List the currently available assemblies for a species, along with toplevel sequences, chromosomes and cytogenetic bands.
| Name | Type | Description | Default | Example Values |
|---|---|---|---|---|
| species | String | Species name/alias | - |
homo_sapiens human |
| Name | Type | Description | Default | Example Values |
|---|---|---|---|---|
| bands | Boolean(0,1) | If set to 1, include karyotype band information. Only display if band information is available | 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 |
| synonyms | Boolean(0,1) | If set to 1, include information about known synonyms. | 0 | - |
use strict;
use warnings;
use HTTP::Tiny;
my $http = HTTP::Tiny->new();
my $server = 'http://rest.ensembl.org';
my $ext = '/info/assembly/homo_sapiens?';
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 = "/info/assembly/homo_sapiens?"
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 = "/info/assembly/homo_sapiens?"
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 = '/info/assembly/homo_sapiens?'
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 = "/info/assembly/homo_sapiens?";
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 <- "/info/assembly/homo_sapiens?"
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/info/assembly/homo_sapiens?' -H 'Content-type:application/json'
wget -q --header='Content-type:application/json' 'http://rest.ensembl.org/info/assembly/homo_sapiens?' -O -
use strict;
use warnings;
use HTTP::Tiny;
my $http = HTTP::Tiny->new();
my $server = 'http://rest.ensembl.org';
my $ext = '/info/assembly/human?';
my $response = $http->get($server.$ext, {
headers => { 'Content-type' => 'text/xml' }
});
die "Failed!\n" unless $response->{success};
print "$response->{content}\n";
import requests, sys
server = "http://rest.ensembl.org"
ext = "/info/assembly/human?"
r = requests.get(server+ext, headers={ "Content-Type" : "text/xml"})
if not r.ok:
r.raise_for_status()
sys.exit()
print r.text
import requests, sys
server = "http://rest.ensembl.org"
ext = "/info/assembly/human?"
r = requests.get(server+ext, headers={ "Content-Type" : "text/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 = '/info/assembly/human?'
url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)
request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/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 = "/info/assembly/human?";
URL url = new URL(server + ext);
URLConnection connection = url.openConnection();
HttpURLConnection httpConnection = (HttpURLConnection)connection;
httpConnection.setRequestProperty("Content-Type", "text/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 <- "/info/assembly/human?"
r <- GET(paste(server, ext, sep = ""), content_type("text/xml"))
stop_for_status(r)
print(content(r))
curl 'http://rest.ensembl.org/info/assembly/human?' -H 'Content-type:text/xml'
wget -q --header='Content-type:text/xml' 'http://rest.ensembl.org/info/assembly/human?' -O -