GET genetree/id/:id

Retrieves a gene tree for a gene tree stable identifier

Parameters

Required

NameTypeDescriptionDefaultExample Values
id String An Ensembl genetree ID - ENSGT00390000003602

Optional

NameTypeDescriptionDefaultExample 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 -

Example Requests

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


  1. use strict;
  2. use warnings;
  3.  
  4. use HTTP::Tiny;
  5.  
  6. my $http = HTTP::Tiny->new();
  7.  
  8. my $server = 'https://jan2020.rest.ensembl.org';
  9. my $ext = '/genetree/id/ENSGT00390000003602?';
  10. my $response = $http->get($server.$ext, {
  11. headers => { 'Content-type' => 'application/json' }
  12. });
  13.  
  14. die "Failed!\n" unless $response->{success};
  15.  
  16.  
  17. use JSON;
  18. use Data::Dumper;
  19. if(length $response->{content}) {
  20. my $hash = decode_json($response->{content});
  21. local $Data::Dumper::Terse = 1;
  22. local $Data::Dumper::Indent = 1;
  23. print Dumper $hash;
  24. print "\n";
  25. }
  26.  
  1. import requests, sys
  2.  
  3. server = "https://jan2020.rest.ensembl.org"
  4. ext = "/genetree/id/ENSGT00390000003602?"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})
  7.  
  8. if not r.ok:
  9. r.raise_for_status()
  10. sys.exit()
  11.  
  12. decoded = r.json()
  13. print repr(decoded)
  14.  
  1. import requests, sys
  2.  
  3. server = "https://jan2020.rest.ensembl.org"
  4. ext = "/genetree/id/ENSGT00390000003602?"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})
  7.  
  8. if not r.ok:
  9. r.raise_for_status()
  10. sys.exit()
  11.  
  12. decoded = r.json()
  13. print(repr(decoded))
  14.  
  1. require 'net/http'
  2. require 'uri'
  3.  
  4. server='https://jan2020.rest.ensembl.org'
  5. path = '/genetree/id/ENSGT00390000003602?'
  6.  
  7. url = URI.parse(server)
  8. http = Net::HTTP.new(url.host, url.port)
  9.  
  10. request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'})
  11.  
  12. response = http.request(request)
  13.  
  14. if response.code != "200"
  15. puts "Invalid response: #{response.code}"
  16. puts response.body
  17. exit
  18. end
  19.  
  20.  
  21. require 'rubygems'
  22. require 'json'
  23. require 'yaml'
  24.  
  25. result = JSON.parse(response.body)
  26. puts YAML::dump(result)
  27.  
  1. import java.net.URL;
  2. import java.net.URLConnection;
  3. import java.net.HttpURLConnection;
  4. import java.io.BufferedReader;
  5. import java.io.InputStream;
  6. import java.io.InputStreamReader;
  7. import java.io.IOException;
  8. import java.io.Reader;
  9.  
  10.  
  11. public class EnsemblRest {
  12.  
  13. public static void main(String[] args) throws Exception {
  14. String server = "https://jan2020.rest.ensembl.org";
  15. String ext = "/genetree/id/ENSGT00390000003602?";
  16. URL url = new URL(server + ext);
  17.  
  18. URLConnection connection = url.openConnection();
  19. HttpURLConnection httpConnection = (HttpURLConnection)connection;
  20. httpConnection.setRequestProperty("Content-Type", "application/json");
  21.  
  22. InputStream response = connection.getInputStream();
  23. int responseCode = httpConnection.getResponseCode();
  24.  
  25. if(responseCode != 200) {
  26. throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
  27. }
  28.  
  29. String output;
  30. Reader reader = null;
  31. try {
  32. reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
  33. StringBuilder builder = new StringBuilder();
  34. char[] buffer = new char[8192];
  35. int read;
  36. while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
  37. builder.append(buffer, 0, read);
  38. }
  39. output = builder.toString();
  40. }
  41. finally {
  42. if (reader != null) try {
  43. reader.close();
  44. } catch (IOException logOrIgnore) {
  45. logOrIgnore.printStackTrace();
  46. }
  47. }
  48.  
  49. System.out.println(output);
  50. }
  51. }
  52.  
  1. library(httr)
  2. library(jsonlite)
  3. library(xml2)
  4.  
  5. server <- "https://jan2020.rest.ensembl.org"
  6. ext <- "/genetree/id/ENSGT00390000003602?"
  7.  
  8. r <- GET(paste(server, ext, sep = ""), content_type("application/json"))
  9.  
  10. stop_for_status(r)
  11.  
  12. # use this if you get a simple nested list back, otherwise inspect its structure
  13. # head(data.frame(t(sapply(content(r),c))))
  14. head(fromJSON(toJSON(content(r))))
  15.  
  1.  
  2. curl 'https://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?' -H 'Content-type:application/json'
  3.  
  1. wget -q --header='Content-type:application/json' 'https://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?' -O -
  2.  

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


  1. use strict;
  2. use warnings;
  3.  
  4. use HTTP::Tiny;
  5.  
  6. my $http = HTTP::Tiny->new();
  7.  
  8. my $server = 'https://jan2020.rest.ensembl.org';
  9. my $ext = '/genetree/id/ENSGT00390000003602?nh_format=simple;prune_species=cow;prune_taxon=9526';
  10. my $response = $http->get($server.$ext, {
  11. headers => { 'Content-type' => 'text/x-nh' }
  12. });
  13.  
  14. die "Failed!\n" unless $response->{success};
  15.  
  16.  
  17. print "$response->{status} $response->{reason}\n";
  18.  
  1. import requests, sys
  2.  
  3. server = "https://jan2020.rest.ensembl.org"
  4. ext = "/genetree/id/ENSGT00390000003602?nh_format=simple;prune_species=cow;prune_taxon=9526"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-nh"})
  7.  
  8. if not r.ok:
  9. r.raise_for_status()
  10. sys.exit()
  11.  
  12.  
  13. print r.text
  14.  
  1. import requests, sys
  2.  
  3. server = "https://jan2020.rest.ensembl.org"
  4. ext = "/genetree/id/ENSGT00390000003602?nh_format=simple;prune_species=cow;prune_taxon=9526"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-nh"})
  7.  
  8. if not r.ok:
  9. r.raise_for_status()
  10. sys.exit()
  11.  
  12.  
  13. print(r.text)
  14.  
  1. require 'net/http'
  2. require 'uri'
  3.  
  4. server='https://jan2020.rest.ensembl.org'
  5. path = '/genetree/id/ENSGT00390000003602?nh_format=simple;prune_species=cow;prune_taxon=9526'
  6.  
  7. url = URI.parse(server)
  8. http = Net::HTTP.new(url.host, url.port)
  9.  
  10. request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-nh'})
  11.  
  12. response = http.request(request)
  13.  
  14. if response.code != "200"
  15. puts "Invalid response: #{response.code}"
  16. puts response.body
  17. exit
  18. end
  19.  
  20.  
  21. puts response.body
  22.  
  1. import java.net.URL;
  2. import java.net.URLConnection;
  3. import java.net.HttpURLConnection;
  4. import java.io.BufferedReader;
  5. import java.io.InputStream;
  6. import java.io.InputStreamReader;
  7. import java.io.IOException;
  8. import java.io.Reader;
  9.  
  10.  
  11. public class EnsemblRest {
  12.  
  13. public static void main(String[] args) throws Exception {
  14. String server = "https://jan2020.rest.ensembl.org";
  15. String ext = "/genetree/id/ENSGT00390000003602?nh_format=simple;prune_species=cow;prune_taxon=9526";
  16. URL url = new URL(server + ext);
  17.  
  18. URLConnection connection = url.openConnection();
  19. HttpURLConnection httpConnection = (HttpURLConnection)connection;
  20. httpConnection.setRequestProperty("Content-Type", "text/x-nh");
  21.  
  22. InputStream response = connection.getInputStream();
  23. int responseCode = httpConnection.getResponseCode();
  24.  
  25. if(responseCode != 200) {
  26. throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
  27. }
  28.  
  29. String output;
  30. Reader reader = null;
  31. try {
  32. reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
  33. StringBuilder builder = new StringBuilder();
  34. char[] buffer = new char[8192];
  35. int read;
  36. while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
  37. builder.append(buffer, 0, read);
  38. }
  39. output = builder.toString();
  40. }
  41. finally {
  42. if (reader != null) try {
  43. reader.close();
  44. } catch (IOException logOrIgnore) {
  45. logOrIgnore.printStackTrace();
  46. }
  47. }
  48.  
  49. System.out.println(output);
  50. }
  51. }
  52.  
  1. library(httr)
  2. library(jsonlite)
  3. library(xml2)
  4.  
  5. server <- "https://jan2020.rest.ensembl.org"
  6. ext <- "/genetree/id/ENSGT00390000003602?nh_format=simple;prune_species=cow;prune_taxon=9526"
  7.  
  8. r <- GET(paste(server, ext, sep = ""), content_type("text/x-nh"))
  9.  
  10. stop_for_status(r)
  11.  
  12.  
  13. print(content(r))
  14.  
  1.  
  2. curl 'https://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?nh_format=simple;prune_species=cow;prune_taxon=9526' -H 'Content-type:text/x-nh'
  3.  
  1. 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 -
  2.  

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


  1. use strict;
  2. use warnings;
  3.  
  4. use HTTP::Tiny;
  5.  
  6. my $http = HTTP::Tiny->new();
  7.  
  8. my $server = 'https://jan2020.rest.ensembl.org';
  9. my $ext = '/genetree/id/ENSGT00390000003602?';
  10. my $response = $http->get($server.$ext, {
  11. headers => { 'Content-type' => 'text/x-orthoxml+xml' }
  12. });
  13.  
  14. die "Failed!\n" unless $response->{success};
  15.  
  16.  
  17. print "$response->{status} $response->{reason}\n";
  18.  
  1. import requests, sys
  2.  
  3. server = "https://jan2020.rest.ensembl.org"
  4. ext = "/genetree/id/ENSGT00390000003602?"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-orthoxml+xml"})
  7.  
  8. if not r.ok:
  9. r.raise_for_status()
  10. sys.exit()
  11.  
  12.  
  13. print r.text
  14.  
  1. import requests, sys
  2.  
  3. server = "https://jan2020.rest.ensembl.org"
  4. ext = "/genetree/id/ENSGT00390000003602?"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-orthoxml+xml"})
  7.  
  8. if not r.ok:
  9. r.raise_for_status()
  10. sys.exit()
  11.  
  12.  
  13. print(r.text)
  14.  
  1. require 'net/http'
  2. require 'uri'
  3.  
  4. server='https://jan2020.rest.ensembl.org'
  5. path = '/genetree/id/ENSGT00390000003602?'
  6.  
  7. url = URI.parse(server)
  8. http = Net::HTTP.new(url.host, url.port)
  9.  
  10. request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-orthoxml+xml'})
  11.  
  12. response = http.request(request)
  13.  
  14. if response.code != "200"
  15. puts "Invalid response: #{response.code}"
  16. puts response.body
  17. exit
  18. end
  19.  
  20.  
  21. puts response.body
  22.  
  1. import java.net.URL;
  2. import java.net.URLConnection;
  3. import java.net.HttpURLConnection;
  4. import java.io.BufferedReader;
  5. import java.io.InputStream;
  6. import java.io.InputStreamReader;
  7. import java.io.IOException;
  8. import java.io.Reader;
  9.  
  10.  
  11. public class EnsemblRest {
  12.  
  13. public static void main(String[] args) throws Exception {
  14. String server = "https://jan2020.rest.ensembl.org";
  15. String ext = "/genetree/id/ENSGT00390000003602?";
  16. URL url = new URL(server + ext);
  17.  
  18. URLConnection connection = url.openConnection();
  19. HttpURLConnection httpConnection = (HttpURLConnection)connection;
  20. httpConnection.setRequestProperty("Content-Type", "text/x-orthoxml+xml");
  21.  
  22. InputStream response = connection.getInputStream();
  23. int responseCode = httpConnection.getResponseCode();
  24.  
  25. if(responseCode != 200) {
  26. throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
  27. }
  28.  
  29. String output;
  30. Reader reader = null;
  31. try {
  32. reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
  33. StringBuilder builder = new StringBuilder();
  34. char[] buffer = new char[8192];
  35. int read;
  36. while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
  37. builder.append(buffer, 0, read);
  38. }
  39. output = builder.toString();
  40. }
  41. finally {
  42. if (reader != null) try {
  43. reader.close();
  44. } catch (IOException logOrIgnore) {
  45. logOrIgnore.printStackTrace();
  46. }
  47. }
  48.  
  49. System.out.println(output);
  50. }
  51. }
  52.  
  1. library(httr)
  2. library(jsonlite)
  3. library(xml2)
  4.  
  5. server <- "https://jan2020.rest.ensembl.org"
  6. ext <- "/genetree/id/ENSGT00390000003602?"
  7.  
  8. r <- GET(paste(server, ext, sep = ""), content_type("text/x-orthoxml+xml"))
  9.  
  10. stop_for_status(r)
  11.  
  12.  
  13. print(content(r))
  14.  
  1.  
  2. curl 'https://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?' -H 'Content-type:text/x-orthoxml+xml'
  3.  
  1. wget -q --header='Content-type:text/x-orthoxml+xml' 'https://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?' -O -
  2.  

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


  1. use strict;
  2. use warnings;
  3.  
  4. use HTTP::Tiny;
  5.  
  6. my $http = HTTP::Tiny->new();
  7.  
  8. my $server = 'https://jan2020.rest.ensembl.org';
  9. my $ext = '/genetree/id/ENSGT00390000003602?';
  10. my $response = $http->get($server.$ext, {
  11. headers => { 'Content-type' => 'text/x-phyloxml+xml' }
  12. });
  13.  
  14. die "Failed!\n" unless $response->{success};
  15.  
  16.  
  17. print "$response->{status} $response->{reason}\n";
  18.  
  1. import requests, sys
  2.  
  3. server = "https://jan2020.rest.ensembl.org"
  4. ext = "/genetree/id/ENSGT00390000003602?"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-phyloxml+xml"})
  7.  
  8. if not r.ok:
  9. r.raise_for_status()
  10. sys.exit()
  11.  
  12.  
  13. print r.text
  14.  
  1. import requests, sys
  2.  
  3. server = "https://jan2020.rest.ensembl.org"
  4. ext = "/genetree/id/ENSGT00390000003602?"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-phyloxml+xml"})
  7.  
  8. if not r.ok:
  9. r.raise_for_status()
  10. sys.exit()
  11.  
  12.  
  13. print(r.text)
  14.  
  1. require 'net/http'
  2. require 'uri'
  3.  
  4. server='https://jan2020.rest.ensembl.org'
  5. path = '/genetree/id/ENSGT00390000003602?'
  6.  
  7. url = URI.parse(server)
  8. http = Net::HTTP.new(url.host, url.port)
  9.  
  10. request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-phyloxml+xml'})
  11.  
  12. response = http.request(request)
  13.  
  14. if response.code != "200"
  15. puts "Invalid response: #{response.code}"
  16. puts response.body
  17. exit
  18. end
  19.  
  20.  
  21. puts response.body
  22.  
  1. import java.net.URL;
  2. import java.net.URLConnection;
  3. import java.net.HttpURLConnection;
  4. import java.io.BufferedReader;
  5. import java.io.InputStream;
  6. import java.io.InputStreamReader;
  7. import java.io.IOException;
  8. import java.io.Reader;
  9.  
  10.  
  11. public class EnsemblRest {
  12.  
  13. public static void main(String[] args) throws Exception {
  14. String server = "https://jan2020.rest.ensembl.org";
  15. String ext = "/genetree/id/ENSGT00390000003602?";
  16. URL url = new URL(server + ext);
  17.  
  18. URLConnection connection = url.openConnection();
  19. HttpURLConnection httpConnection = (HttpURLConnection)connection;
  20. httpConnection.setRequestProperty("Content-Type", "text/x-phyloxml+xml");
  21.  
  22. InputStream response = connection.getInputStream();
  23. int responseCode = httpConnection.getResponseCode();
  24.  
  25. if(responseCode != 200) {
  26. throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
  27. }
  28.  
  29. String output;
  30. Reader reader = null;
  31. try {
  32. reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
  33. StringBuilder builder = new StringBuilder();
  34. char[] buffer = new char[8192];
  35. int read;
  36. while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
  37. builder.append(buffer, 0, read);
  38. }
  39. output = builder.toString();
  40. }
  41. finally {
  42. if (reader != null) try {
  43. reader.close();
  44. } catch (IOException logOrIgnore) {
  45. logOrIgnore.printStackTrace();
  46. }
  47. }
  48.  
  49. System.out.println(output);
  50. }
  51. }
  52.  
  1. library(httr)
  2. library(jsonlite)
  3. library(xml2)
  4.  
  5. server <- "https://jan2020.rest.ensembl.org"
  6. ext <- "/genetree/id/ENSGT00390000003602?"
  7.  
  8. r <- GET(paste(server, ext, sep = ""), content_type("text/x-phyloxml+xml"))
  9.  
  10. stop_for_status(r)
  11.  
  12.  
  13. print(content(r))
  14.  
  1.  
  2. curl 'https://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?' -H 'Content-type:text/x-phyloxml+xml'
  3.  
  1. wget -q --header='Content-type:text/x-phyloxml+xml' 'https://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?' -O -
  2.  

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


  1. use strict;
  2. use warnings;
  3.  
  4. use HTTP::Tiny;
  5.  
  6. my $http = HTTP::Tiny->new();
  7.  
  8. my $server = 'https://jan2020.rest.ensembl.org';
  9. my $ext = '/genetree/id/ENSGT00390000003602?sequence=cdna;aligned=1';
  10. my $response = $http->get($server.$ext, {
  11. headers => { 'Content-type' => 'text/x-phyloxml+xml' }
  12. });
  13.  
  14. die "Failed!\n" unless $response->{success};
  15.  
  16.  
  17. print "$response->{status} $response->{reason}\n";
  18.  
  1. import requests, sys
  2.  
  3. server = "https://jan2020.rest.ensembl.org"
  4. ext = "/genetree/id/ENSGT00390000003602?sequence=cdna;aligned=1"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-phyloxml+xml"})
  7.  
  8. if not r.ok:
  9. r.raise_for_status()
  10. sys.exit()
  11.  
  12.  
  13. print r.text
  14.  
  1. import requests, sys
  2.  
  3. server = "https://jan2020.rest.ensembl.org"
  4. ext = "/genetree/id/ENSGT00390000003602?sequence=cdna;aligned=1"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-phyloxml+xml"})
  7.  
  8. if not r.ok:
  9. r.raise_for_status()
  10. sys.exit()
  11.  
  12.  
  13. print(r.text)
  14.  
  1. require 'net/http'
  2. require 'uri'
  3.  
  4. server='https://jan2020.rest.ensembl.org'
  5. path = '/genetree/id/ENSGT00390000003602?sequence=cdna;aligned=1'
  6.  
  7. url = URI.parse(server)
  8. http = Net::HTTP.new(url.host, url.port)
  9.  
  10. request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-phyloxml+xml'})
  11.  
  12. response = http.request(request)
  13.  
  14. if response.code != "200"
  15. puts "Invalid response: #{response.code}"
  16. puts response.body
  17. exit
  18. end
  19.  
  20.  
  21. puts response.body
  22.  
  1. import java.net.URL;
  2. import java.net.URLConnection;
  3. import java.net.HttpURLConnection;
  4. import java.io.BufferedReader;
  5. import java.io.InputStream;
  6. import java.io.InputStreamReader;
  7. import java.io.IOException;
  8. import java.io.Reader;
  9.  
  10.  
  11. public class EnsemblRest {
  12.  
  13. public static void main(String[] args) throws Exception {
  14. String server = "https://jan2020.rest.ensembl.org";
  15. String ext = "/genetree/id/ENSGT00390000003602?sequence=cdna;aligned=1";
  16. URL url = new URL(server + ext);
  17.  
  18. URLConnection connection = url.openConnection();
  19. HttpURLConnection httpConnection = (HttpURLConnection)connection;
  20. httpConnection.setRequestProperty("Content-Type", "text/x-phyloxml+xml");
  21.  
  22. InputStream response = connection.getInputStream();
  23. int responseCode = httpConnection.getResponseCode();
  24.  
  25. if(responseCode != 200) {
  26. throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
  27. }
  28.  
  29. String output;
  30. Reader reader = null;
  31. try {
  32. reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
  33. StringBuilder builder = new StringBuilder();
  34. char[] buffer = new char[8192];
  35. int read;
  36. while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
  37. builder.append(buffer, 0, read);
  38. }
  39. output = builder.toString();
  40. }
  41. finally {
  42. if (reader != null) try {
  43. reader.close();
  44. } catch (IOException logOrIgnore) {
  45. logOrIgnore.printStackTrace();
  46. }
  47. }
  48.  
  49. System.out.println(output);
  50. }
  51. }
  52.  
  1. library(httr)
  2. library(jsonlite)
  3. library(xml2)
  4.  
  5. server <- "https://jan2020.rest.ensembl.org"
  6. ext <- "/genetree/id/ENSGT00390000003602?sequence=cdna;aligned=1"
  7.  
  8. r <- GET(paste(server, ext, sep = ""), content_type("text/x-phyloxml+xml"))
  9.  
  10. stop_for_status(r)
  11.  
  12.  
  13. print(content(r))
  14.  
  1.  
  2. curl 'https://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?sequence=cdna;aligned=1' -H 'Content-type:text/x-phyloxml+xml'
  3.  
  1. wget -q --header='Content-type:text/x-phyloxml+xml' 'https://jan2020.rest.ensembl.org/genetree/id/ENSGT00390000003602?sequence=cdna;aligned=1' -O -
  2.  

Resource Information

MethodsGET
Response formatsphyloxml
orthoxml
nh
json
jsonp