Convert from cDNA coordinates to genomic coordinates. Output reflects forward orientation coordinates as returned from the Ensembl API.
Name | Type | Description | Default | Example Values |
---|---|---|---|---|
id | String | An Ensembl stable ID | - |
ENST00000288602 |
region | String | Query region | - |
100..300 |
Name | Type | Description | Default | Example Values |
---|---|---|---|---|
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 |
include_original_region | Boolean(0,1) | Include original input region (cDNA coordinates) along with the target region (genomic coordinates) mappings. | 0 | - |
species | String | Species name/alias | - |
homo_sapiens human |
{
"mappings": [
{
"start": 140924566,
"end": 140924633,
"assembly_name": "GRCh38",
"seq_region_name": "7",
"gap": 0,
"rank": 0,
"strand": -1,
"coord_system": "chromosome"
},
{
"start": 140850111,
"assembly_name": "GRCh38",
"end": 140850212,
"seq_region_name": "7",
"gap": 0,
"strand": -1,
"rank": 0,
"coord_system": "chromosome"
},
{
"end": 140834872,
"assembly_name": "GRCh38",
"start": 140834842,
"seq_region_name": "7",
"gap": 0,
"coord_system": "chromosome",
"strand": -1,
"rank": 0
}
]
}
- use strict;
- use warnings;
- use HTTP::Tiny;
- my $http = HTTP::Tiny->new();
- my $server = 'https://jan2020.rest.ensembl.org';
- my $ext = '/map/cdna/ENST00000288602/100..300?';
- 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://jan2020.rest.ensembl.org"
- ext = "/map/cdna/ENST00000288602/100..300?"
- 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://jan2020.rest.ensembl.org"
- ext = "/map/cdna/ENST00000288602/100..300?"
- 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://jan2020.rest.ensembl.org'
- path = '/map/cdna/ENST00000288602/100..300?'
- 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://jan2020.rest.ensembl.org";
- String ext = "/map/cdna/ENST00000288602/100..300?";
- 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://jan2020.rest.ensembl.org"
- ext <- "/map/cdna/ENST00000288602/100..300?"
- 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://jan2020.rest.ensembl.org/map/cdna/ENST00000288602/100..300?' -H 'Content-type:application/json'
- wget -q --header='Content-type:application/json' 'https://jan2020.rest.ensembl.org/map/cdna/ENST00000288602/100..300?' -O -
Methods | GET |
Response formats | json xml jsonp |