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-8/genetree/member/id/WBGene00221255?content-type=text/x-phyloxml%2Bxml


use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'http://parasite.wormbase.org';
my $ext = '/rest-8/genetree/member/id/WBGene00221255?';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/x-phyloxml+xml' }
});

die "Failed!\n" unless $response->{success};


print "$response->{status} $response->{reason}\n";

import requests, sys

server = "http://parasite.wormbase.org"
ext = "/rest-8/genetree/member/id/WBGene00221255?"

r = requests.get(server+ext, headers={ "Content-Type" : "text/x-phyloxml+xml"})

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


print r.text

import requests, sys

server = "http://parasite.wormbase.org"
ext = "/rest-8/genetree/member/id/WBGene00221255?"

r = requests.get(server+ext, headers={ "Content-Type" : "text/x-phyloxml+xml"})

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


print r.text

require 'net/http'
require 'uri'

server='http://parasite.wormbase.org'
path = '/rest-8/genetree/member/id/WBGene00221255?'

url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)

request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-phyloxml+xml'})

response = http.request(request)

if response.code != "200"
  puts "Invalid response: #{response.code}"
  puts response.body
  exit
end


puts response.body

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://parasite.wormbase.org";
    String ext = "/rest-8/genetree/member/id/WBGene00221255?";
    URL url = new URL(server + ext);

    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "text/x-phyloxml+xml");
    

    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://parasite.wormbase.org/rest-8/genetree/member/id/WBGene00221255?' -H 'Content-type:text/x-phyloxml+xml'

wget -q --header='Content-type:text/x-phyloxml+xml' 'http://parasite.wormbase.org/rest-8/genetree/member/id/WBGene00221255?'  -O -

Resource Information

MethodsGET
Response formatsphyloxml
nh
json
jsonp