GET genetree/member/id/:id

Retrieves a gene tree that contains the stable identifier

Parameters

Required

Name	Type	Description	Default	Example Values
id	`String`	A stable ID	`-`	`WBGene00221255`

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`
db_type	`String`	Restrict the search to a database other than the default. Useful if you need to use a DB other than core	`-`	`core`
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`	`-`
object_type	`String`	Filter by feature type	`-`	`gene` `transcript`
sequence	`Enum(none, cdna, protein)`	The type of sequence to bring back. Setting it to none results in no sequence being returned	`protein`	`-`
species	`String`	Species name/alias	`-`	`brugia_malayi_prjna10729`

Example Requests

/rest-19/genetree/member/id/WBGene00221255?content-type=text/x-phyloxml%2Bxml

<?xml version="1.0" encoding="UTF-8"?><phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.phyloxml.org" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd">
  <phylogeny type="gene tree" rooted="true">
    <clade branch_length="0">
      <taxonomy>
        <id>6296</id>
        <scientific_name>Onchocercidae</scientific_name>
      </taxonomy>
      <clade branch_length="0">
        <confidence type="bootstrap">73</confidence>
        <taxonomy>
          <id>6296</id>
          <scientific_name>Onchocercidae</scientific_name>
        </taxonomy>
        <clade branch_length="0.05556">
          <confidence type="bootstrap">85</confidence>
          <taxonomy>
            <id>6296</id>
            <scientific_name>Onchocercidae</scientific_name>
          </taxonomy>
          <clade branch_length="0.100909">
            <name>CJOHNSTONI_LOCUS9362</name>
            <taxonomy>
              <id>2874296</id>
              <scientific_name>Cercopithifilaria johnstoni</scientific_name>
              <common_name>Cercopithifilaria johnstoni (PRJEB47283)</common_name>
            </taxonomy>
            <sequence>
              <accession source="Ensembl">rna-CJOHNSTONI_LOCUS9362</accession>
              <location>scaffold77_size169672:15082-17073</location>
              <mol_seq is_aligned="0">MQKTNKPTVSGIHGQTLLKRIEHINELFPTNLQQNSSTNNSSSSSLSSTKQCQNDNLLVEIRSGVQLRHVIPNAHKQCIKMLYDNTCEKLFITENENERKLETEKQTDIGNIILNAMRKRRLLMGFGQLAFIVFRFNDSMIKNDHCPLKSSSTSNEDGNERKLEQWSDTDDKGYGDDQ</mol_seq>
            </sequence>
            <property datatype="xsd:string" ref="Compara:genome_db_name" applies_to="clade">cercopithifilaria_johnstoni_prjeb47283</property>
          </clade>
          <clade branch_length="0.280408">
            <name>nLs.2.1.2.g06925</name>
            <taxonomy>
              <id>42156</id>
              <scientific_name>Litomosoides sigmodontis strain Bain lab strain</scientific_name>
              <common_name>Litomosoides sigmodontis (PRJEB3075)</common_name>
            </taxonomy>
            <sequence>
              <accession source="Ensembl">nLs.2.1.2.t06925-RA</accession>
              <location>nLs.2.1.scaf00656:4793-6244</location>
              <mol_seq is_aligned="0">MSEKMPLDRAERIEQHKHELISTDPQQNNLISTNYSASSSSSPPSTQQQRQNDKLLTEINKGIHLRHVIPNAHKQCISMLYDKKCEKSSTTEKDSVKEDETKLEMEKSTDIGNVLLNAMRKRRLLVEFESSSISNEDGNERRLEQWSDSDDTDSNAGKFRN</mol_seq>
            </sequence>
            <property datatype="xsd:string" ref="Compara:genome_db_name" applies_to="clade">litomosoides_sigmodontis_prjeb3075</property>
          </clade>
        </clade>
        <clade branch_length="0.153362">
          <confidence type="duplication_confidence_score">0.6667</confidence>
          <taxonomy>
            <id>6296</id>
            <scientific_name>Onchocercidae</scientific_name>
          </taxonomy>
          <events>
            <type>speciation_or_duplication</type>
            <duplications>1</duplications>
          </events>
          <clade branch_length="0">
            <confidence type="bootstrap">3</confidence>
            <taxonomy>
              <id>6296</id>
              <scientific_name>Onchocercidae</scientific_name>
            </taxonomy>
            <clade branch_length="0.06168">
              <confidence type="bootstrap">98</confidence>
              <taxonomy>
                <id>6278</id>
                <scientific_name>Brugia</scientific_name>
              </taxonomy>
              <clade branch_length="0.128164">
                <confidence type="bootstrap">100</confidence>
                <confidence type="duplication_confidence_score">1</confidence>
                <taxonomy>
                  <id>6280</id>
                  <scientific_name>Brugia pahangi strain Scotland/Glasgow</scientific_name>
                  <common_name>Brugia pahangi (PRJEB497)</common_name>
                </taxonomy>
                <events>
                  <type>speciation_or_duplication</type>
                  <duplications>1</duplications>
                </events>
                <clade branch_length="0">
                  <name>BPAG_0000674301</name>
                  <taxonomy>
                    <id>6280</id>
                    <scientific_name>Brugia pahangi strain Scotland/Glasgow</scientific_name>
                    <common_name>Brugia pahangi (PRJEB497)</common_name>
                  </taxonomy>
                  <sequence>
                    <accession source="Ensembl">BPAG_0000674301-mRNA-1</accession>
                    <location>BPAG_contig0006494:24-205</location>
                    <mol_seq is_aligned="0">MQKQVKRQQHVDELLPSVIQQEDPTNDSLSPLSSARCTDQYQSDKLLAVSVNVLTFEKY</mol_seq>
                  </sequence>
                  <property datatype="xsd:string" ref="Compara:genome_db_name" applies_to="clade">brugia_pahangi_prjeb497</property>
                </clade>
                <clade branch_length="0.004885">
                  <name>BPAG_0000621901</name>
                  <taxonomy>
                    <id>6280</id>
                    <scientific_name>Brugia pahangi strain Scotland/Glasgow</scientific_name>
                    <common_name>Brugia pahangi (PRJEB497)</common_name>
                  </taxonomy>
                  <sequence>
                    <accession source="Ensembl">BPAG_0000621901-mRNA-1</accession>
                    <location>BPAG_contig0005308:317-498</location>
                    <mol_seq is_aligned="0">MQKQVKRQQHIDELLPSVIQQEDPTNDSLSPLSSARCTDQYQSDKLLAVSVNVLTFEKY</mol_seq>
                  </sequence>
                  <property datatype="xsd:string" ref="Compara:genome_db_name" applies_to="clade">brugia_pahangi_prjeb497</property>
                </clade>
              </clade>
              <clade branch_length="0.006247">
                <name>WBGene00221255</name>
                <taxonomy>
                  <id>6279</id>
                  <scientific_name>Brugia malayi strain FR3</scientific_name>
                  <common_name>Brugia malayi (PRJNA10729)</common_name>
                </taxonomy>
                <sequence>
                  <accession source="Ensembl">Bm994.1</accession>
                  <name>Bm994.1</name>
                  <location>Bm_007:479867-484217</location>
                  <mol_seq is_aligned="0">MQKQVKGQQHVNELLPSVIQQEDPTNDSLSPLSSARCTDQYQSDKLLAEIRNGVQLRHVIPNDHKQCAKMLYDKACEKKEENNINEKETKLETEKAINIGNILLNAMQKRRLLMHFG</mol_seq>
                </sequence>
                <property datatype="xsd:string" ref="Compara:genome_db_name" applies_to="clade">brugia_malayi_prjna10729</property>
              </clade>
            </clade>
            <clade branch_length="0.024003">
              <name>Wban_10481</name>
              <taxonomy>
                <id>6293</id>
                <scientific_name>Wuchereria bancrofti strain 17-3</scientific_name>
                <common_name>Wuchereria bancrofti (PRJNA275548)</common_name>
              </taxonomy>
              <sequence>
                <accession source="Ensembl">mrna-Wban_10481</accession>
                <location>Wb_ChrX_3:313070-314224</location>
                <mol_seq is_aligned="0">MQSQVKRQQHVDELLPPVLQQKDPTNDSLSPSSFARCTDQYQSDKLLAQIRSGVQLRHVIPNDHKQCTKMLYDKACEKEENNINEKEVKLETEKTIDIGNILLNAMHKRRLLMRFG</mol_seq>
              </sequence>
              <property datatype="xsd:string" ref="Compara:genome_db_name" applies_to="clade">wuchereria_bancrofti_prjna275548</property>
            </clade>
          </clade>
          <clade branch_length="0">
            <taxonomy>
              <id>6296</id>
              <scientific_name>Onchocercidae</scientific_name>
            </taxonomy>
            <clade branch_length="0.064776">
              <name>Wban_03022</name>
              <taxonomy>
                <id>6293</id>
                <scientific_name>Wuchereria bancrofti strain 17-3</scientific_name>
                <common_name>Wuchereria bancrofti (PRJNA275548)</common_name>
              </taxonomy>
              <sequence>
                <accession source="Ensembl">mrna-Wban_03022</accession>
                <location>Wb_ChrX_0:23866265-23867089</location>
                <mol_seq is_aligned="0">MQSQVKRQQHVDELLPPVLQQKDPTNNSLSPSSSARCTDPYQSDKLLAVIQLRHVIPNDHKQCTKMLYDKACEKEENNINEKETKLETEKKRLETKKN</mol_seq>
              </sequence>
              <property datatype="xsd:string" ref="Compara:genome_db_name" applies_to="clade">wuchereria_bancrofti_prjna275548</property>
            </clade>
            <clade branch_length="0.108173">
              <name>BPAG_0000765501</name>
              <taxonomy>
                <id>6280</id>
                <scientific_name>Brugia pahangi strain Scotland/Glasgow</scientific_name>
                <common_name>Brugia pahangi (PRJEB497)</common_name>
              </taxonomy>
              <sequence>
                <accession source="Ensembl">BPAG_0000765501-mRNA-1</accession>
                <location>BPAG_contig0008935:106-1027</location>
                <mol_seq is_aligned="0">MRNFYIEIRNGVQLRHVIPNDHKQCAKMLYDKACEKKEENNINEKETKLETERAINIGNILLNAMHKRRLLMHSESSSSSDENINEQKLELWSDTDDNYDDNNDNDNNYNDINKSMNKTQM</mol_seq>
              </sequence>
              <property datatype="xsd:string" ref="Compara:genome_db_name" applies_to="clade">brugia_pahangi_prjeb497</property>
            </clade>
          </clade>
        </clade>
      </clade>
      <clade branch_length="0.113862">
        <confidence type="bootstrap">100</confidence>
        <taxonomy>
          <id>6296</id>
          <scientific_name>Onchocercidae</scientific_name>
        </taxonomy>
        <clade branch_length="0.184259">
          <name>WBGene00239008</name>
          <taxonomy>
            <id>6282</id>
            <scientific_name>Onchocerca volvulus strain O. volvulus Cameroon isolate</scientific_name>
            <common_name>Onchocerca volvulus (PRJEB513)</common_name>
          </taxonomy>
          <sequence>
            <accession source="Ensembl">OVOC2199.1</accession>
            <name>OVOC2199.1</name>
            <location>OVOC_OM1b:16714030-16717575</location>
            <mol_seq is_aligned="0">MNDLSSSSHTDRYVDQNQNNKLLTEIRSRIHLRHVIPNEHKQCTKMLYDKTFDKAIISNEDNVSKKETKLDEQKRIHAENLLINAMRKRRFVMRFESSSSDENETEQELEH</mol_seq>
          </sequence>
          <property datatype="xsd:string" ref="Compara:genome_db_name" applies_to="clade">onchocerca_volvulus_prjeb513</property>
        </clade>
        <clade branch_length="0.230279">
          <name>nDi.2.2.2.g04666</name>
          <taxonomy>
            <id>6287</id>
            <scientific_name>Dirofilaria immitis nDi.2.2</scientific_name>
            <common_name>Dirofilaria immitis (PRJEB1797)</common_name>
          </taxonomy>
          <sequence>
            <accession source="Ensembl">nDi.2.2.2.t04666</accession>
            <location>nDi.2.2.scaf00098:142364-144204</location>
            <mol_seq is_aligned="0">MQKVNKAAISDKQIKALLKRISQKEQVREFHAINIQGENSTNDQSLSSSSNHCNDQYQYDKLLTEIRNGIELRHVIPNEHKRCAKMLYDKTIEELFISGEDKINDKQIKLCEQKSTDDIDIENILINAMCKRRFAMRFESSSSDENVSGRELEHWYDADDGNDDE</mol_seq>
          </sequence>
          <property datatype="xsd:string" ref="Compara:genome_db_name" applies_to="clade">dirofilaria_immitis_prjeb1797</property>
        </clade>
      </clade>
    </clade>
    <property datatype="xsd:string" ref="Compara:gene_tree_stable_id" applies_to="phylogeny">WBGT00000000028368</property>
  </phylogeny>
</phyloxml>

use strict;
use warnings;
 
use HTTP::Tiny;
 
my $http = HTTP::Tiny->new();
 
my $server = 'https://parasite.wormbase.org';
my $ext = '/rest-19/genetree/member/id/WBGene00221255?';
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://parasite.wormbase.org"
ext = "/rest-19/genetree/member/id/WBGene00221255?"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-phyloxml+xml", "Accept" : ""})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print r.text

import requests, sys
 
server = "https://parasite.wormbase.org"
ext = "/rest-19/genetree/member/id/WBGene00221255?"
 
r = requests.get(server+ext, headers={ "Content-Type" : "text/x-phyloxml+xml", "Accept" : ""})
 
if not r.ok:
  r.raise_for_status()
  sys.exit()
 
 
print(r.text)

require 'net/http'
require 'uri'
 
server='https://parasite.wormbase.org'
path = '/rest-19/genetree/member/id/WBGene00221255?'
 
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://parasite.wormbase.org";
    String ext = "/rest-19/genetree/member/id/WBGene00221255?";
    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);
  }
}

 
curl 'https://parasite.wormbase.org/rest-19/genetree/member/id/WBGene00221255?' -H 'Content-type:text/x-phyloxml+xml'

wget -q --header='Content-type:text/x-phyloxml+xml' 'https://parasite.wormbase.org/rest-19/genetree/member/id/WBGene00221255?'  -O -

Resource Information

Methods	GET
Response formats	phyloxml nh json jsonp