GET genetree/member/id/:id

Retrieves a gene tree that contains the stable identifier

Parameters

Required

NameTypeDescriptionDefaultExample Values
id String A stable ID - WBGene00221255

Optional

NameTypeDescriptionDefaultExample Values
aligned Boolean Return the aligned string if true. Otherwise, return the original sequence (no insertions) 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
db_type String Restrict the search to a database other than the default. Useful if you need to use a DB other than core - core
nh_format Enum(full, display_label_composite, simple, species, species_short_name, ncbi_taxon, ncbi_name, njtree, phylip) The format of a NH (New Hampshire) request. simple -
object_type String Filter by feature type - gene
transcript
sequence Enum(none, cdna, protein) The type of sequence to bring back. Setting it to none results in no sequence being returned protein -
species String Species name/alias - brugia_malayi_prjna10729

Example Requests

/rest-19/genetree/member/id/WBGene00221255?content-type=text/x-phyloxml%2Bxml


  1. use strict;
  2. use warnings;
  3.  
  4. use HTTP::Tiny;
  5.  
  6. my $http = HTTP::Tiny->new();
  7.  
  8. my $server = 'https://parasite.wormbase.org';
  9. my $ext = '/rest-19/genetree/member/id/WBGene00221255?';
  10. my $response = $http->get($server.$ext, {
  11. headers => { 'Content-type' => 'text/x-phyloxml+xml' }
  12. });
  13.  
  14. die "Failed!\n" unless $response->{success};
  15.  
  16.  
  17. print "$response->{status} $response->{reason}\n";
  18.  
  1. import requests, sys
  2.  
  3. server = "https://parasite.wormbase.org"
  4. ext = "/rest-19/genetree/member/id/WBGene00221255?"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-phyloxml+xml", "Accept" : ""})
  7.  
  8. if not r.ok:
  9. r.raise_for_status()
  10. sys.exit()
  11.  
  12.  
  13. print r.text
  14.  
  1. import requests, sys
  2.  
  3. server = "https://parasite.wormbase.org"
  4. ext = "/rest-19/genetree/member/id/WBGene00221255?"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-phyloxml+xml", "Accept" : ""})
  7.  
  8. if not r.ok:
  9. r.raise_for_status()
  10. sys.exit()
  11.  
  12.  
  13. print(r.text)
  14.  
  1. require 'net/http'
  2. require 'uri'
  3.  
  4. server='https://parasite.wormbase.org'
  5. path = '/rest-19/genetree/member/id/WBGene00221255?'
  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' => 'text/x-phyloxml+xml'})
  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. puts response.body
  22.  
  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 = "https://parasite.wormbase.org";
  15. String ext = "/rest-19/genetree/member/id/WBGene00221255?";
  16. URL url = new URL(server + ext);
  17.  
  18. URLConnection connection = url.openConnection();
  19. HttpURLConnection httpConnection = (HttpURLConnection)connection;
  20. httpConnection.setRequestProperty("Content-Type", "text/x-phyloxml+xml");
  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.  
  2. curl 'https://parasite.wormbase.org/rest-19/genetree/member/id/WBGene00221255?' -H 'Content-type:text/x-phyloxml+xml'
  3.  
  1. wget -q --header='Content-type:text/x-phyloxml+xml' 'https://parasite.wormbase.org/rest-19/genetree/member/id/WBGene00221255?' -O -
  2.  

Resource Information

MethodsGET
Response formatsphyloxml
nh
json
jsonp