Retrieves a gene tree for a gene tree stable identifier
Name | Type | Description | Default | Example Values |
---|---|---|---|---|
id | String | An Ensembl genetree ID | - |
ENSGT00390000003602 |
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, njtree, phylip) | 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 cow |
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 | - |
use strict; use warnings; use HTTP::Tiny; my $http = HTTP::Tiny->new(); my $server = 'http://jan2020.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://jan2020.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://jan2020.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://jan2020.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://jan2020.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://jan2020.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://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?' -H 'Content-type:application/json'
wget -q --header='Content-type:application/json' 'http://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?' -O -
use strict; use warnings; use HTTP::Tiny; my $http = HTTP::Tiny->new(); my $server = 'http://jan2020.rest.ensembl.org'; my $ext = '/genetree/id/ENSGT00390000003602?nh_format=simple;prune_taxon=9526;prune_species=cow'; 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://jan2020.rest.ensembl.org" ext = "/genetree/id/ENSGT00390000003602?nh_format=simple;prune_taxon=9526;prune_species=cow" 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://jan2020.rest.ensembl.org" ext = "/genetree/id/ENSGT00390000003602?nh_format=simple;prune_taxon=9526;prune_species=cow" 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://jan2020.rest.ensembl.org' path = '/genetree/id/ENSGT00390000003602?nh_format=simple;prune_taxon=9526;prune_species=cow' 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://jan2020.rest.ensembl.org"; String ext = "/genetree/id/ENSGT00390000003602?nh_format=simple;prune_taxon=9526;prune_species=cow"; 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://jan2020.rest.ensembl.org" ext <- "/genetree/id/ENSGT00390000003602?nh_format=simple;prune_taxon=9526;prune_species=cow" r <- GET(paste(server, ext, sep = ""), content_type("text/x-nh")) stop_for_status(r) print(content(r))
curl 'http://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?nh_format=simple;prune_taxon=9526;prune_species=cow' -H 'Content-type:text/x-nh'
wget -q --header='Content-type:text/x-nh' 'http://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?nh_format=simple;prune_taxon=9526;prune_species=cow' -O -
use strict; use warnings; use HTTP::Tiny; my $http = HTTP::Tiny->new(); my $server = 'http://jan2020.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->{status} $response->{reason}\n";
import requests, sys server = "http://jan2020.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://jan2020.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://jan2020.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://jan2020.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://jan2020.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://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?' -H 'Content-type:text/x-orthoxml+xml'
wget -q --header='Content-type:text/x-orthoxml+xml' 'http://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?' -O -
use strict; use warnings; use HTTP::Tiny; my $http = HTTP::Tiny->new(); my $server = 'http://jan2020.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->{status} $response->{reason}\n";
import requests, sys server = "http://jan2020.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://jan2020.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://jan2020.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://jan2020.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://jan2020.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://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?' -H 'Content-type:text/x-phyloxml+xml'
wget -q --header='Content-type:text/x-phyloxml+xml' 'http://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?' -O -
use strict; use warnings; use HTTP::Tiny; my $http = HTTP::Tiny->new(); my $server = 'http://jan2020.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->{status} $response->{reason}\n";
import requests, sys server = "http://jan2020.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://jan2020.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://jan2020.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://jan2020.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://jan2020.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://jan2020.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://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?sequence=cdna;aligned=1' -O -
Methods | GET |
Response formats | phyloxml orthoxml nh json jsonp |