GET overlap/region/:species/:region

Retrieves multiple types of features for a given region.

Parameters

Required

Name	Type	Description	Default	Example Values
feature	`Enum(gene, transcript, cds, exon, repeat, simple, misc)`	The type of feature to retrieve. Multiple values are accepted.	`none`	`-`
region	`String`	Query region. A maximum of 5Mb is allowed to be requested at any one time	`-`	`X:1..1000:1` `X:1..1000:-1` `X:1..1000`
species	`String`	Species name/alias.	`-`	`brugia_malayi_prjna10729`

Optional

Name	Type	Description	Default	Example Values
biotype	`String`	Functional classification of the gene or transcript to fetch. Cannot be used in conjunction with logic_name when querying transcripts.	`-`	`protein_coding`
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`
cell_type	`String`	Cell type name in Ensembl's Regulatory Build, required for segmentation feature, optional for regulatory elements.	`-`	`K562`
db_type	`String`	Specify the database type to retrieve features from if not using the core database. We automatically choose the correct type of DB for variation, comparative and regulation features.	`core`	`core`
logic_name	`String`	Limit retrieval of genes, transcripts and exons by the name of analysis.	`-`	`-`
misc_set	`String`	Miscellaneous set which groups together feature entries. Consult the DB or returned data sets to discover what is available.	`-`	`cloneset_30k`
species_set	`String`	The species set name for retrieving constrained elements.	`mammals`	`-`
trim_downstream	`Boolean`	Do not return features which overlap the downstream end of the region.	`0`	`-`
trim_upstream	`Boolean`	Do not return features which overlap upstream end of the region.	`0`	`-`

Example Requests

/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?content-type=application/json;feature=gene;feature=transcript;feature=cds;feature=exon

use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'https://parasite.wormbase.org';
my $ext = '/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon';
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://parasite.wormbase.org"
ext = "/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon"

r = requests.get(server+ext, headers={ "Content-Type" : "application/json", "Accept" : ""})

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

decoded = r.json()
print repr(decoded)

import requests, sys

server = "https://parasite.wormbase.org"
ext = "/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon"

r = requests.get(server+ext, headers={ "Content-Type" : "application/json", "Accept" : ""})

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

decoded = r.json()
print(repr(decoded))

require 'net/http'
require 'uri'

server='https://parasite.wormbase.org'
path = '/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon'

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://parasite.wormbase.org";
    String ext = "/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon";
    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);
  }
}


curl 'https://parasite.wormbase.org/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon' -H 'Content-type:application/json'

wget -q --header='Content-type:application/json' 'https://parasite.wormbase.org/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon'  -O -

/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?content-type=text/x-gff3;feature=gene;feature=transcript;feature=cds;feature=exon

use strict;
use warnings;

use HTTP::Tiny;

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

my $server = 'https://parasite.wormbase.org';
my $ext = '/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'text/x-gff3' }
});

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


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

import requests, sys

server = "https://parasite.wormbase.org"
ext = "/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon"

r = requests.get(server+ext, headers={ "Content-Type" : "text/x-gff3", "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/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon"

r = requests.get(server+ext, headers={ "Content-Type" : "text/x-gff3", "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/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon'

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

request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-gff3'})

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/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon";
    URL url = new URL(server + ext);

    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "text/x-gff3");
    

    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/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon' -H 'Content-type:text/x-gff3'

wget -q --header='Content-type:text/x-gff3' 'https://parasite.wormbase.org/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon'  -O -

Resource Information

Methods	GET
Response formats	json xml gff3 bed jsonp
Slice length	5e6