GET map/:species/:asm_one/:region/:asm_two

Convert the co-ordinates of one assembly to another

Parameters

Required

NameTypeDescriptionDefaultExample Values
asm_one String Version of the input assembly - TAIR9
asm_two String Version of the output assembly - TAIR10
region String Query region - 1:8001..18000:1
1:8001..18000:1
1:8001..18000
species String Species name/alias - arabidopsis_thaliana
Arabidopsis thaliana

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
coord_system String Name of the input coordinate system chromosome chromosome
target_coord_system String Name of the output coordinate system chromosome chromosome

Example Requests

/map/Arabidopsis thaliana/TAIR9/1:8001..18000:1/TAIR10?content-type=application/json


use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'http://rest.ensemblgenomes.org';
my $ext = '/map/Arabidopsis%20thaliana/TAIR9/1:8001..18000:1/TAIR10?';
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 = "http://rest.ensemblgenomes.org"
ext = "/map/Arabidopsis thaliana/TAIR9/1:8001..18000:1/TAIR10?"

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 = "http://rest.ensemblgenomes.org"
ext = "/map/Arabidopsis thaliana/TAIR9/1:8001..18000:1/TAIR10?"

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='http://rest.ensemblgenomes.org'
path = '/map/Arabidopsis%20thaliana/TAIR9/1:8001..18000:1/TAIR10?'

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 = "http://rest.ensemblgenomes.org";
    String ext = "/map/Arabidopsis%20thaliana/TAIR9/1:8001..18000:1/TAIR10?";
    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);
  }
}


curl 'http://rest.ensemblgenomes.org/map/Arabidopsis%20thaliana/TAIR9/1:8001..18000:1/TAIR10?' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'http://rest.ensemblgenomes.org/map/Arabidopsis thaliana/TAIR9/1:8001..18000:1/TAIR10?'  -O -

Resource Information

MethodsGET
Response formatsjson
xml
jsonp