ensemblrest 1.1.0 → 1.1.1

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Files changed (17) hide show
  1. checksums.yaml +4 -4
  2. data/lib/ensemblrest/archive.rb +4 -4
  3. data/lib/ensemblrest/comparativegenomics.rb +15 -15
  4. data/lib/ensemblrest/connect.rb +1 -1
  5. data/lib/ensemblrest/info.rb +20 -20
  6. data/lib/ensemblrest/lookup.rb +10 -10
  7. data/lib/ensemblrest/map.rb +14 -14
  8. data/lib/ensemblrest/ontoandtaxo.rb +16 -16
  9. data/lib/ensemblrest/overlap.rb +9 -9
  10. data/lib/ensemblrest/regulation.rb +3 -3
  11. data/lib/ensemblrest/sequence.rb +10 -10
  12. data/lib/ensemblrest/variation.rb +6 -5
  13. data/lib/ensemblrest/variationga4gh.rb +7 -7
  14. data/lib/ensemblrest/vep.rb +16 -16
  15. data/lib/ensemblrest/version.rb +1 -1
  16. data/lib/ensemblrest/xref.rb +8 -8
  17. metadata +1 -1
checksums.yaml CHANGED
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+ data.tar.gz: 6b4f7c42b9f91ed52b15d70a861476ed29df3066c82e128284e93a9aad8b32a14c2336cccd1603be7613ccdf060bf908c234e6df0491772709c363ea808881ef
data/lib/ensemblrest/archive.rb CHANGED
@@ -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
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- # @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
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+ # @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
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  return EnsemblREST.post("archive/id", {"id" => ids}, {format: 'json'}.merge(options))
data/lib/ensemblrest/comparativegenomics.rb CHANGED
@@ -17,8 +17,8 @@ module EnsemblREST
17
17
 
18
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  # 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
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  # @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))
data/lib/ensemblrest/connect.rb CHANGED
@@ -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)
data/lib/ensemblrest/info.rb CHANGED
@@ -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))
data/lib/ensemblrest/lookup.rb CHANGED
@@ -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))
data/lib/ensemblrest/map.rb CHANGED
@@ -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))
data/lib/ensemblrest/ontoandtaxo.rb CHANGED
@@ -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))
data/lib/ensemblrest/overlap.rb CHANGED
@@ -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))
data/lib/ensemblrest/regulation.rb CHANGED
@@ -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))
data/lib/ensemblrest/sequence.rb CHANGED
@@ -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))
data/lib/ensemblrest/variation.rb CHANGED
@@ -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))
data/lib/ensemblrest/variationga4gh.rb CHANGED
@@ -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))
data/lib/ensemblrest/vep.rb CHANGED
@@ -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))
data/lib/ensemblrest/version.rb CHANGED
@@ -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
data/lib/ensemblrest/xref.rb CHANGED
@@ -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