POST ga4gh/beacon/query

Return the Beacon response for allele information

Parameters

Required

NameTypeDescriptionDefaultExample Values
alternateBases String The bases that appear instead of the reference bases. Accepted values: see the ALT field in VCF 4.2 specification (http://samtools.github.io/hts-specs/VCFv4.2.pdf). - C
assemblyId String Assembly identifier (GRC notation, e.g. GRCh38). - GRCh38
referenceBases String Reference bases for this variant (starting from start). Accepted values: see the REF field in VCF 4.2 specification (http://samtools.github.io/hts-specs/VCFv4.2.pdf). - G
referenceName String Reference name (chromosome). Accepted values: 1-22, X, Y. - 9
start Int Position, allele locus (0-based). Accepted values: non-negative integers smaller than reference length. - 22125503

Optional

NameTypeDescriptionDefaultExample 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
datasetIds array of strings Identifiers of datasets. Option not used currently as single dataset. - -
includeDatasetResponses boolean Indicator of whether responses for individual datasets should be included. false -

Message

Content-typeFormatExample
application/json{ "referenceName": string, "start": integer, "referenceBases": string, "alternateBases": string, "assemblyId": string}{ "referenceName": "9", "start" : 22125503, "referenceBases": "G", "alternateBases": "C","assemblyId" : "GRCh38","includeDatasetResponses": "true" }

Example Requests

/ga4gh/beacon/query


{ "referenceName": "9", "start" : 22125503, "referenceBases": "G", "alternateBases": "C","assemblyId" : "GRCh38" }
        
use strict;
use warnings;

use HTTP::Tiny;

my $http = HTTP::Tiny->new();

my $server = 'http://rest.ensembl.org';
my $ext = '/ga4gh/beacon/query';
my $response = $http->request('POST', $server.$ext, {
  headers => { 
  	'Content-type' => 'application/json',
  	'Accept' => 'application/json'
  },
  content => '{ "referenceName": "9", "start" : 22125503, "referenceBases": "G", "alternateBases": "C","assemblyId" : "GRCh38" }'
});

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 = "http://rest.ensembl.org"
ext = "/ga4gh/beacon/query"
headers={ "Content-Type" : "application/json", "Accept" : "application/json"}
r = requests.post(server+ext, headers=headers, data='{ "referenceName": "9", "start" : 22125503, "referenceBases": "G", "alternateBases": "C","assemblyId" : "GRCh38" }')

if not r.ok:
  r.raise_for_status()
  sys.exit()

decoded = r.json()
print repr(decoded)

import requests, sys

server = "http://rest.ensembl.org"
ext = "/ga4gh/beacon/query"
headers={ "Content-Type" : "application/json", "Accept" : "application/json"}
r = requests.post(server+ext, headers=headers, data='{ "referenceName": "9", "start" : 22125503, "referenceBases": "G", "alternateBases": "C","assemblyId" : "GRCh38" }')

if not r.ok:
  r.raise_for_status()
  sys.exit()

decoded = r.json()
print(repr(decoded))

require 'net/http'
require 'uri'

server='http://rest.ensembl.org'
path = '/ga4gh/beacon/query'

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 = '{ "referenceName": "9", "start" : 22125503, "referenceBases": "G", "alternateBases": "C","assemblyId" : "GRCh38" }'

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 = "http://rest.ensembl.org";
    String ext = "/ga4gh/beacon/query";
    URL url = new URL(server + ext);

    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    String postBody = "{ \"referenceName\": \"9\", \"start\" : 22125503, \"referenceBases\": \"G\", \"alternateBases\": \"C\",\"assemblyId\" : \"GRCh38\" }";
    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);
  }
}

curl 'http://rest.ensembl.org/ga4gh/beacon/query' -H 'Content-type:application/json' \
-H 'Accept:application/json' -X POST -d '{ "referenceName": "9", "start" : 22125503, "referenceBases": "G", "alternateBases": "C","assemblyId" : "GRCh38" }'

wget -q --header='Content-type:application/json' --header='Accept:application/json' \
--post-data='{ "referenceName": "9", "start" : 22125503, "referenceBases": "G", "alternateBases": "C","assemblyId" : "GRCh38" }' \
'http://rest.ensembl.org/ga4gh/beacon/query'  -O -

/ga4gh/beacon/query


{ "referenceName": "9", "start" : 22125503, "referenceBases": "G", "alternateBases": "C","assemblyId" : "GRCh38","includeDatasetResponses": "true"  }
        
use strict;
use warnings;

use HTTP::Tiny;

my $http = HTTP::Tiny->new();

my $server = 'http://rest.ensembl.org';
my $ext = '/ga4gh/beacon/query';
my $response = $http->request('POST', $server.$ext, {
  headers => { 
  	'Content-type' => 'application/json',
  	'Accept' => 'application/json'
  },
  content => '{ "referenceName": "9", "start" : 22125503, "referenceBases": "G", "alternateBases": "C","assemblyId" : "GRCh38","includeDatasetResponses": "true"  }'
});

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 = "http://rest.ensembl.org"
ext = "/ga4gh/beacon/query"
headers={ "Content-Type" : "application/json", "Accept" : "application/json"}
r = requests.post(server+ext, headers=headers, data='{ "referenceName": "9", "start" : 22125503, "referenceBases": "G", "alternateBases": "C","assemblyId" : "GRCh38","includeDatasetResponses": "true"  }')

if not r.ok:
  r.raise_for_status()
  sys.exit()

decoded = r.json()
print repr(decoded)

import requests, sys

server = "http://rest.ensembl.org"
ext = "/ga4gh/beacon/query"
headers={ "Content-Type" : "application/json", "Accept" : "application/json"}
r = requests.post(server+ext, headers=headers, data='{ "referenceName": "9", "start" : 22125503, "referenceBases": "G", "alternateBases": "C","assemblyId" : "GRCh38","includeDatasetResponses": "true"  }')

if not r.ok:
  r.raise_for_status()
  sys.exit()

decoded = r.json()
print(repr(decoded))

require 'net/http'
require 'uri'

server='http://rest.ensembl.org'
path = '/ga4gh/beacon/query'

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 = '{ "referenceName": "9", "start" : 22125503, "referenceBases": "G", "alternateBases": "C","assemblyId" : "GRCh38","includeDatasetResponses": "true"  }'

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 = "http://rest.ensembl.org";
    String ext = "/ga4gh/beacon/query";
    URL url = new URL(server + ext);

    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    String postBody = "{ \"referenceName\": \"9\", \"start\" : 22125503, \"referenceBases\": \"G\", \"alternateBases\": \"C\",\"assemblyId\" : \"GRCh38\",\"includeDatasetResponses\": \"true\"  }";
    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);
  }
}

curl 'http://rest.ensembl.org/ga4gh/beacon/query' -H 'Content-type:application/json' \
-H 'Accept:application/json' -X POST -d '{ "referenceName": "9", "start" : 22125503, "referenceBases": "G", "alternateBases": "C","assemblyId" : "GRCh38","includeDatasetResponses": "true"  }'

wget -q --header='Content-type:application/json' --header='Accept:application/json' \
--post-data='{ "referenceName": "9", "start" : 22125503, "referenceBases": "G", "alternateBases": "C","assemblyId" : "GRCh38","includeDatasetResponses": "true"  }' \
'http://rest.ensembl.org/ga4gh/beacon/query'  -O -

Resource Information

MethodsPOST
Response formatsjson
jsonp