VectorBase Rest API - GET alignment/region/:species/:region

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

Parameters

Required

Name	Type	Description	Default	Example Values
region	`String`	Query region. A maximum of 10Mb is allowed to be requested at any one time	`-`	`2L:2000000-2000100:1` `2L:2000000-2000100:-1` `2L:2000000-2000100`
species	`String`	Species name/alias	`-`	`anopheles_gambiae` `Anopheles_gambiae`

Optional

Name	Type	Description	Default	Example 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`
compact	`Boolean`	Applicable to EPO_LOW_COVERAGE alignments. If true, concatenate the low coverage species sequences together to create a single sequence. Otherwise, separates out all sequences.	`1`	`-`
compara	`String`	Name of the compara database to use. Multiple comparas can exist on a server if you are accessing Ensembl Genomes data	`vb`	`vb`
display_species_set	`String`	Subset of species in the alignment to be displayed (multiple values). All the species in the alignment will be displayed if this is not set. Any valid alias may be used.	`-`	`human` `chimp` `gorilla`
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(EPO, EPO_LOW_COVERAGE, PECAN, LASTZ_NET, BLASTZ_NET, TRANSLATED_BLAT_NET)`	The alignment method	`LASTZ_NET`	`LASTZ_NET`
species_set	`String`	The set of species used to define the pairwise alignment (multiple values). Should not be used with the species_set_group parameter. Use /info/compara/species_sets/:method with one of the methods listed above to obtain a valid list of species sets. Any valid alias may be used.	`-`	`__VAR(compara_set_species_1)__` `__VAR(compara_set_species_2)__`
species_set_group	`String`	The species set group name of the multiple alignment. Should not be used with the species_set parameter. Use /info/compara/species_sets/:method with one of the methods listed above to obtain a valid list of group names.	`mammals`	`mammals, amniotes, fish, sauropsids`

Example Requests

/rest/alignment/region/anopheles_gambiae/2L:2269888-2519887?content-type=application/json;method=LASTZ_NET;species_set=anopheles_gambiae;species_set=anopheles_farauti

use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'https://www.vectorbase.org/rest';
my $ext = '/alignment/region/anopheles_gambiae/2L:2269888-2519887?method=LASTZ_NET;species_set=anopheles_gambiae;species_set=anopheles_farauti';
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://www.vectorbase.org/rest"
ext = "/alignment/region/anopheles_gambiae/2L:2269888-2519887?method=LASTZ_NET;species_set=anopheles_gambiae;species_set=anopheles_farauti"

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://www.vectorbase.org/rest"
ext = "/alignment/region/anopheles_gambiae/2L:2269888-2519887?method=LASTZ_NET;species_set=anopheles_gambiae;species_set=anopheles_farauti"

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://www.vectorbase.org/rest'
path = '/alignment/region/anopheles_gambiae/2L:2269888-2519887?method=LASTZ_NET;species_set=anopheles_gambiae;species_set=anopheles_farauti'

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://www.vectorbase.org/rest";
    String ext = "/alignment/region/anopheles_gambiae/2L:2269888-2519887?method=LASTZ_NET;species_set=anopheles_gambiae;species_set=anopheles_farauti";
    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);
  }
}

# Note: curl version 7.34.0 or above is required

curl 'https://www.vectorbase.org/rest/alignment/region/anopheles_gambiae/2L:2269888-2519887?method=LASTZ_NET;species_set=anopheles_gambiae;species_set=anopheles_farauti' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'https://www.vectorbase.org/rest/alignment/region/anopheles_gambiae/2L:2269888-2519887?method=LASTZ_NET;species_set=anopheles_gambiae;species_set=anopheles_farauti'  -O -

/rest/alignment/region/anopheles_gambiae/2L:2269888-2519887?content-type=text/x-phyloxml;method=LASTZ_NET;species_set=anopheles_gambiae;species_set=anopheles_farauti

use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'https://www.vectorbase.org/rest';
my $ext = '/alignment/region/anopheles_gambiae/2L:2269888-2519887?method=LASTZ_NET;species_set=anopheles_gambiae;species_set=anopheles_farauti';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/x-phyloxml' }
});

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


print "$response->{status} $response->{reason}\n";

import requests, sys

server = "https://www.vectorbase.org/rest"
ext = "/alignment/region/anopheles_gambiae/2L:2269888-2519887?method=LASTZ_NET;species_set=anopheles_gambiae;species_set=anopheles_farauti"

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://www.vectorbase.org/rest"
ext = "/alignment/region/anopheles_gambiae/2L:2269888-2519887?method=LASTZ_NET;species_set=anopheles_gambiae;species_set=anopheles_farauti"

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://www.vectorbase.org/rest'
path = '/alignment/region/anopheles_gambiae/2L:2269888-2519887?method=LASTZ_NET;species_set=anopheles_gambiae;species_set=anopheles_farauti'

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://www.vectorbase.org/rest";
    String ext = "/alignment/region/anopheles_gambiae/2L:2269888-2519887?method=LASTZ_NET;species_set=anopheles_gambiae;species_set=anopheles_farauti";
    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);
  }
}

# Note: curl version 7.34.0 or above is required

curl 'https://www.vectorbase.org/rest/alignment/region/anopheles_gambiae/2L:2269888-2519887?method=LASTZ_NET;species_set=anopheles_gambiae;species_set=anopheles_farauti' -H 'Content-type:text/x-phyloxml'

wget -q --header='Content-type:text/x-phyloxml' 'https://www.vectorbase.org/rest/alignment/region/anopheles_gambiae/2L:2269888-2519887?method=LASTZ_NET;species_set=anopheles_gambiae;species_set=anopheles_farauti'  -O -

Resource Information

Methods	GET
Response formats	json xml phyloxml jsonp