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GET alignment/region/:species/:region

Retrieves genomic alignments as separate blocks based on a region and species

Parameters

Required

NameTypeDescriptionDefaultExample Values
region String Query region. A maximum of 10Mb is allowed to be requested at any one time - X:1000000..1000100:1
X:1000000..1000100:-1
X:1000000..1000100
species String Species name/alias - homo_sapiens
human

Optional

NameTypeDescriptionDefaultExample Values
aligned Boolean Return the aligned string if true. Otherwise, return the original sequence (no insertions) 1 -
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
mask Enum(hard,soft) Request the sequence masked for repeat sequences. Hard will mask all repeats as N's and soft will mask repeats as lowercased characters. - hard
method Enum(LASTZ_PATCH, LASTZ_NET) The alignment method LASTZ_NET LASTZ_PATCH

Example Requests

/alignment/region/homo_sapiens/17:64155265-64255266?content-type=application/json


use strict;
use warnings;

use HTTP::Tiny;

my $http = HTTP::Tiny->new();

my $server = 'https://grch37.rest.ensembl.org';
my $ext = '/alignment/region/homo_sapiens/17:64155265-64255266?';
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://grch37.rest.ensembl.org"
ext = "/alignment/region/homo_sapiens/17:64155265-64255266?"

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://grch37.rest.ensembl.org"
ext = "/alignment/region/homo_sapiens/17:64155265-64255266?"

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://grch37.rest.ensembl.org'
path = '/alignment/region/homo_sapiens/17:64155265-64255266?'

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://grch37.rest.ensembl.org";
    String ext = "/alignment/region/homo_sapiens/17:64155265-64255266?";
    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://grch37.rest.ensembl.org"
ext <- "/alignment/region/homo_sapiens/17:64155265-64255266?"

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://grch37.rest.ensembl.org/alignment/region/homo_sapiens/17:64155265-64255266?' -H 'Content-type:application/json'


wget -q --header='Content-type:application/json' 'https://grch37.rest.ensembl.org/alignment/region/homo_sapiens/17:64155265-64255266?'  -O -

/alignment/region/homo_sapiens/17:64155265-64255266?content-type=text/x-phyloxml


use strict;
use warnings;

use HTTP::Tiny;

my $http = HTTP::Tiny->new();

my $server = 'https://grch37.rest.ensembl.org';
my $ext = '/alignment/region/homo_sapiens/17:64155265-64255266?';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/x-phyloxml' }
});

die "Failed!\n" unless $response->{success};


print "$response->{content}\n";


import requests, sys

server = "https://grch37.rest.ensembl.org"
ext = "/alignment/region/homo_sapiens/17:64155265-64255266?"

r = requests.get(server+ext, headers={ "Content-Type" : "text/x-phyloxml"})

if not r.ok:
  r.raise_for_status()
  sys.exit()


print r.text


import requests, sys

server = "https://grch37.rest.ensembl.org"
ext = "/alignment/region/homo_sapiens/17:64155265-64255266?"

r = requests.get(server+ext, headers={ "Content-Type" : "text/x-phyloxml"})

if not r.ok:
  r.raise_for_status()
  sys.exit()


print(r.text)


require 'net/http'
require 'uri'

server='https://grch37.rest.ensembl.org'
path = '/alignment/region/homo_sapiens/17:64155265-64255266?'

url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)

request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-phyloxml'})

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://grch37.rest.ensembl.org";
    String ext = "/alignment/region/homo_sapiens/17:64155265-64255266?";
    URL url = new URL(server + ext);

    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "text/x-phyloxml");
    

    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://grch37.rest.ensembl.org"
ext <- "/alignment/region/homo_sapiens/17:64155265-64255266?"

r <- GET(paste(server, ext, sep = ""), content_type("text/x-phyloxml"))

stop_for_status(r)


print(content(r))



curl 'https://grch37.rest.ensembl.org/alignment/region/homo_sapiens/17:64155265-64255266?' -H 'Content-type:text/x-phyloxml'


wget -q --header='Content-type:text/x-phyloxml' 'https://grch37.rest.ensembl.org/alignment/region/homo_sapiens/17:64155265-64255266?'  -O -

/alignment/region/homo_sapiens/17:39090535-39196497?method=LASTZ_PATCH;content-type=application/json


use strict;
use warnings;

use HTTP::Tiny;

my $http = HTTP::Tiny->new();

my $server = 'https://grch37.rest.ensembl.org';
my $ext = '/alignment/region/homo_sapiens/17:39090535-39196497?method=LASTZ_PATCH';
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://grch37.rest.ensembl.org"
ext = "/alignment/region/homo_sapiens/17:39090535-39196497?method=LASTZ_PATCH"

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://grch37.rest.ensembl.org"
ext = "/alignment/region/homo_sapiens/17:39090535-39196497?method=LASTZ_PATCH"

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://grch37.rest.ensembl.org'
path = '/alignment/region/homo_sapiens/17:39090535-39196497?method=LASTZ_PATCH'

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://grch37.rest.ensembl.org";
    String ext = "/alignment/region/homo_sapiens/17:39090535-39196497?method=LASTZ_PATCH";
    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://grch37.rest.ensembl.org"
ext <- "/alignment/region/homo_sapiens/17:39090535-39196497?method=LASTZ_PATCH"

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://grch37.rest.ensembl.org/alignment/region/homo_sapiens/17:39090535-39196497?method=LASTZ_PATCH' -H 'Content-type:application/json'


wget -q --header='Content-type:application/json' 'https://grch37.rest.ensembl.org/alignment/region/homo_sapiens/17:39090535-39196497?method=LASTZ_PATCH'  -O -

Resource Information

MethodsGET
Response formatsjson
xml
phyloxml
jsonp