GET genetree/member/symbol/:species/:symbol

Retrieves a gene tree containing the gene identified by a symbol

Parameters

Required

Name	Type	Description	Default	Example Values
species	`String`	Species name/alias	`-`	`brugia_malayi_prjna10729`
symbol	`String`	Symbol or display name of a gene	`-`	`Bm994`

Optional

Name	Type	Description	Default	Example 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`	`core`
external_db	`String`	Filter by external database	`-`	`EntrezGene`
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`	`-`

Example Requests

/rest-19/genetree/member/symbol/brugia_malayi_prjna10729/Bm994?content-type=text/x-phyloxml%2Bxml

use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'https://parasite.wormbase.org';
my $ext = '/rest-19/genetree/member/symbol/brugia_malayi_prjna10729/Bm994?';
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 = "https://parasite.wormbase.org"
ext = "/rest-19/genetree/member/symbol/brugia_malayi_prjna10729/Bm994?"

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

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


print r.text

import requests, sys

server = "https://parasite.wormbase.org"
ext = "/rest-19/genetree/member/symbol/brugia_malayi_prjna10729/Bm994?"

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

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


print(r.text)

require 'net/http'
require 'uri'

server='https://parasite.wormbase.org'
path = '/rest-19/genetree/member/symbol/brugia_malayi_prjna10729/Bm994?'

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 = "https://parasite.wormbase.org";
    String ext = "/rest-19/genetree/member/symbol/brugia_malayi_prjna10729/Bm994?";
    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 'https://parasite.wormbase.org/rest-19/genetree/member/symbol/brugia_malayi_prjna10729/Bm994?' -H 'Content-type:text/x-phyloxml+xml'

wget -q --header='Content-type:text/x-phyloxml+xml' 'https://parasite.wormbase.org/rest-19/genetree/member/symbol/brugia_malayi_prjna10729/Bm994?'  -O -

Resource Information

Methods	GET
Response formats	phyloxml nh json jsonp