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 = 'https://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 = "https://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 = "https://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='https://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 = "https://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 <- "https://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 'https://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?' -H 'Content-type:application/json'
- wget -q --header='Content-type:application/json' 'https://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?' -O -
- use strict;
- use warnings;
- use HTTP::Tiny;
- my $http = HTTP::Tiny->new();
- my $server = 'https://jan2020.rest.ensembl.org';
- my $ext = '/genetree/id/ENSGT00390000003602?nh_format=simple;prune_species=cow;prune_taxon=9526';
- 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 = "https://jan2020.rest.ensembl.org"
- ext = "/genetree/id/ENSGT00390000003602?nh_format=simple;prune_species=cow;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 = "https://jan2020.rest.ensembl.org"
- ext = "/genetree/id/ENSGT00390000003602?nh_format=simple;prune_species=cow;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='https://jan2020.rest.ensembl.org'
- path = '/genetree/id/ENSGT00390000003602?nh_format=simple;prune_species=cow;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 = "https://jan2020.rest.ensembl.org";
- String ext = "/genetree/id/ENSGT00390000003602?nh_format=simple;prune_species=cow;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 <- "https://jan2020.rest.ensembl.org"
- ext <- "/genetree/id/ENSGT00390000003602?nh_format=simple;prune_species=cow;prune_taxon=9526"
- r <- GET(paste(server, ext, sep = ""), content_type("text/x-nh"))
- stop_for_status(r)
- print(content(r))
- curl 'https://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?nh_format=simple;prune_species=cow;prune_taxon=9526' -H 'Content-type:text/x-nh'
- wget -q --header='Content-type:text/x-nh' 'https://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?nh_format=simple;prune_species=cow;prune_taxon=9526' -O -
- use strict;
- use warnings;
- use HTTP::Tiny;
- my $http = HTTP::Tiny->new();
- my $server = 'https://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 = "https://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 = "https://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='https://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 = "https://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 <- "https://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 'https://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?' -H 'Content-type:text/x-orthoxml+xml'
- wget -q --header='Content-type:text/x-orthoxml+xml' 'https://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?' -O -
- use strict;
- use warnings;
- use HTTP::Tiny;
- my $http = HTTP::Tiny->new();
- my $server = 'https://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 = "https://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 = "https://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='https://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 = "https://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 <- "https://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 'https://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?' -H 'Content-type:text/x-phyloxml+xml'
- wget -q --header='Content-type:text/x-phyloxml+xml' 'https://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?' -O -
- use strict;
- use warnings;
- use HTTP::Tiny;
- my $http = HTTP::Tiny->new();
- my $server = 'https://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 = "https://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 = "https://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='https://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 = "https://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 <- "https://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 'https://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' 'https://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?sequence=cdna;aligned=1' -O -
Methods | GET |
Response formats | phyloxml orthoxml nh json jsonp |