POST ga4gh/variants/search

Return variant call information in GA4GH format for a region on a reference sequence

Parameters

Required

NameTypeDescriptionDefaultExample Values
end Int End position of region (zero-based, exclusive) - 25455087
referenceName String Reference sequence name - 22
start Int Start position of region (zero-based, inclusive) - 25455086
variantSetId String Return variant data for specific variantSets - 3

Optional

NameTypeDescriptionDefaultExample Values
callSetIds String Return variant data for specific callSets - [ 3:NA19777 ]
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
pageSize Int Number of variants to show per page 10 -
pageToken Int Identifier showing which page of data to retrieve next null -

Message

Content-typeFormatExample
application/json{"variantSetId": string, "callSetIds": array, "referenceName": string, "start": long, "end": long, "pageToken": string, "pageSize": long }{ "variantSetId": 3, "callSetIds":[ "3:NA19777" , "3:HG01242" , "3:HG01142" ], "referenceName": 22,"start": 17190024 ,"end": 17671934 , "pageToken":"", "pageSize": 3 }

Example Requests

/ga4gh/variants/search


{ "variantSetId": 3, "callSetIds":[ "3:NA19777"  , "3:HG01242" , "3:HG01142"   ], "referenceName": 22,"start": 17190024 ,"end":  17671934 ,  "pageToken":"", "pageSize": 3 }
        
use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'http://grch37.rest.ensembl.org';
my $ext = '/ga4gh/variants/search';
my $response = $http->request('POST', $server.$ext, {
  headers => { 
  	'Content-type' => 'application/json',
  	'Accept' => 'application/json'
  },
  content => '{ "variantSetId": 3, "callSetIds":[ "3:NA19777"  , "3:HG01242" , "3:HG01142"   ], "referenceName": 22,"start": 17190024 ,"end":  17671934 ,  "pageToken":"", "pageSize": 3 }'
});

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://grch37.rest.ensembl.org"
ext = "/ga4gh/variants/search"
headers={ "Content-Type" : "application/json", "Accept" : "application/json"}
r = requests.post(server+ext, headers=headers, data='{ "variantSetId": 3, "callSetIds":[ "3:NA19777"  , "3:HG01242" , "3:HG01142"   ], "referenceName": 22,"start": 17190024 ,"end":  17671934 ,  "pageToken":"", "pageSize": 3 }')

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

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

import requests, sys

server = "http://grch37.rest.ensembl.org"
ext = "/ga4gh/variants/search"
headers={ "Content-Type" : "application/json", "Accept" : "application/json"}
r = requests.post(server+ext, headers=headers, data='{ "variantSetId": 3, "callSetIds":[ "3:NA19777"  , "3:HG01242" , "3:HG01142"   ], "referenceName": 22,"start": 17190024 ,"end":  17671934 ,  "pageToken":"", "pageSize": 3 }')

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

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

require 'net/http'
require 'uri'

server='http://grch37.rest.ensembl.org'
path = '/ga4gh/variants/search'

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 = '{ "variantSetId": 3, "callSetIds":[ "3:NA19777"  , "3:HG01242" , "3:HG01142"   ], "referenceName": 22,"start": 17190024 ,"end":  17671934 ,  "pageToken":"", "pageSize": 3 }'

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://grch37.rest.ensembl.org";
    String ext = "/ga4gh/variants/search";
    URL url = new URL(server + ext);

    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    String postBody = "{ \"variantSetId\": 3, \"callSetIds\":[ \"3:NA19777\"  , \"3:HG01242\" , \"3:HG01142\"   ], \"referenceName\": 22,\"start\": 17190024 ,\"end\":  17671934 ,  \"pageToken\":\"\", \"pageSize\": 3 }";
    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://grch37.rest.ensembl.org/ga4gh/variants/search' -H 'Content-type:application/json' \
-H 'Accept:application/json' -X POST -d '{ "variantSetId": 3, "callSetIds":[ "3:NA19777"  , "3:HG01242" , "3:HG01142"   ], "referenceName": 22,"start": 17190024 ,"end":  17671934 ,  "pageToken":"", "pageSize": 3 }'

wget -q --header='Content-type:application/json' --header='Accept:application/json' \
--post-data='{ "variantSetId": 3, "callSetIds":[ "3:NA19777"  , "3:HG01242" , "3:HG01142"   ], "referenceName": 22,"start": 17190024 ,"end":  17671934 ,  "pageToken":"", "pageSize": 3 }' \
'http://grch37.rest.ensembl.org/ga4gh/variants/search'  -O -

Resource Information

MethodsPOST
Response formatsjson
jsonp