Retrieves features (e.g. genes, transcripts, variants and more) that overlap a given region.
Name | Type | Description | Default | Example Values |
---|---|---|---|---|
feature | Enum(band, gene, transcript, cds, exon, repeat, simple, misc, variation, somatic_variation, structural_variation, somatic_structural_variation, constrained, regulatory, motif, mane) | The type of feature to retrieve. Multiple values are accepted. | none | - |
region | String | Query region. A maximum of 5Mb is allowed to be requested at any one time | - |
X:1..1000:1 X:1..1000:-1 X:1..1000 |
species | String | Species name/alias. | - |
homo_sapiens |
Name | Type | Description | Default | Example Values |
---|---|---|---|---|
biotype | String | Functional classification of the gene or transcript to fetch. Cannot be used in conjunction with logic_name when querying transcripts. | - |
protein_coding |
callback | String | Name of the callback subroutine to be returned by the requested JSONP response. Required ONLY when using JSONP as the serialisation method. Please see the user guide. | - |
randomlygeneratedname |
db_type | String | Specify the database type to retrieve features from if not using the core database. We automatically choose the correct type of DB for variation, comparative and regulation features. | core |
core otherfeatures |
logic_name | String | Limit retrieval of genes, transcripts and exons by the name of analysis. | - | - |
misc_set | String | Miscellaneous set which groups together feature entries. Consult the DB or returned data sets to discover what is available. | - |
cloneset_30k |
so_term | String | Sequence Ontology term to restrict the variants found. Its descendants are also included in the search. | - |
SO:0001650 |
species_set | String | The species set name for retrieving constrained elements. | mammals | - |
trim_downstream | Boolean | Do not return features which overlap the downstream end of the region. | 0 | - |
trim_upstream | Boolean | Do not return features which overlap upstream end of the region. | 0 | - |
variant_set | String | Short name of a set to restrict the variants found. (See list of short set names) | - |
ClinVar |
use strict; use warnings; use HTTP::Tiny; my $http = HTTP::Tiny->new(); my $server = 'https://grch37.rest.ensembl.org'; my $ext = '/overlap/region/human/7:140424943-140624564?feature=gene;feature=transcript;feature=cds;feature=exon'; my $response = $http->get($server.$ext, { headers => { 'Content-type' => 'application/json' } }); die "Failed!\n" unless $response->{success}; use JSON; use Data::Dumper; if(length $response->{content}) { my $hash = decode_json($response->{content}); local $Data::Dumper::Terse = 1; local $Data::Dumper::Indent = 1; print Dumper $hash; print "\n"; }
import requests, sys server = "https://grch37.rest.ensembl.org" ext = "/overlap/region/human/7:140424943-140624564?feature=gene;feature=transcript;feature=cds;feature=exon" r = requests.get(server+ext, headers={ "Content-Type" : "application/json"}) if not r.ok: r.raise_for_status() sys.exit() decoded = r.json() print repr(decoded)
import requests, sys server = "https://grch37.rest.ensembl.org" ext = "/overlap/region/human/7:140424943-140624564?feature=gene;feature=transcript;feature=cds;feature=exon" r = requests.get(server+ext, headers={ "Content-Type" : "application/json"}) if not r.ok: r.raise_for_status() sys.exit() decoded = r.json() print(repr(decoded))
require 'net/http' require 'uri' server='https://grch37.rest.ensembl.org' path = '/overlap/region/human/7:140424943-140624564?feature=gene;feature=transcript;feature=cds;feature=exon' url = URI.parse(server) http = Net::HTTP.new(url.host, url.port) request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'}) response = http.request(request) if response.code != "200" puts "Invalid response: #{response.code}" puts response.body exit end require 'rubygems' require 'json' require 'yaml' result = JSON.parse(response.body) puts YAML::dump(result)
import java.net.URL; import java.net.URLConnection; import java.net.HttpURLConnection; import java.io.BufferedReader; import java.io.InputStream; import java.io.InputStreamReader; import java.io.IOException; import java.io.Reader; public class EnsemblRest { public static void main(String[] args) throws Exception { String server = "https://grch37.rest.ensembl.org"; String ext = "/overlap/region/human/7:140424943-140624564?feature=gene;feature=transcript;feature=cds;feature=exon"; URL url = new URL(server + ext); URLConnection connection = url.openConnection(); HttpURLConnection httpConnection = (HttpURLConnection)connection; httpConnection.setRequestProperty("Content-Type", "application/json"); InputStream response = connection.getInputStream(); int responseCode = httpConnection.getResponseCode(); if(responseCode != 200) { throw new RuntimeException("Response code was not 200. Detected response was "+responseCode); } String output; Reader reader = null; try { reader = new BufferedReader(new InputStreamReader(response, "UTF-8")); StringBuilder builder = new StringBuilder(); char[] buffer = new char[8192]; int read; while ((read = reader.read(buffer, 0, buffer.length)) > 0) { builder.append(buffer, 0, read); } output = builder.toString(); } finally { if (reader != null) try { reader.close(); } catch (IOException logOrIgnore) { logOrIgnore.printStackTrace(); } } System.out.println(output); } }
library(httr) library(jsonlite) library(xml2) server <- "https://grch37.rest.ensembl.org" ext <- "/overlap/region/human/7:140424943-140624564?feature=gene;feature=transcript;feature=cds;feature=exon" r <- GET(paste(server, ext, sep = ""), content_type("application/json")) stop_for_status(r) # use this if you get a simple nested list back, otherwise inspect its structure # head(data.frame(t(sapply(content(r),c)))) head(fromJSON(toJSON(content(r))))
curl 'https://grch37.rest.ensembl.org/overlap/region/human/7:140424943-140624564?feature=gene;feature=transcript;feature=cds;feature=exon' -H 'Content-type:application/json'
wget -q --header='Content-type:application/json' 'https://grch37.rest.ensembl.org/overlap/region/human/7:140424943-140624564?feature=gene;feature=transcript;feature=cds;feature=exon' -O -
use strict; use warnings; use HTTP::Tiny; my $http = HTTP::Tiny->new(); my $server = 'https://grch37.rest.ensembl.org'; my $ext = '/overlap/region/human/7:140424943-140624564?feature=gene;feature=transcript;feature=cds;feature=exon'; my $response = $http->get($server.$ext, { headers => { 'Content-type' => 'text/x-gff3' } }); die "Failed!\n" unless $response->{success}; print "$response->{content}\n";
import requests, sys server = "https://grch37.rest.ensembl.org" ext = "/overlap/region/human/7:140424943-140624564?feature=gene;feature=transcript;feature=cds;feature=exon" r = requests.get(server+ext, headers={ "Content-Type" : "text/x-gff3"}) if not r.ok: r.raise_for_status() sys.exit() print r.text
import requests, sys server = "https://grch37.rest.ensembl.org" ext = "/overlap/region/human/7:140424943-140624564?feature=gene;feature=transcript;feature=cds;feature=exon" r = requests.get(server+ext, headers={ "Content-Type" : "text/x-gff3"}) if not r.ok: r.raise_for_status() sys.exit() print(r.text)
require 'net/http' require 'uri' server='https://grch37.rest.ensembl.org' path = '/overlap/region/human/7:140424943-140624564?feature=gene;feature=transcript;feature=cds;feature=exon' url = URI.parse(server) http = Net::HTTP.new(url.host, url.port) request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-gff3'}) response = http.request(request) if response.code != "200" puts "Invalid response: #{response.code}" puts response.body exit end puts response.body
import java.net.URL; import java.net.URLConnection; import java.net.HttpURLConnection; import java.io.BufferedReader; import java.io.InputStream; import java.io.InputStreamReader; import java.io.IOException; import java.io.Reader; public class EnsemblRest { public static void main(String[] args) throws Exception { String server = "https://grch37.rest.ensembl.org"; String ext = "/overlap/region/human/7:140424943-140624564?feature=gene;feature=transcript;feature=cds;feature=exon"; URL url = new URL(server + ext); URLConnection connection = url.openConnection(); HttpURLConnection httpConnection = (HttpURLConnection)connection; httpConnection.setRequestProperty("Content-Type", "text/x-gff3"); InputStream response = connection.getInputStream(); int responseCode = httpConnection.getResponseCode(); if(responseCode != 200) { throw new RuntimeException("Response code was not 200. Detected response was "+responseCode); } String output; Reader reader = null; try { reader = new BufferedReader(new InputStreamReader(response, "UTF-8")); StringBuilder builder = new StringBuilder(); char[] buffer = new char[8192]; int read; while ((read = reader.read(buffer, 0, buffer.length)) > 0) { builder.append(buffer, 0, read); } output = builder.toString(); } finally { if (reader != null) try { reader.close(); } catch (IOException logOrIgnore) { logOrIgnore.printStackTrace(); } } System.out.println(output); } }
library(httr) library(jsonlite) library(xml2) server <- "https://grch37.rest.ensembl.org" ext <- "/overlap/region/human/7:140424943-140624564?feature=gene;feature=transcript;feature=cds;feature=exon" r <- GET(paste(server, ext, sep = ""), content_type("text/x-gff3")) stop_for_status(r) print(content(r))
curl 'https://grch37.rest.ensembl.org/overlap/region/human/7:140424943-140624564?feature=gene;feature=transcript;feature=cds;feature=exon' -H 'Content-type:text/x-gff3'
wget -q --header='Content-type:text/x-gff3' 'https://grch37.rest.ensembl.org/overlap/region/human/7:140424943-140624564?feature=gene;feature=transcript;feature=cds;feature=exon' -O -
Methods | GET |
Response formats | json xml gff3 bed jsonp |
Slice length | 5e6 |