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GET overlap/region/:species/:region

Retrieves multiple types of features for a given region.

Parameters

Required

NameTypeDescriptionDefaultExample 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

NameTypeDescriptionDefaultExample 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


  1. use strict;
  2. use warnings;
  3.  
  4. use HTTP::Tiny;
  5.  
  6. my $http = HTTP::Tiny->new();
  7.  
  8. my $server = 'https://parasite.wormbase.org';
  9. my $ext = '/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon';
  10. my $response = $http->get($server.$ext, {
  11.   headers => { 'Content-type' => 'application/json' }
  12. });
  13.  
  14. die "Failed!\n" unless $response->{success};
  15.  
  16.  
  17. use JSON;
  18. use Data::Dumper;
  19. if(length $response->{content}) {
  20.   my $hash = decode_json($response->{content});
  21.   local $Data::Dumper::Terse = 1;
  22.   local $Data::Dumper::Indent = 1;
  23.   print Dumper $hash;
  24.   print "\n";
  25. }
  26.  
  1. import requests, sys
  2.  
  3. server = "https://parasite.wormbase.org"
  4. ext = "/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "application/json", "Accept" : ""})
  7.  
  8. if not r.ok:
  9.   r.raise_for_status()
  10.   sys.exit()
  11.  
  12. decoded = r.json()
  13. print repr(decoded)
  14.  
  1. import requests, sys
  2.  
  3. server = "https://parasite.wormbase.org"
  4. ext = "/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "application/json", "Accept" : ""})
  7.  
  8. if not r.ok:
  9.   r.raise_for_status()
  10.   sys.exit()
  11.  
  12. decoded = r.json()
  13. print(repr(decoded))
  14.  
  1. require 'net/http'
  2. require 'uri'
  3.  
  4. server='https://parasite.wormbase.org'
  5. path = '/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon'
  6.  
  7. url = URI.parse(server)
  8. http = Net::HTTP.new(url.host, url.port)
  9.  
  10. request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'})
  11.  
  12. response = http.request(request)
  13.  
  14. if response.code != "200"
  15.   puts "Invalid response: #{response.code}"
  16.   puts response.body
  17.   exit
  18. end
  19.  
  20.  
  21. require 'rubygems'
  22. require 'json'
  23. require 'yaml'
  24.  
  25. result = JSON.parse(response.body)
  26. puts YAML::dump(result)
  27.  
  1. import java.net.URL;
  2. import java.net.URLConnection;
  3. import java.net.HttpURLConnection;
  4. import java.io.BufferedReader;
  5. import java.io.InputStream;
  6. import java.io.InputStreamReader;
  7. import java.io.IOException;
  8. import java.io.Reader;
  9.  
  10.  
  11. public class EnsemblRest {
  12.  
  13.   public static void main(String[] args) throws Exception {
  14.     String server = "https://parasite.wormbase.org";
  15.     String ext = "/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon";
  16.     URL url = new URL(server + ext);
  17.  
  18.     URLConnection connection = url.openConnection();
  19.     HttpURLConnection httpConnection = (HttpURLConnection)connection;
  20.     
  21.     httpConnection.setRequestProperty("Content-Type", "application/json");
  22.     
  23.  
  24.     InputStream response = connection.getInputStream();
  25.     int responseCode = httpConnection.getResponseCode();
  26.  
  27.     if(responseCode != 200) {
  28.       throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
  29.     }
  30.  
  31.     String output;
  32.     Reader reader = null;
  33.     try {
  34.       reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
  35.       StringBuilder builder = new StringBuilder();
  36.       char[] buffer = new char[8192];
  37.       int read;
  38.       while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
  39.         builder.append(buffer, 0, read);
  40.       }
  41.       output = builder.toString();
  42.     } 
  43.     finally {
  44.         if (reader != null) try {
  45.           reader.close(); 
  46.         } catch (IOException logOrIgnore) {
  47.           logOrIgnore.printStackTrace();
  48.         }
  49.     }
  50.  
  51.     System.out.println(output);
  52.   }
  53. }
  54.  
  1.  
  2. 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'
  3.  
  1. 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 -
  2.  

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


  1. use strict;
  2. use warnings;
  3.  
  4. use HTTP::Tiny;
  5.  
  6. my $http = HTTP::Tiny->new();
  7.  
  8. my $server = 'https://parasite.wormbase.org';
  9. my $ext = '/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon';
  10. my $response = $http->get($server.$ext, {
  11.   headers => { 'Content-type' => 'text/x-gff3' }
  12. });
  13.  
  14. die "Failed!\n" unless $response->{success};
  15.  
  16.  
  17. print "$response->{status} $response->{reason}\n";
  18.  
  1. import requests, sys
  2.  
  3. server = "https://parasite.wormbase.org"
  4. ext = "/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-gff3", "Accept" : ""})
  7.  
  8. if not r.ok:
  9.   r.raise_for_status()
  10.   sys.exit()
  11.  
  12.  
  13. print r.text
  14.  
  1. import requests, sys
  2.  
  3. server = "https://parasite.wormbase.org"
  4. ext = "/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-gff3", "Accept" : ""})
  7.  
  8. if not r.ok:
  9.   r.raise_for_status()
  10.   sys.exit()
  11.  
  12.  
  13. print(r.text)
  14.  
  1. require 'net/http'
  2. require 'uri'
  3.  
  4. server='https://parasite.wormbase.org'
  5. path = '/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon'
  6.  
  7. url = URI.parse(server)
  8. http = Net::HTTP.new(url.host, url.port)
  9.  
  10. request = Net::HTTP::Get.new(path, {'Content-Type' => 'text/x-gff3'})
  11.  
  12. response = http.request(request)
  13.  
  14. if response.code != "200"
  15.   puts "Invalid response: #{response.code}"
  16.   puts response.body
  17.   exit
  18. end
  19.  
  20.  
  21. puts response.body
  22.  
  1. import java.net.URL;
  2. import java.net.URLConnection;
  3. import java.net.HttpURLConnection;
  4. import java.io.BufferedReader;
  5. import java.io.InputStream;
  6. import java.io.InputStreamReader;
  7. import java.io.IOException;
  8. import java.io.Reader;
  9.  
  10.  
  11. public class EnsemblRest {
  12.  
  13.   public static void main(String[] args) throws Exception {
  14.     String server = "https://parasite.wormbase.org";
  15.     String ext = "/rest-19/overlap/region/brugia_malayi_prjna10729/Bm_v4_Chr2_contig_001:13847151-13862157?feature=gene;feature=transcript;feature=cds;feature=exon";
  16.     URL url = new URL(server + ext);
  17.  
  18.     URLConnection connection = url.openConnection();
  19.     HttpURLConnection httpConnection = (HttpURLConnection)connection;
  20.     
  21.     httpConnection.setRequestProperty("Content-Type", "text/x-gff3");
  22.     
  23.  
  24.     InputStream response = connection.getInputStream();
  25.     int responseCode = httpConnection.getResponseCode();
  26.  
  27.     if(responseCode != 200) {
  28.       throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
  29.     }
  30.  
  31.     String output;
  32.     Reader reader = null;
  33.     try {
  34.       reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
  35.       StringBuilder builder = new StringBuilder();
  36.       char[] buffer = new char[8192];
  37.       int read;
  38.       while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
  39.         builder.append(buffer, 0, read);
  40.       }
  41.       output = builder.toString();
  42.     } 
  43.     finally {
  44.         if (reader != null) try {
  45.           reader.close(); 
  46.         } catch (IOException logOrIgnore) {
  47.           logOrIgnore.printStackTrace();
  48.         }
  49.     }
  50.  
  51.     System.out.println(output);
  52.   }
  53. }
  54.  
  1.  
  2. 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'
  3.  
  1. 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 -
  2.  

Resource Information

MethodsGET
Response formatsjson
xml
gff3
bed
jsonp
Slice length5e6