GET cafe/genetree/id/:id

Retrieves a cafe tree of the gene tree using the gene tree stable identifier

Parameters

Required

NameTypeDescriptionDefaultExample Values
id String An Ensembl genetree ID - ENSGT00390000003602

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
compara String Name of the compara database to use. Multiple comparas can exist on a server if you are accessing Ensembl Genomes data multi (if using Ensembl) multi
nh_format String The format of a NH (New Hampshire) request. Available only with the default setting to allow us to return the cafe tree with Taxa names appended with number of members and the p_value. example : homo_sapiens_3_0.123 where 3 is the number of members and 0.123 is the p value Preset with default cafe parameters -

Example Requests

/cafe/genetree/id/ENSGT00390000003602?content-type=application/json


use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'http://grch37.rest.ensembl.org';
my $ext = '/cafe/genetree/id/ENSGT00390000003602?';
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://grch37.rest.ensembl.org"
ext = "/cafe/genetree/id/ENSGT00390000003602?"

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://grch37.rest.ensembl.org"
ext = "/cafe/genetree/id/ENSGT00390000003602?"

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://grch37.rest.ensembl.org'
path = '/cafe/genetree/id/ENSGT00390000003602?'

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://grch37.rest.ensembl.org";
    String ext = "/cafe/genetree/id/ENSGT00390000003602?";
    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);
  }
}

library(httr)
library(jsonlite)
library(xml2)

server <- "http://grch37.rest.ensembl.org"
ext <- "/cafe/genetree/id/ENSGT00390000003602?"

r <- GET(paste(server, ext, sep = ""), content_type("application/json"))

stop_for_status(r)

# use this if you get a simple nested list back, otherwise inspect its structure
# head(data.frame(t(sapply(content(r),c))))
head(fromJSON(toJSON(content(r))))


curl 'http://grch37.rest.ensembl.org/cafe/genetree/id/ENSGT00390000003602?' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'http://grch37.rest.ensembl.org/cafe/genetree/id/ENSGT00390000003602?'  -O -

/cafe/genetree/id/ENSGT00390000003602?content-type=text/x-nh;nh_format=simple


use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'http://grch37.rest.ensembl.org';
my $ext = '/cafe/genetree/id/ENSGT00390000003602?nh_format=simple';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/x-nh' }
});

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


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

import requests, sys

server = "http://grch37.rest.ensembl.org"
ext = "/cafe/genetree/id/ENSGT00390000003602?nh_format=simple"

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

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


print r.text

import requests, sys

server = "http://grch37.rest.ensembl.org"
ext = "/cafe/genetree/id/ENSGT00390000003602?nh_format=simple"

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

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


print r.text

require 'net/http'
require 'uri'

server='http://grch37.rest.ensembl.org'
path = '/cafe/genetree/id/ENSGT00390000003602?nh_format=simple'

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

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

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://grch37.rest.ensembl.org";
    String ext = "/cafe/genetree/id/ENSGT00390000003602?nh_format=simple";
    URL url = new URL(server + ext);

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

    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);
  }
}

library(httr)
library(jsonlite)
library(xml2)

server <- "http://grch37.rest.ensembl.org"
ext <- "/cafe/genetree/id/ENSGT00390000003602?nh_format=simple"

r <- GET(paste(server, ext, sep = ""), content_type("text/x-nh"))

stop_for_status(r)


print(content(r))


curl 'http://grch37.rest.ensembl.org/cafe/genetree/id/ENSGT00390000003602?nh_format=simple' -H 'Content-type:text/x-nh'

wget -q --header='Content-type:text/x-nh' 'http://grch37.rest.ensembl.org/cafe/genetree/id/ENSGT00390000003602?nh_format=simple'  -O -

Resource Information

MethodsGET
Response formatsnh
json
jsonp