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 - GRCh37
asm_two String Version of the output assembly - GRCh38
region String Query region - X:1000000..1000100:1
X:1000000..1000100:-1
X:1000000..1000100
species String Species name/alias - homo_sapiens
human

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/human/GRCh37/X:1000000..1000100:1/GRCh38?content-type=application/json


  1. use strict;
  2. use warnings;
  3.  
  4. use HTTP::Tiny;
  5.  
  6. my $http = HTTP::Tiny->new();
  7.  
  8. my $server = 'http://rest.ensembl.org';
  9. my $ext = '/map/human/GRCh37/X:1000000..1000100:1/GRCh38?';
  10. my $response = $http->get($server.$ext, {
  11. headers => { 'Content-type' => 'application/json' }
  12. });
  13.  
  14. die "Failed!\n" unless $response->{success};
  15.  
  16.  
  17. use JSON;
  18. use Data::Dumper;
  19. if(length $response->{content}) {
  20. my $hash = decode_json($response->{content});
  21. local $Data::Dumper::Terse = 1;
  22. local $Data::Dumper::Indent = 1;
  23. print Dumper $hash;
  24. print "\n";
  25. }
  26.  
  1. import requests, sys
  2.  
  3. server = "http://rest.ensembl.org"
  4. ext = "/map/human/GRCh37/X:1000000..1000100:1/GRCh38?"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})
  7.  
  8. if not r.ok:
  9. r.raise_for_status()
  10. sys.exit()
  11.  
  12. decoded = r.json()
  13. print repr(decoded)
  14.  
  1. import requests, sys
  2.  
  3. server = "http://rest.ensembl.org"
  4. ext = "/map/human/GRCh37/X:1000000..1000100:1/GRCh38?"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})
  7.  
  8. if not r.ok:
  9. r.raise_for_status()
  10. sys.exit()
  11.  
  12. decoded = r.json()
  13. print(repr(decoded))
  14.  
  1. require 'net/http'
  2. require 'uri'
  3.  
  4. server='http://rest.ensembl.org'
  5. path = '/map/human/GRCh37/X:1000000..1000100:1/GRCh38?'
  6.  
  7. url = URI.parse(server)
  8. http = Net::HTTP.new(url.host, url.port)
  9.  
  10. request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'})
  11.  
  12. response = http.request(request)
  13.  
  14. if response.code != "200"
  15. puts "Invalid response: #{response.code}"
  16. puts response.body
  17. exit
  18. end
  19.  
  20.  
  21. require 'rubygems'
  22. require 'json'
  23. require 'yaml'
  24.  
  25. result = JSON.parse(response.body)
  26. puts YAML::dump(result)
  27.  
  1. import java.net.URL;
  2. import java.net.URLConnection;
  3. import java.net.HttpURLConnection;
  4. import java.io.BufferedReader;
  5. import java.io.InputStream;
  6. import java.io.InputStreamReader;
  7. import java.io.IOException;
  8. import java.io.Reader;
  9.  
  10.  
  11. public class EnsemblRest {
  12.  
  13. public static void main(String[] args) throws Exception {
  14. String server = "http://rest.ensembl.org";
  15. String ext = "/map/human/GRCh37/X:1000000..1000100:1/GRCh38?";
  16. URL url = new URL(server + ext);
  17.  
  18. URLConnection connection = url.openConnection();
  19. HttpURLConnection httpConnection = (HttpURLConnection)connection;
  20. httpConnection.setRequestProperty("Content-Type", "application/json");
  21.  
  22. InputStream response = connection.getInputStream();
  23. int responseCode = httpConnection.getResponseCode();
  24.  
  25. if(responseCode != 200) {
  26. throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
  27. }
  28.  
  29. String output;
  30. Reader reader = null;
  31. try {
  32. reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
  33. StringBuilder builder = new StringBuilder();
  34. char[] buffer = new char[8192];
  35. int read;
  36. while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
  37. builder.append(buffer, 0, read);
  38. }
  39. output = builder.toString();
  40. }
  41. finally {
  42. if (reader != null) try {
  43. reader.close();
  44. } catch (IOException logOrIgnore) {
  45. logOrIgnore.printStackTrace();
  46. }
  47. }
  48.  
  49. System.out.println(output);
  50. }
  51. }
  52.  
  1. library(httr)
  2. library(jsonlite)
  3. library(xml2)
  4.  
  5. server <- "http://rest.ensembl.org"
  6. ext <- "/map/human/GRCh37/X:1000000..1000100:1/GRCh38?"
  7.  
  8. r <- GET(paste(server, ext, sep = ""), content_type("application/json"))
  9.  
  10. stop_for_status(r)
  11.  
  12. # use this if you get a simple nested list back, otherwise inspect its structure
  13. # head(data.frame(t(sapply(content(r),c))))
  14. head(fromJSON(toJSON(content(r))))
  15.  
  1.  
  2. curl 'http://rest.ensembl.org/map/human/GRCh37/X:1000000..1000100:1/GRCh38?' -H 'Content-type:application/json'
  3.  
  1. wget -q --header='Content-type:application/json' 'http://rest.ensembl.org/map/human/GRCh37/X:1000000..1000100:1/GRCh38?' -O -
  2.  

Resource Information

MethodsGET
Response formatsjson
xml
jsonp