Request multiple types of sequence by a list of regions.
Name | Type | Description | Default | Example Values |
---|---|---|---|---|
species | String | Species name/alias | - |
homo_sapiens human |
Name | Type | Description | Default | Example Values |
---|---|---|---|---|
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 |
coord_system | String | Filter by coordinate system name | - |
contig seqlevel |
coord_system_version | String | Filter by coordinate system version | - |
GRCh37 |
expand_3prime | Int | Expand the sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type. | - |
1000 |
expand_5prime | Int | Expand the sequence upstream of the sequence by this many basepairs. Only available when using genomic sequence type. | - |
1000 |
format | Enum(fasta) | Format of the data. | - |
fasta |
mask | Enum(hard,soft) | Request the sequence masked for repeat sequences. Hard will mask all repeats as N's and soft will mask repeats as lower cased characters. Only available when using genomic sequence type. | - |
hard |
mask_feature | Boolean | Mask features on the sequence. If sequence is genomic, mask introns. If sequence is cDNA, mask UTRs. Incompatible with the 'mask' option | 0 |
1 |
Content-type | Format | Example |
application/json | { "regions": array } | { "regions" : ["X:1000000..1000100:1", "ABBA01004489.1:1..100"] } |
{ "regions" : ["X:1000000..1000100:1", "ABBA01004489.1:1..100"] }
use strict; use warnings; use HTTP::Tiny; my $http = HTTP::Tiny->new(); my $server = 'https://grch37.rest.ensembl.org'; my $ext = '/sequence/region/human'; my $response = $http->request('POST', $server.$ext, { headers => { 'Content-type' => 'application/json', 'Accept' => 'application/json' }, content => '{ "regions" : ["X:1000000..1000100:1", "ABBA01004489.1:1..100"] }' }); 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 = "/sequence/region/human" headers={ "Content-Type" : "application/json", "Accept" : "application/json"} r = requests.post(server+ext, headers=headers, data='{ "regions" : ["X:1000000..1000100:1", "ABBA01004489.1:1..100"] }') 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 = "/sequence/region/human" headers={ "Content-Type" : "application/json", "Accept" : "application/json"} r = requests.post(server+ext, headers=headers, data='{ "regions" : ["X:1000000..1000100:1", "ABBA01004489.1:1..100"] }') 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 = '/sequence/region/human' url = URI.parse(server) http = Net::HTTP.new(url.host, url.port) request = Net::HTTP::Post.new(path, {'Content-Type' => 'application/json', 'Accept' => 'application/json'}) request.body = '{ "regions" : ["X:1000000..1000100:1", "ABBA01004489.1:1..100"] }' 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; import java.io.DataOutputStream; public class EnsemblRest { public static void main(String[] args) throws Exception { String server = "https://grch37.rest.ensembl.org"; String ext = "/sequence/region/human"; URL url = new URL(server + ext); URLConnection connection = url.openConnection(); HttpURLConnection httpConnection = (HttpURLConnection)connection; String postBody = "{ \"regions\" : [\"X:1000000..1000100:1\", \"ABBA01004489.1:1..100\"] }"; httpConnection.setRequestMethod("POST"); httpConnection.setRequestProperty("Content-Type", "application/json"); httpConnection.setRequestProperty("Accept", "application/json"); httpConnection.setRequestProperty("Content-Length", Integer.toString(postBody.getBytes().length)); httpConnection.setUseCaches(false); httpConnection.setDoInput(true); httpConnection.setDoOutput(true); DataOutputStream wr = new DataOutputStream(httpConnection.getOutputStream()); wr.writeBytes(postBody); wr.flush(); wr.close(); 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 <- "/sequence/region/human" r <- POST(paste(server, ext, sep = ""), content_type("application/json"), accept("application/json"), body = '{ "regions" : ["X:1000000..1000100:1", "ABBA01004489.1:1..100"] }') 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/sequence/region/human' -H 'Content-type:application/json' \ -H 'Accept:application/json' -X POST -d '{ "regions" : ["X:1000000..1000100:1", "ABBA01004489.1:1..100"] }'
wget -q --header='Content-type:application/json' --header='Accept:application/json' \ --post-data='{ "regions" : ["X:1000000..1000100:1", "ABBA01004489.1:1..100"] }' \ 'https://grch37.rest.ensembl.org/sequence/region/human' -O -
Methods | POST |
Response formats | json jsonp |
Maximum POST size | 50 |
Slice length | 1e7 |