GET ld/:species/:id/:population_name

Computes and returns LD values between the given variant and all other variants in a window centered around the given variant. The window size is set to 500 kb.

Parameters

Required

NameTypeDescriptionDefaultExample Values
id String Variant id - 2L.2422652
population_name String Population for which to compute LD. Use GET /info/variation/populations/:species?filter=LD to retrieve a list of all populations with LD data. - field isolates, Antula, Guinea-Bissau 1993
species String Species name/alias - anopheles_gambiae
Anopheles_gambiae

Optional

NameTypeDescriptionDefaultExample Values
attribs Boolean Add variation attributes for the variation which is used to compute LD data with the input variation: chr, start, end, strand, consequence_type, clinical_significance 0 -
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
d_prime Float Measure of LD. If D' is provided only return pairs of variants whose D' value is equal to or greater than the value provided. 0 0.666121
r2 Float Measure of LD. If r-squared is provided only return pairs of variants whose r-squared value is equal to or greater than the value provided. 0 __VAR(r2)__
window_size Integer Window size in kb. The maximum allowed value for the window size is 500 kb. LD is computed for the given variant and all variants that are located within the specified window. 500 500

Example Requests

/rest/ld/Anopheles_gambiae/2L.2402774/field isolates, Antula, Guinea-Bissau 1993?content-type=application/json


use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'https://www.vectorbase.org/rest';
my $ext = '/ld/Anopheles_gambiae/2L.2402774/field%20isolates,%20Antula,%20Guinea-Bissau%201993?';
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://www.vectorbase.org/rest"
ext = "/ld/Anopheles_gambiae/2L.2402774/field isolates, Antula, Guinea-Bissau 1993?"

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://www.vectorbase.org/rest"
ext = "/ld/Anopheles_gambiae/2L.2402774/field isolates, Antula, Guinea-Bissau 1993?"

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://www.vectorbase.org/rest'
path = '/ld/Anopheles_gambiae/2L.2402774/field%20isolates,%20Antula,%20Guinea-Bissau%201993?'

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://www.vectorbase.org/rest";
    String ext = "/ld/Anopheles_gambiae/2L.2402774/field%20isolates,%20Antula,%20Guinea-Bissau%201993?";
    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);
  }
}

# Note: curl version 7.34.0 or above is required

curl 'https://www.vectorbase.org/rest/ld/Anopheles_gambiae/2L.2402774/field isolates, Antula, Guinea-Bissau 1993?' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'https://www.vectorbase.org/rest/ld/Anopheles_gambiae/2L.2402774/field isolates, Antula, Guinea-Bissau 1993?'  -O -

/rest/ld/Anopheles_gambiae/2L.2402774/field isolates, Antula, Guinea-Bissau 1993?content-type=application/json;d_prime=0.666121


use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'https://www.vectorbase.org/rest';
my $ext = '/ld/Anopheles_gambiae/2L.2402774/field%20isolates,%20Antula,%20Guinea-Bissau%201993?d_prime=0.666121';
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://www.vectorbase.org/rest"
ext = "/ld/Anopheles_gambiae/2L.2402774/field isolates, Antula, Guinea-Bissau 1993?d_prime=0.666121"

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://www.vectorbase.org/rest"
ext = "/ld/Anopheles_gambiae/2L.2402774/field isolates, Antula, Guinea-Bissau 1993?d_prime=0.666121"

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://www.vectorbase.org/rest'
path = '/ld/Anopheles_gambiae/2L.2402774/field%20isolates,%20Antula,%20Guinea-Bissau%201993?d_prime=0.666121'

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://www.vectorbase.org/rest";
    String ext = "/ld/Anopheles_gambiae/2L.2402774/field%20isolates,%20Antula,%20Guinea-Bissau%201993?d_prime=0.666121";
    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);
  }
}

# Note: curl version 7.34.0 or above is required

curl 'https://www.vectorbase.org/rest/ld/Anopheles_gambiae/2L.2402774/field isolates, Antula, Guinea-Bissau 1993?d_prime=0.666121' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'https://www.vectorbase.org/rest/ld/Anopheles_gambiae/2L.2402774/field isolates, Antula, Guinea-Bissau 1993?d_prime=0.666121'  -O -

/rest/ld/Anopheles_gambiae/2L.2402774/field isolates, Antula, Guinea-Bissau 1993?content-type=application/json;d_prime=0.666121;window_size=500


use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'https://www.vectorbase.org/rest';
my $ext = '/ld/Anopheles_gambiae/2L.2402774/field%20isolates,%20Antula,%20Guinea-Bissau%201993?d_prime=0.666121;window_size=500';
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://www.vectorbase.org/rest"
ext = "/ld/Anopheles_gambiae/2L.2402774/field isolates, Antula, Guinea-Bissau 1993?d_prime=0.666121;window_size=500"

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://www.vectorbase.org/rest"
ext = "/ld/Anopheles_gambiae/2L.2402774/field isolates, Antula, Guinea-Bissau 1993?d_prime=0.666121;window_size=500"

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://www.vectorbase.org/rest'
path = '/ld/Anopheles_gambiae/2L.2402774/field%20isolates,%20Antula,%20Guinea-Bissau%201993?d_prime=0.666121;window_size=500'

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://www.vectorbase.org/rest";
    String ext = "/ld/Anopheles_gambiae/2L.2402774/field%20isolates,%20Antula,%20Guinea-Bissau%201993?d_prime=0.666121;window_size=500";
    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);
  }
}

# Note: curl version 7.34.0 or above is required

curl 'https://www.vectorbase.org/rest/ld/Anopheles_gambiae/2L.2402774/field isolates, Antula, Guinea-Bissau 1993?d_prime=0.666121;window_size=500' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'https://www.vectorbase.org/rest/ld/Anopheles_gambiae/2L.2402774/field isolates, Antula, Guinea-Bissau 1993?d_prime=0.666121;window_size=500'  -O -

Resource Information

MethodsGET
Response formatsjson
xml
jsonp