_id
47
+ # @param [String] name An ontology term identifier
48
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_id
49
49
  # @return [JSON] an ontological term
50
50
  def id(name, options = {})
51
51
  return EnsemblREST.get("ontology/id/#{name}", {format: 'json'}.merge(options))
@@ -53,8 +53,8 @@ module EnsemblREST
53
53
 
54
54
  # Search for a list of ontological terms by their name
55
55
  #
56
- # @param [String] An ontology name. SQL wildcards are supported
57
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_name
56
+ # @param [String] name An ontology name. SQL wildcards are supported
57
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ontology_name
58
58
  # @return [JSON] a list of ontological terms
59
59
  def name(name, options = {})
60
60
  return EnsemblREST.get("ontology/name/#{URI.escape(name)}", {format: 'json'}.merge(options))
@@ -67,8 +67,8 @@ module EnsemblREST
67
67
 
68
68
  # Return the taxonomic classification of a taxon node
69
69
  #
70
- # @param [String] A taxon identifier. Can be a NCBI taxon id or a name
71
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/taxonomy_classification
70
+ # @param [String] id A taxon identifier. Can be a NCBI taxon id or a name
71
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/taxonomy_classification
72
72
  # @return [JSON] the taxonomic classification
73
73
  def classification(id, options = {})
74
74
  return EnsemblREST.get("taxonomy/classification/#{id}", {format: 'json'}.merge(options))
@@ -76,8 +76,8 @@ module EnsemblREST
76
76
 
77
77
  # Search for a taxonomic term by its identifier or name
78
78
  #
79
- # @param [String] A taxon identifier. Can be a NCBI taxon id or a name
80
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/taxonomy_id
79
+ # @param [String] id A taxon identifier. Can be a NCBI taxon id or a name
80
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/taxonomy_id
81
81
  # @return [JSON] the taxonomic classification
82
82
  def id(id, options = {})
83
83
  return EnsemblREST.get("taxonomy/id/#{id}", {format: 'json'}.merge(options))
@@ -85,8 +85,8 @@ module EnsemblREST
85
85
 
86
86
  # Search for a taxonomic id by a non-scientific name
87
87
  #
88
- # @param [String] A non-scientific species name. Can include SQL wildcards
89
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/taxonomy_name
88
+ # @param [String] name A non-scientific species name. Can include SQL wildcards
89
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/taxonomy_name
90
90
  # @return [JSON] the taxonomic classification
91
91
  def name(name, options = {})
92
92
  return EnsemblREST.get("taxonomy/name/#{URI.escape(name)}", {format: 'json'}.merge(options))
@@ -14,11 +14,11 @@ module EnsemblREST
14
14
 
15
15
  # Request multiple types of sequence by a list of regions.
16
16
  #
17
- # @param [Array] Query regions. A maximum of 10Mb is allowed to be requested at any one time
18
- # @param [Array] The type of feature to retrieve. Multiple values are accepted. Array of gene, transcript, cds, exon, repeat, simple, misc, variation, somatic_variation,
17
+ # @param [Array] region Query regions. A maximum of 10Mb is allowed to be requested at any one time
18
+ # @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,
19
19
  # structural_variation, somatic_structural_variation, constrained, regulatory, segmentation, motif, chipseq, array_probe
20
- # @param [String] Species name/alias
21
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/overlap_region
20
+ # @param [String] species Species name/alias
21
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/overlap_region
22
22
  # @return [JSON] Requested response
23
23
  def region(region, features = [], species = 'human', options = {})
24
24
  return EnsemblREST.get("overlap/region/#{species}/#{region}", {format: 'json', feature: features}.merge(options))
@@ -26,10 +26,10 @@ module EnsemblREST
26
26
 
27
27
  # Retrieves features (e.g. genes, transcripts, variations etc.) that overlap a region defined by the given identifier.
28
28
  #
29
- # @param [String] An Ensembl stable ID
30
- # @param [Array] The type of feature to retrieve. Multiple values are accepted. Array of gene, transcript, cds, exon, repeat, simple, misc, variation, somatic_variation,
29
+ # @param [String] id An Ensembl stable ID
30
+ # @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,
31
31
  # structural_variation, somatic_structural_variation, constrained, regulatory, segmentation, motif, chipseq, array_probe
32
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/overlap_id
32
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/overlap_id
33
33
  # @return [JSON] Requested response
34
34
  def id(id, features = [], options = {})
35
35
  return EnsemblREST.get("overlap/id/#{id}", {format: 'json', feature: features}.merge(options))
@@ -37,8 +37,8 @@ module EnsemblREST
37
37
 
38
38
  # Retrieve features related to a specific Translation as described by its stable ID (e.g. domains, variations).
39
39
  #
40
- # @param [String] An Ensembl stable ID
41
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/overlap_translation
40
+ # @param [String] id An Ensembl stable ID
41
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/overlap_translation
42
42
  # @return [JSON] Requested response
43
43
  def translation(id, options = {})
44
44
  return EnsemblREST.get("overlap/translation/#{id}", {format: 'json'}.merge(options))
@@ -16,9 +16,9 @@ module EnsemblREST
16
16
 
17
17
  # Returns a RegulatoryFeature given its stable ID (e.g. ENSR00001348195)
18
18
  #
19
- # @param [String] RegulatoryFeature stable ID
20
- # @param [String] Species name/alias
21
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/regulatory_id
19
+ # @param [String] id RegulatoryFeature stable ID
20
+ # @param [String] species Species name/alias
21
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/regulatory_id
22
22
  # @return [JSON] the entire ancestry of a term
23
23
  def id(id, species = 'human', options = {})
24
24
  return EnsemblREST.get("regulatory/#{species}/#{id}", {format: 'json'}.merge(options))
@@ -16,8 +16,8 @@ module EnsemblREST
16
16
 
17
17
  # Request multiple types of sequence by stable identifier.
18
18
  #
19
- # @param [String] An Ensembl stable ID
20
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_id
19
+ # @param [String] id An Ensembl stable ID
20
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_id
21
21
  # @return [FastaFormat] requested sequence
22
22
  def id(id, options = {})
23
23
  return EnsemblREST.get("sequence/id/#{id}", {format: 'fasta'}.merge(options))
@@ -25,9 +25,9 @@ module EnsemblREST
25
25
 
26
26
  # Returns the genomic sequence of the specified region of the given species.
27
27
  #
28
- # @param [String] Query region. A maximum of 10Mb is allowed to be requested at any one time
29
- # @param [String] Species name/alias
30
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_region
28
+ # @param [String] regionQuery region. A maximum of 10Mb is allowed to be requested at any one time
29
+ # @param [String] species Species name/alias
30
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_region
31
31
  # @return [FastaFormat] requested sequence
32
32
  def region(region, species = 'human', options = {})
33
33
  return EnsemblREST.get("sequence/region/#{species}/#{region}", {format: 'fasta'}.merge(options))
@@ -35,8 +35,8 @@ module EnsemblREST
35
35
 
36
36
  # Request multiple types of sequence by a stable identifier list.
37
37
  #
38
- # @param [Array] Ensembl stable IDs
39
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_id_post
38
+ # @param [Array] ids Ensembl stable IDs
39
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_id_post
40
40
  # @return [JSON] Requested response
41
41
  def id_post(ids, options = {})
42
42
  return EnsemblREST.post("sequence/id", {"ids" => ids}, {format: 'json'}.merge(options))
@@ -44,9 +44,9 @@ module EnsemblREST
44
44
 
45
45
  # Request multiple types of sequence by a list of regions.
46
46
  #
47
- # @param [Array] Query regions. A maximum of 10Mb is allowed to be requested at any one time
48
- # @param [String] Species name/alias
49
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_region_post
47
+ # @param [Array] regions Query regions. A maximum of 10Mb is allowed to be requested at any one time
48
+ # @param [String] species Species name/alias
49
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/sequence_region_post
50
50
  # @return [JSON] Requested response
51
51
  def region_post(regions, species = 'human', options = {})
52
52
  return EnsemblREST.post("sequence/region/#{species}", {"regions" => regions}, {format: 'json'}.merge(options))
@@ -16,9 +16,9 @@ module EnsemblREST
16
16
 
17
17
  # Uses a variation identifier (e.g. rsID) to return the variation features
18
18
  #
19
- # @param [String] RegulatoryFeature stable ID
20
- # @param [String] Species name/alias
21
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/variation_id
19
+ # @param [String] id RegulatoryFeature stable ID
20
+ # @param [String] species Species name/alias
21
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/variation_id
22
22
  # @return [JSON] the variation features
23
23
  def id(id, species = 'human', options = {})
24
24
  return EnsemblREST.get("variation/#{species}/#{id}", {format: 'json'}.merge(options))
@@ -26,8 +26,9 @@ module EnsemblREST
26
26
 
27
27
  # Uses a list of variation identifiers (e.g. rsID) to return the variation features
28
28
  #
29
- # @param [String] Species name/alias
30
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/variation_post
29
+ # @param [Array] ids RegulatoryFeature stable IDs
30
+ # @param [String] species Species name/alias
31
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/variation_post
31
32
  # @return [JSON] the variation features
32
33
  def post(ids, species = 'human', options = {})
33
34
  return EnsemblREST.post("variation/#{species}", {"ids" => ids}, {format: 'json'}.merge(options))
@@ -16,7 +16,7 @@ module EnsemblREST
16
16
 
17
17
  # Return a list of sets of genotype calls for specific samples in GA4GH format
18
18
  #
19
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gacallSet
19
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gacallSet
20
20
  # @return [JSON] a list of sets of genotype calls for specific samples
21
21
  def gacallSet(options = {})
22
22
  return EnsemblREST.post("ga4gh/callsets/search", {}, {format: 'json'}.merge(options))
@@ -24,11 +24,11 @@ module EnsemblREST
24
24
 
25
25
  # Return variant call information in GA4GH format for a region on a reference sequence
26
26
  #
27
- # @param [Integer] Start position of region (zero-based, inclusive)
28
- # @param [Integer] End position of region (zero-based, exclusive)
29
- # @param [String] Reference sequence name
30
- # @param [String] Return variant data for specific variantSets
31
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gavariants
27
+ # @param [Integer] start Start position of region (zero-based, inclusive)
28
+ # @param [Integer] stop End position of region (zero-based, exclusive)
29
+ # @param [String] referenceName Reference sequence name
30
+ # @param [Array] variantSetIds Return variant data for specific variantSets
31
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gavariants
32
32
  # @return [JSON] variant call information in GA4GH format
33
33
  def gavariants(start, stop, referenceName, variantSetIds, options = {})
34
34
  return EnsemblREST.post("ga4gh/variants/search", {"variantSetIds" => variantSetIds, "referenceName" => referenceName,"start" => start ,"end" => stop}, {format: 'json'}.merge(options))
@@ -36,7 +36,7 @@ module EnsemblREST
36
36
 
37
37
  # Return a list of variant sets in GA4GH format
38
38
  #
39
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gavariantset
39
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gavariantset
40
40
  # @return [JSON] a list of variant sets in GA4GH format
41
41
  def gavariantset(options = {})
42
42
  return EnsemblREST.post("ga4gh/variantsets/search", {}, {format: 'json'}.merge(options))
@@ -17,10 +17,10 @@ module EnsemblREST
17
17
 
18
18
  # Fetch variant consequences
19
19
  #
20
- # @param [String] Variation allele, Example Values: 'C', 'DUP'
21
- # @param [String] Query region. Example Values: '9:22125503-22125502:1', '7:100318423-100321323:1'
22
- # @param [String] Species name/alias
23
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_region_get
20
+ # @param [String] allele Variation allele, Example Values: 'C', 'DUP'
21
+ # @param [String] region Query region. Example Values: '9:22125503-22125502:1', '7:100318423-100321323:1'
22
+ # @param [String] species Species name/alias
23
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_region_get
24
24
  # @return [JSON] Variants consequences
25
25
  def region_get(allele, region, species = 'human', options = {})
26
26
  return EnsemblREST.get("vep/#{species}/region/#{region}/#{allele}", {format: 'json'}.merge(options))
@@ -28,9 +28,9 @@ module EnsemblREST
28
28
 
29
29
  # Fetch variant consequences based on a variation identifier
30
30
  #
31
- # @param [String] Query ID. Supports dbSNP, COSMIC and HGMD identifiers
32
- # @param [String] Species name/alias
33
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_region_get
31
+ # @param [String] id Query ID. Supports dbSNP, COSMIC and HGMD identifiers
32
+ # @param [String] species Species name/alias
33
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_region_get
34
34
  # @return [JSON] Variants consequences
35
35
  def id_get(id, species = 'human', options = {})
36
36
  return EnsemblREST.get("vep/#{species}/id/#{id}", {format: 'json'}.merge(options))
@@ -38,9 +38,9 @@ module EnsemblREST
38
38
 
39
39
  # Fetch variant consequences based on a HGVS notation
40
40
  #
41
- # @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.
42
- # @param [String] Species name/alias
43
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_hgvs_get
41
+ # @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.
42
+ # @param [String] species Species name/alias
43
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_hgvs_get
44
44
  # @return [JSON] Variants consequences
45
45
  def hgvs_get(hgvs_notation, species = 'human', options = {})
46
46
  return EnsemblREST.get("vep/#{species}/hgvs/#{hgvs_notation}", {format: 'json'}.merge(options))
@@ -48,9 +48,9 @@ module EnsemblREST
48
48
 
49
49
  # Fetch variant consequences for multiple ids
50
50
  #
51
- # @param [Array] Query IDs. Supports dbSNP, COSMIC and HGMD identifiers
52
- # @param [String] Species name/alias
53
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_id_post
51
+ # @param [Array] ids Query IDs. Supports dbSNP, COSMIC and HGMD identifiers
52
+ # @param [String] species Species name/alias
53
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_id_post
54
54
  # @return [JSON] Variants consequences
55
55
  def id_post(ids, species = 'human', options = {})
56
56
  return EnsemblREST.post("vep/#{species}/id", {"ids" => ids}, {format: 'json'}.merge(options))
@@ -58,9 +58,9 @@ module EnsemblREST
58
58
 
59
59
  # Fetch variant consequences for multiple regions
60
60
  #
61
- # @param [Array] input lines for VEP. Example Values: ["21 26960070 rs116645811 G A . . .", "21 26965148 rs1135638 G A . . ." ]
62
- # @param [String] Species name/alias
63
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_region_get
61
+ # @param [Array] variants input lines for VEP. Example Values: ["21 26960070 rs116645811 G A . . .", "21 26965148 rs1135638 G A . . ." ]
62
+ # @param [String] species Species name/alias
63
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/vep_region_get
64
64
  # @return [JSON] Variants consequences
65
65
  def region_post(variants, species = 'human', options = {})
66
66
  return EnsemblREST.post("vep/#{species}/region", {"variants" => variants}, {format: 'json'}.merge(options))
@@ -11,5 +11,5 @@
11
11
 
12
12
 
13
13
  module EnsemblREST
14
- VERSION = "1.1.0"
14
+ VERSION = "1.1.1"
15
15
  end
@@ -18,9 +18,9 @@ module EnsemblREST
18
18
  # This can be a display name for a gene/transcript/translation, a synonym or an externally linked reference.
19
19
  # If a gene's transcript is linked to the supplied symbol the service will return both gene and transcript (it supports transient links).
20
20
  #
21
- # @param [String] Symbol or display name of a gene
22
- # @param [String] Species name/alias
23
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/xref_external
21
+ # @param [String] symbol Symbol or display name of a gene
22
+ # @param [String] species Species name/alias
23
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/xref_external
24
24
  # @return [JSON] Cross references
25
25
  def external(symbol, species = 'human', options = {})
26
26
  return EnsemblREST.get("xrefs/symbol/#{species}/#{symbol}", {format: 'json'}.merge(options))
@@ -28,8 +28,8 @@ module EnsemblREST
28
28
 
29
29
  # Perform lookups of Ensembl Identifiers and retrieve their external references in other databases
30
30
  #
31
- # @param [String] An Ensembl Stable ID
32
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/xref_id
31
+ # @param [String] id An Ensembl Stable ID
32
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/xref_id
33
33
  # @return [JSON] Cross references
34
34
  def id(id, options = {})
35
35
  return EnsemblREST.get("xrefs/id/#{id}", {format: 'json'}.merge(options))
@@ -38,9 +38,9 @@ module EnsemblREST
38
38
  # Performs a lookup based upon the primary accession or display label of
39
39
  # an external reference and returning the information we hold about the entry
40
40
  #
41
- # @param [String] Symbol or display name of a gene
42
- # @param [String] Species name/alias
43
- # @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/xref_name
41
+ # @param [String] name Symbol or display name of a gene
42
+ # @param [String] species Species name/alias
43
+ # @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/xref_name
44
44
  # @return [JSON] Cross references
45
45
  def name(name, species = 'human', options = {})
46
46
  return EnsemblREST.get("xrefs/name/#{species}/#{name}", {format: 'json'}.merge(options))
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: ensemblrest
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.1.0
4
+ version: 1.1.1
5
5
  platform: ruby
6
6
  authors:
7
7
  - Natapol Pornputtapong