ensemblrest 1.1.0 → 1.1.1
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- checksums.yaml +4 -4
- data/lib/ensemblrest/archive.rb +4 -4
- data/lib/ensemblrest/comparativegenomics.rb +15 -15
- data/lib/ensemblrest/connect.rb +1 -1
- data/lib/ensemblrest/info.rb +20 -20
- data/lib/ensemblrest/lookup.rb +10 -10
- data/lib/ensemblrest/map.rb +14 -14
- data/lib/ensemblrest/ontoandtaxo.rb +16 -16
- data/lib/ensemblrest/overlap.rb +9 -9
- data/lib/ensemblrest/regulation.rb +3 -3
- data/lib/ensemblrest/sequence.rb +10 -10
- data/lib/ensemblrest/variation.rb +6 -5
- data/lib/ensemblrest/variationga4gh.rb +7 -7
- data/lib/ensemblrest/vep.rb +16 -16
- data/lib/ensemblrest/version.rb +1 -1
- data/lib/ensemblrest/xref.rb +8 -8
- metadata +1 -1
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 7a5efeea2ea4a92716b931614be8456de09ee9df
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4
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+
data.tar.gz: 73c7fb0a3ab39f3560672d555ec1d99bf4256901
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 874dfb83b62b9be675d43253d1328699eb38e5a0729762f42a8381474ed5a439585b834d24a4c04beb54459e1537e29cfc5744af885c51ef3e1b640360fcbe83
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7
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+
data.tar.gz: 6b4f7c42b9f91ed52b15d70a861476ed29df3066c82e128284e93a9aad8b32a14c2336cccd1603be7613ccdf060bf908c234e6df0491772709c363ea808881ef
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data/lib/ensemblrest/archive.rb
CHANGED
@@ -15,8 +15,8 @@ module EnsemblREST
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module_function
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# Uses the given identifier to return the archived sequence
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#
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-
# @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
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+
# @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
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# @return [JSON] Variants consequences
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def id_get(id, options = {})
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return EnsemblREST.get("archive/id/#{id}", {format: 'json'}.merge(options))
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@@ -24,8 +24,8 @@ module EnsemblREST
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# Retrieve the archived sequence for a set of identifiers
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#
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-
# @param [Array] Ensembl stable IDs
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-
# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/archive_id_post
|
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+
# @param [Array] ids Ensembl stable IDs
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+
# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/archive_id_post
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# @return [JSON] Requested response
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def id_post(ids, options = {})
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return EnsemblREST.post("archive/id", {"id" => ids}, {format: 'json'}.merge(options))
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@@ -17,8 +17,8 @@ module EnsemblREST
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# Retrieves a gene tree dump for a gene tree stable identifier
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#
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-
# @param [String] An Ensembl genetree ID
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-
# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree
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+
# @param [String] id An Ensembl genetree ID
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+
# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree
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# @return [JSON] a gene tree
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def genetree(id, options = {})
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return EnsemblREST.get("genetree/id/#{id}", {format: 'json'}.merge(options))
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@@ -26,8 +26,8 @@ module EnsemblREST
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# Retrieves a gene tree that contains the stable identifier
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#
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# @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/genetree_member_id
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+
# @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/genetree_member_id
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# @return [JSON] gene trees
|
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def genetree_member_id(id, options = {})
|
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return EnsemblREST.get("genetree/member/id/#{id}", {format: 'json'}.merge(options))
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@@ -35,9 +35,9 @@ module EnsemblREST
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# Retrieves a gene tree containing the gene identified by a symbol
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#
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# @param [String] Symbol or display name of a gene
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# @param [String] Species name/alias
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-
# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree_member_symbol
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# @param [String] symbol Symbol or display name of a gene
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# @param [String] species Species name/alias
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# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genetree_member_symbol
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# @return [JSON] gene trees
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def genetree_member_symbol(symbol, species = 'human', options = {})
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return EnsemblREST.get("genetree/member/symbol/#{species}/#{symbol}", {format: 'json'}.merge(options))
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@@ -45,9 +45,9 @@ module EnsemblREST
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# Retrieves genomic alignments as separate blocks based on a region and species
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#
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# @param [String] Query region. A maximum of 10Mb is allowed to be requested at any one time
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# @param [String] Species name/alias
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# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genomic_alignment_region
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+
# @param [String] region Query region. A maximum of 10Mb is allowed to be requested at any one time
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# @param [String] species Species name/alias
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# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/genomic_alignment_region
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# @return [JSON] an alignment
|
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def genomic_alignment_region(region, species = 'human', options = {})
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return EnsemblREST.get("alignment/region/#{species}/#{region}", {format: 'json'}.merge(options))
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@@ -55,8 +55,8 @@ module EnsemblREST
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# Retrieves homology information (orthologs) by Ensembl gene id
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#
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# @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/homology_ensemblgene
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+
# @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/homology_ensemblgene
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# @return [JSON] a homology information
|
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def homology_ensemblgene(id, options = {})
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return EnsemblREST.get("homology/id/#{id}", {format: 'json'}.merge(options))
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@@ -64,9 +64,9 @@ module EnsemblREST
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# Retrieves homology information (orthologs) by symbol
|
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#
|
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-
# @param [String] Symbol or display name of a gene
|
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-
# @param [String] Species name/alias
|
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-
# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/homology_symbol
|
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+
# @param [String] symbol Symbol or display name of a gene
|
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+
# @param [String] species Species name/alias
|
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+
# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/homology_symbol
|
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# @return [JSON] gene trees
|
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def homology_symbol(symbol, species = 'human', options = {})
|
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return EnsemblREST.get("homology/symbol/#{species}/#{symbol}", {format: 'json'}.merge(options))
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data/lib/ensemblrest/connect.rb
CHANGED
@@ -40,7 +40,7 @@ module EnsemblREST
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# Connect to Ensembl REST Service
|
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#
|
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-
# @param [String] Base Ensembl REST Service URL
|
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+
# @param [String] server Base Ensembl REST Service URL
|
44
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def connect(server)
|
45
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@@url = URI.parse(server)
|
46
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@@http_connect = Net::HTTP.new(@@url.host, @@url.port)
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data/lib/ensemblrest/info.rb
CHANGED
@@ -16,8 +16,8 @@ module EnsemblREST
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16
16
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17
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# List the names of analyses involved in generating Ensembl data.
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#
|
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-
# @param [String] Species name/alias
|
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-
# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/analysis
|
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+
# @param [String] species Species name/alias
|
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+
# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/analysis
|
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# @return [JSON] List the names of analyses
|
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def analysis(species = 'human', options = {})
|
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return EnsemblREST.get("info/analysis/#{species}", {format: 'json'}.merge(options))
|
@@ -25,8 +25,8 @@ module EnsemblREST
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# List the currently available assemblies for a species.
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#
|
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-
# @param [String] Species name/alias
|
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-
# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_info
|
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+
# @param [String] species Species name/alias
|
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+
# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_info
|
30
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# @return [JSON] List the currently available assemblies
|
31
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def assembly_info(species = 'human', options = {})
|
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return EnsemblREST.get("info/assembly/#{species}", {format: 'json'}.merge(options))
|
@@ -34,9 +34,9 @@ module EnsemblREST
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# Returns information about the specified toplevel sequence region for the given species.
|
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#
|
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-
# @param [String] The (top level) sequence region name.
|
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# @param [String] Species name/alias
|
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-
# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_stats
|
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+
# @param [String] region_name The (top level) sequence region name.
|
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+
# @param [String] species Species name/alias
|
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# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/assembly_stats
|
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# @return [JSON] Returns information about the specified toplevel sequence region
|
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def assembly_stats(region_name, species = 'human', options = {})
|
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return EnsemblREST.get("info/assembly/#{species}/#{region_name}", {format: 'json'}.merge(options))
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@@ -45,8 +45,8 @@ module EnsemblREST
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# List the functional classifications of gene models that Ensembl associates with a particular species.
|
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# Useful for restricting the type of genes/transcripts retrieved by other endpoints.
|
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#
|
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-
# @param [String] Species name/alias
|
49
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-
# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/biotypes
|
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+
# @param [String] species Species name/alias
|
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+
# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/biotypes
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# @return [JSON] List the currently available assemblies
|
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def biotypes(species = 'human', options = {})
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return EnsemblREST.get("info/biotypes/#{species}", {format: 'json'}.merge(options))
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@@ -54,7 +54,7 @@ module EnsemblREST
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# List all compara analyses available (an analysis defines the type of comparative data).
|
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#
|
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# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/compara_methods
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# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/compara_methods
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# @return [JSON] List all compara analyses
|
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def compara_methods(options = {})
|
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return EnsemblREST.get("info/compara/methods", {format: 'json'}.merge(options))
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@@ -62,8 +62,8 @@ module EnsemblREST
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# List all collections of species analysed with the specified compara method.
|
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#
|
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# @param [String] Filter by compara method. Use one the methods returned by /info/compara/methods endpoint.
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# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/compara_species_sets
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+
# @param [String] method Filter by compara method. Use one the methods returned by /info/compara/methods endpoint.
|
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+
# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/compara_species_sets
|
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# @return [JSON] List the currently available assemblies
|
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def compara_species_sets(method, options = {})
|
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return EnsemblREST.get("info/compara/species_sets/#{method}", {format: 'json'}.merge(options))
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@@ -71,7 +71,7 @@ module EnsemblREST
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# Lists all available comparative genomics databases and their data release.
|
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#
|
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# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/comparas
|
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# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/comparas
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# @return [JSON] List all compara analyses
|
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def comparas(options = {})
|
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return EnsemblREST.get("info/comparas", {format: 'json'}.merge(options))
|
@@ -79,7 +79,7 @@ module EnsemblREST
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# Shows the data releases available on this REST server. May return more than one release (unfrequent non-standard Ensembl configuration).
|
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#
|
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-
# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/data
|
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# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/data
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# @return [JSON] Shows the data releases available on this REST server
|
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def data(options = {})
|
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return EnsemblREST.get("info/data", {format: 'json'}.merge(options))
|
@@ -87,8 +87,8 @@ module EnsemblREST
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# Lists all available external sources for a species.
|
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#
|
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-
# @param [String] Species name/alias
|
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-
# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/external_dbs
|
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|
+
# @param [String] species Species name/alias
|
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+
# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/external_dbs
|
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# @return [JSON] Lists all available external sources
|
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def external_dbs(species = 'human', options = {})
|
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return EnsemblREST.get("info/external_dbs/#{species}", {format: 'json'}.merge(options))
|
@@ -96,7 +96,7 @@ module EnsemblREST
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|
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|
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# Checks if the service is alive.
|
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#
|
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-
# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ping
|
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+
# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/ping
|
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# @return [Boolean] True/False
|
101
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|
def ping(options = {})
|
102
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|
begin
|
@@ -109,7 +109,7 @@ module EnsemblREST
|
|
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# Shows the current version of the Ensembl REST API.
|
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#
|
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|
-
# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/rest
|
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+
# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/rest
|
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# @return [String] version of this REST server
|
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def rest(options = {})
|
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return EnsemblREST.get("info/rest", {format: 'json'}.merge(options))["release"]
|
@@ -117,7 +117,7 @@ module EnsemblREST
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|
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# Shows the current version of the Ensembl API used by the REST server.
|
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#
|
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-
# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/software
|
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+
# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/software
|
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# @return [String] the current version of the Ensembl API
|
122
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def software(options = {})
|
123
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return EnsemblREST.get("info/software", {format: 'json'}.merge(options))["release"]
|
@@ -125,7 +125,7 @@ module EnsemblREST
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# Lists all available species, their aliases, available adaptor groups and data release.
|
127
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|
#
|
128
|
-
# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/species
|
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+
# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/species
|
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# @return [String] Lists all available species
|
130
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|
def species(options = {})
|
131
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return EnsemblREST.get("info/species", {format: 'json'}.merge(options))
|
data/lib/ensemblrest/lookup.rb
CHANGED
@@ -15,9 +15,9 @@ module EnsemblREST
|
|
15
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|
|
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
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|
35
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|
# Find the species and database for a set of symbols in a linked external database. Unknown symbols are omitted from the response.
|
36
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|
#
|
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
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|
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))
|
@@ -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))
|
@@ -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]
|
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
|
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|
# @return [JSON] the variation features
|
23
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|
def id(id, species = 'human', options = {})
|
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|
return EnsemblREST.get("variation/#{species}/#{id}", {format: 'json'}.merge(options))
|
@@ -26,8 +26,9 @@ module EnsemblREST
|
|
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|
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# Uses a list of variation identifiers (e.g. rsID) to return the variation features
|
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|
#
|
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-
# @param [
|
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-
# @param [
|
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+
# @param [Array] ids RegulatoryFeature stable IDs
|
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+
# @param [String] species Species name/alias
|
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+
# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/variation_post
|
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# @return [JSON] the variation features
|
32
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|
def post(ids, species = 'human', options = {})
|
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return EnsemblREST.post("variation/#{species}", {"ids" => ids}, {format: 'json'}.merge(options))
|
@@ -16,7 +16,7 @@ module EnsemblREST
|
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# Return a list of sets of genotype calls for specific samples in GA4GH format
|
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#
|
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-
# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gacallSet
|
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|
+
# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gacallSet
|
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# @return [JSON] a list of sets of genotype calls for specific samples
|
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def gacallSet(options = {})
|
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return EnsemblREST.post("ga4gh/callsets/search", {}, {format: 'json'}.merge(options))
|
@@ -24,11 +24,11 @@ module EnsemblREST
|
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|
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|
# Return variant call information in GA4GH format for a region on a reference sequence
|
26
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#
|
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-
# @param [Integer] Start position of region (zero-based, inclusive)
|
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|
-
# @param [Integer] End position of region (zero-based, exclusive)
|
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|
-
# @param [String] Reference sequence name
|
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-
# @param [
|
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-
# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gavariants
|
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|
+
# @param [Integer] start Start position of region (zero-based, inclusive)
|
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+
# @param [Integer] stop End position of region (zero-based, exclusive)
|
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+
# @param [String] referenceName Reference sequence name
|
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+
# @param [Array] variantSetIds Return variant data for specific variantSets
|
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+
# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gavariants
|
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# @return [JSON] variant call information in GA4GH format
|
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|
def gavariants(start, stop, referenceName, variantSetIds, options = {})
|
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|
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
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|
|
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|
# Return a list of variant sets in GA4GH format
|
38
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|
#
|
39
|
-
# @param [Hash] Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gavariantset
|
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|
+
# @param [Hash] options Optional arguments for the service please goto http://rest.ensembl.org/documentation/info/gavariantset
|
40
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|
# @return [JSON] a list of variant sets in GA4GH format
|
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|
def gavariantset(options = {})
|
42
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|
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
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|
#
|
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
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))
|