GET genetree/id/:id

Retrieves a gene tree for a gene tree stable identifier

Parameters

Required

Name	Type	Description	Default	Example Values
id	`String`	An Ensembl genetree ID	`-`	`ENSGT00390000003602`

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`
cigar_line	`Boolean`	Return the aligned sequence encoded in CIGAR format	`0`	`-`
clusterset_id	`String`	Name of the gene-tree resource being queried. Common values are "default" for the standard multi-clade trees (which exclude all non-reference strains) and "murinae" for the trees spanning all mouse strains. By default, the most inclusive analysis will be selected	`-`	`default` `murinae`
compara	`String`	Name of the compara database to use. Multiple comparas exist on a server for separate species divisions	`vertebrates`	`vertebrates`
nh_format	`Enum(full, display_label_composite, simple, species, species_short_name, ncbi_taxon, ncbi_name, phylip, gene_stable_id, genome_gene_stable_id, genome_product_stable_id)`	The format of a NH (New Hampshire) request.	`simple`	`-`
prune_species	`String`	Prune the tree by species. Supports all species aliases. Will return a tree with only the species given	`-`	`human` `bos_taurus`
prune_taxon	`Integer`	Prune the tree by taxon. Will return a tree with only the taxons given	`-`	`9606` `10090`
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

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

Example output
Perl
Python2
Python3
Ruby
Java
R
Curl
Wget

use strict;
use warnings;
use HTTP::Tiny;
my $http = HTTP::Tiny->new();
my $server = 'http://rest.ensembl.org';
my $ext = '/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://rest.ensembl.org"
ext = "/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://rest.ensembl.org"
ext = "/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://rest.ensembl.org'
path = '/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://rest.ensembl.org";
 String ext = "/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://rest.ensembl.org"
ext <- "/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://rest.ensembl.org/genetree/id/ENSGT00390000003602?' -H 'Content-type:application/json'

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

/genetree/id/ENSGT00390000003602?content-type=text/x-nh;prune_taxon=9526;prune_species=bos_taurus;nh_format=simple

Example output
Perl
Python2
Python3
Ruby
Java
R
Curl
Wget

use strict;
use warnings;
use HTTP::Tiny;
my $http = HTTP::Tiny->new();
my $server = 'http://rest.ensembl.org';
my $ext = '/genetree/id/ENSGT00390000003602?prune_species=bos_taurus;nh_format=simple;prune_taxon=9526';
my $response = $http->get($server.$ext, {
 headers => { 'Content-type' => 'text/x-nh' }
});
die "Failed!\n" unless $response->{success};
print "$response->{content}\n";

import requests, sys
server = "http://rest.ensembl.org"
ext = "/genetree/id/ENSGT00390000003602?prune_species=bos_taurus;nh_format=simple;prune_taxon=9526"
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://rest.ensembl.org"
ext = "/genetree/id/ENSGT00390000003602?prune_species=bos_taurus;nh_format=simple;prune_taxon=9526"
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://rest.ensembl.org'
path = '/genetree/id/ENSGT00390000003602?prune_species=bos_taurus;nh_format=simple;prune_taxon=9526'
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://rest.ensembl.org";
 String ext = "/genetree/id/ENSGT00390000003602?prune_species=bos_taurus;nh_format=simple;prune_taxon=9526";
 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://rest.ensembl.org"
ext <- "/genetree/id/ENSGT00390000003602?prune_species=bos_taurus;nh_format=simple;prune_taxon=9526"
r <- GET(paste(server, ext, sep = ""), content_type("text/x-nh"))
stop_for_status(r)
print(content(r))

curl 'http://rest.ensembl.org/genetree/id/ENSGT00390000003602?prune_species=bos_taurus;nh_format=simple;prune_taxon=9526' -H 'Content-type:text/x-nh'

wget -q --header='Content-type:text/x-nh' 'http://rest.ensembl.org/genetree/id/ENSGT00390000003602?prune_species=bos_taurus;nh_format=simple;prune_taxon=9526' -O -

/genetree/id/ENSGT00390000003602?content-type=text/x-orthoxml%2Bxml

Example output
Perl
Python2
Python3
Ruby
Java
R
Curl
Wget

use strict;
use warnings;
use HTTP::Tiny;
my $http = HTTP::Tiny->new();
my $server = 'http://rest.ensembl.org';
my $ext = '/genetree/id/ENSGT00390000003602?';
my $response = $http->get($server.$ext, {
 headers => { 'Content-type' => 'text/x-orthoxml+xml' }
});
die "Failed!\n" unless $response->{success};
print "$response->{content}\n";

import requests, sys
server = "http://rest.ensembl.org"
ext = "/genetree/id/ENSGT00390000003602?"
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-orthoxml+xml"})
if not r.ok:
 r.raise_for_status()
 sys.exit()
print r.text

import requests, sys
server = "http://rest.ensembl.org"
ext = "/genetree/id/ENSGT00390000003602?"
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-orthoxml+xml"})
if not r.ok:
 r.raise_for_status()
 sys.exit()
print(r.text)

require 'net/http'
require 'uri'
server='http://rest.ensembl.org'
path = '/genetree/id/ENSGT00390000003602?'
url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)
request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-orthoxml+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://rest.ensembl.org";
 String ext = "/genetree/id/ENSGT00390000003602?";
 URL url = new URL(server + ext);
 URLConnection connection = url.openConnection();
 HttpURLConnection httpConnection = (HttpURLConnection)connection;
 
 httpConnection.setRequestProperty("Content-Type", "text/x-orthoxml+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);
 }
}

library(httr)
library(jsonlite)
library(xml2)
server <- "http://rest.ensembl.org"
ext <- "/genetree/id/ENSGT00390000003602?"
r <- GET(paste(server, ext, sep = ""), content_type("text/x-orthoxml+xml"))
stop_for_status(r)
print(content(r))

curl 'http://rest.ensembl.org/genetree/id/ENSGT00390000003602?' -H 'Content-type:text/x-orthoxml+xml'

wget -q --header='Content-type:text/x-orthoxml+xml' 'http://rest.ensembl.org/genetree/id/ENSGT00390000003602?' -O -

/genetree/id/ENSGT00390000003602?content-type=text/x-phyloxml%2Bxml

Example output
Perl
Python2
Python3
Ruby
Java
R
Curl
Wget

use strict;
use warnings;
use HTTP::Tiny;
my $http = HTTP::Tiny->new();
my $server = 'http://rest.ensembl.org';
my $ext = '/genetree/id/ENSGT00390000003602?';
my $response = $http->get($server.$ext, {
 headers => { 'Content-type' => 'text/x-phyloxml+xml' }
});
die "Failed!\n" unless $response->{success};
print "$response->{content}\n";

import requests, sys
server = "http://rest.ensembl.org"
ext = "/genetree/id/ENSGT00390000003602?"
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://rest.ensembl.org"
ext = "/genetree/id/ENSGT00390000003602?"
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://rest.ensembl.org'
path = '/genetree/id/ENSGT00390000003602?'
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://rest.ensembl.org";
 String ext = "/genetree/id/ENSGT00390000003602?";
 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);
 }
}

library(httr)
library(jsonlite)
library(xml2)
server <- "http://rest.ensembl.org"
ext <- "/genetree/id/ENSGT00390000003602?"
r <- GET(paste(server, ext, sep = ""), content_type("text/x-phyloxml+xml"))
stop_for_status(r)
print(content(r))

curl 'http://rest.ensembl.org/genetree/id/ENSGT00390000003602?' -H 'Content-type:text/x-phyloxml+xml'

wget -q --header='Content-type:text/x-phyloxml+xml' 'http://rest.ensembl.org/genetree/id/ENSGT00390000003602?' -O -

/genetree/id/ENSGT00390000003602?sequence=cdna;content-type=text/x-phyloxml%2Bxml;aligned=1

Example output
Perl
Python2
Python3
Ruby
Java
R
Curl
Wget

use strict;
use warnings;
use HTTP::Tiny;
my $http = HTTP::Tiny->new();
my $server = 'http://rest.ensembl.org';
my $ext = '/genetree/id/ENSGT00390000003602?sequence=cdna;aligned=1';
my $response = $http->get($server.$ext, {
 headers => { 'Content-type' => 'text/x-phyloxml+xml' }
});
die "Failed!\n" unless $response->{success};
print "$response->{content}\n";

import requests, sys
server = "http://rest.ensembl.org"
ext = "/genetree/id/ENSGT00390000003602?sequence=cdna;aligned=1"
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://rest.ensembl.org"
ext = "/genetree/id/ENSGT00390000003602?sequence=cdna;aligned=1"
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://rest.ensembl.org'
path = '/genetree/id/ENSGT00390000003602?sequence=cdna;aligned=1'
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://rest.ensembl.org";
 String ext = "/genetree/id/ENSGT00390000003602?sequence=cdna;aligned=1";
 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);
 }
}

library(httr)
library(jsonlite)
library(xml2)
server <- "http://rest.ensembl.org"
ext <- "/genetree/id/ENSGT00390000003602?sequence=cdna;aligned=1"
r <- GET(paste(server, ext, sep = ""), content_type("text/x-phyloxml+xml"))
stop_for_status(r)
print(content(r))

curl 'http://rest.ensembl.org/genetree/id/ENSGT00390000003602?sequence=cdna;aligned=1' -H 'Content-type:text/x-phyloxml+xml'

wget -q --header='Content-type:text/x-phyloxml+xml' 'http://rest.ensembl.org/genetree/id/ENSGT00390000003602?sequence=cdna;aligned=1' -O -

Resource Information

Methods GET

Response formats phyloxml
orthoxml
nh
json
jsonp