Service logo

GET sequence/id/:id

Request multiple types of sequence by stable identifier.

Parameters

Required

NameTypeDescriptionDefaultExample Values
id String A stable ID - WBGene00221255
WBGene00221255.fasta (supported on some deployments)

Optional

NameTypeDescriptionDefaultExample 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
db_type String Restrict the search to a database other than the default. Useful if you need to use a DB other than core - core
expand_3prime Int Expand the sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type. - 1000
expand_5prime Int Expand the sequence upstream of the sequence by this many basepairs. Only available when using genomic sequence type. - 1000
format Enum(fasta) Format of the data - fasta
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. Only available when using genomic sequence type. - hard
mask_feature Boolean Mask features on the sequence. If sequence is genomic, mask introns. If sequence is cDNA, mask UTRs. Incompatible with the 'mask' option 0 -
multiple_sequences Boolean Allow the service to return more than 1 sequence per identifier. This is useful when querying for a gene but using a type such as protein. 0 -
object_type String Filter by feature type - gene
species String Species name/alias - brugia_malayi_prjna10729
type Enum(genomic,cds,cdna,protein) Type of sequence. Defaults to genomic where applicable, i.e. not translations. cdna refers to the spliced transcript sequence with UTR; cds refers to the spliced transcript sequence without UTR. genomic cds

Example Requests

/rest-19/sequence/id/WBGene00221255?content-type=text/plain


 AGTATCCAATTCAACAATAGATGGAGCTACAATTTTCTCAATTGTGAATTCCACATGATGATTTGCAGTGTCCACCAGGGTTCACGTTCACCAGGTGGTCCAACTGGTTCATTAGGTTCTGGTTCGTCTCGTTTACCTGGTGGTCCGGTTGGTCCCTTGAAAGTCAGACATAGAAAATATTGAATTACAGAAAGGTATGTAAGAAAAGATGCAAAATGCTCTTAGACAATTCGTTTTGCATTTAAATTAAAAAAAAAAAATTGTTTTTCATTTAAATTTAAATTAATTATAAACCTAAAATGAAGTATAGAATAAATGGCTTCTTAGTGTTATAAAAGGGTTTAATTCAAATATTTTACAATTTTTAATGCAGTTACAATAGTTAGGGAAAAAATGAAATATGCCAAGCAACCATTTCACCAGGAGATGCTGGTGGCCCGAAATTGCTAGATGGAATCATATCTGGTCCTGGTGAACCTTTGGGTCCACGAAGCCCTTGTGATCTTGGTGGCCCGAAATTGCTAGATGGAATCCTATCTGGTCCTGGCGAACCTTTGGATCCACGAGGTCCTTGTGATCCTGGTGGCCCGAAATTGCTAGATGGAATCCTATCTGGTCCTGGTGAACCTTTGGATCCACGAAGTCCTTGTGATCCTGGTGGCCCGAAATTGCTAGATGGAATCCTATCTGGTCCTGGTGAACCTTTGGATCCACGAAGTCCTTGTGATCCTGGTGGCCCGAAATTGCTAGATGGAATCCTATCTGGTCCTGGCGAACCTTTGGATCCACGAGGTCCTTGTGATCCTGGTGGCCCGAAATTGCTAGATGGAATCATATCTGGTCCTGATGAACCTTTGGATCCATCAGGTCCTTGTGATCCTGGTAGACCTTTGATTCCTCTTCCACGATTGTATCATCACCAGGTAGACTCATAATATATAAGTAATAACTTAATGACTTTACTTTACTTTTTTTTTTAATTTACAAATATGCATTATATTGTTCGGTAGTGCATCGATCTCTTCGTATTATTTATTTTCCACTACGATTTTTATTTCTTTGTGGTTCTTATTGTTTAATTGTGCCAGCAAAAATTTCTTTCTAACTTTTTATTAATTTGTATTTTATTTAGTTTCATTCCAACATTATCACTGATCTGATTATAATCCAATTGCAGTATTTTATAGCTAAGTAAAGATTAAAAAAAAAAATTAAAACTTAATCTTTGTCCTTTCAGACATCAATCAAATTACTTTTTATTTTTTTTTTATAGCAGAATGAAATGTACCTTAATGCTAGGCTCACCTTCCTCATCAGAAAAGTCCAGGTGCTTCGGAATCGCCTATCCTACCTCCTTTACCTGGTCTTCCAGGTATGCCGTGATGATCTGGTTCACCAGGTATCCTGGTTCTCCTTTTTCTCCTCTATTTCCTGGTGGTCCTGCAGGATAAATCATGCTTGAAATTCCTTTTTTAATTTGATGCACTACATTTTGCAACAAAGTAGATAAAATCAAAAGAAAAAAAATGATTTAAATGATTTATTTAAATATTAAATATTAAAAAAATTAAATTATAAAAAATTCTTGTGTGAACCAAATTCTGGTTCCAATGAAATATCTAAGTTTGCATTTTCCCTAAATTTATCATTTAATTCTTAATTTATTTCTAATAGATCTACTATGACTTGATGGAAGCTTAGAATTGTTGTCATAAAATGGTTTATAAATAATAATAATACATTGATTATCAGTTAAATTCTCTTAGCATATATTAATTATTTAAAAATTTTTGTCTGAAACCTTTCAGTATTAGAAGTGTTTTTTGAACATATAAGCAAAATTTTAATTTTTTTTAAGAAGAAATTCAAACAATTATAAAACTTTATGCAAATTTGAAATTTGATATTTAAATAAATTAAAAAAAAAAAAAGTTTCATGGTTATTTTGTTTAACTATTACAATAGGAAACGGTAATTTGTGTCTTTACCATATGAAATAAGCAAAAGGTTTAATTAAATGTTATTAGCAAAAAATTTTTGAAAAAATGAATAAAAAATGAAGAAATAATATTGCTATTACAATTATAATAGGAAATTTGATTATTGATTATTTATATTTGGAACTTATAGTAGGAAATTTGATTATTTATTATATATTTGAAACTTATAATAGGAAATTTTGATTATTGATTATCTATATTTGGAACTTATAATAAGAAATTTGATTGTTGATTATCTATATTTGGAACTTATAATAGGAAATTTGATTATTGATTATCTATATTTGGAACTTATAATAGGAAATTTGATTATTGATTATCTATATCTTATAATAGGAATTTTGATTATTGATTATCTATATTTGGAACTTATAATGAGAAATTTGATTGTTGATTATCTATATTTGGAATTATAATAAGAAATTTGATTATTGATTATCTATATTTGGAACTTATAATAGGAAATTTGATTATTGATTATCTATATTTGGAACTTATAATAGGAAATTTGATTATTGATTATCTATATCTTATAATAGGAATTTTGATTATTGATTATCTATATTTGGAACTTATAATGAGAAATTTGATTGTTGATTATCTATATTTGGAACTTATAATAGAAATTTTGATTATTGATTATCACTAAAACTTTATAATTGTCACCAGATACTACTACAATATTTGGAACTTATATAAGAAATTGTAATAGGAAATCTGATTATTGATTATCACTAAAGTTTTATAATTGTCTAGGAATTTTGATTATTGATTATCTATATTTGGAACTTATAATGAGAAATTTGATTGTTGATTATCTATATTTGGAATTATAATAAGAAATTTGATTATTGATTATCTATATTTGGAACTTATAATAGGAAATTTGATTATTGATTATCTATATTTGGAACTTATAATAGGAAATTTGATTATTGATTATCTATATCTTATAATAGGAATTTTGATTATTGATTATCTATATTTGGAACTTATAATGAGAAATTTGATTGTTGATTATCTATATTTGGAACTTATAATAGAAATTTTGATTATTGATTATCACTAAAACTTTATAATTGTCACCAGATACTACTACAATATTTGGAACTTATATAAGAAATTGTAATAGGAAATCTGATTATTGATTATCACTAAAGTTTTATAATTGTTACCAAAACAAGAAGAAAAAGGAAGGAAAAAAAGAAAAAATTTTTTCAGTAATATAATCATTGGAATTGATACTACTTCAAAAATATTACCATATTTTCTGCTCATATTCCGTGTCTTTCCGGATAACAGGATTAAAATATTCCGGTTATGCAGAAACAGGTCAAAGGGCAACAACACGTCAATGAATTACTTCCATCAGTGATACAACAGGAAGATCCAACAAACGATTCACTGTCACCGTTGTCATCTGCTCGTTGCACTGATCAATATCAAAGTGATAAACTGTTAGCTGTAAGTGTTAATGTGTTAACTTTCGAGAAATACTAGTGATAAGGAAGCAATTTGAATATGCCACTTTAAAATGACTGATAAGCAAACTATCAGCTTATCATACACTAGTAAATTAGAAATAATAATGATAAGTTGAATTTTTTTTTTTAATTTTTTCATTTGTTAAAATAATCAGTGCAATTAGTGATATATGATAGTTACAGTATGTTAATAATTCTTCAAAATAACTTTGCAGAATTATTCTCTTCTAGAAAAGCATACTTTTAAAGCGTTGATGGCGTAATCTGACGTAAAAAAAACGTAATCTGACGTAAAAAAAAAGAAAAAAACTATGAAAGAGAAATTTTTACATAGTAAGAAAAAAAATTTTTAAAACAAAAACAAGAAAAAAACTAGCAATTTTAAATTAAATAAATTAAAAAAATTATCATAAAATACTTTAACTGTTGTAGGAGATTCGTAATGGAGTACAATTGCGCCACGTAATACCAAATGATCATAAACAATGCGCTAAAATGCTTTATGATAAAGCATGCGAGAAAAAAGTAATCATTTTGATAAATTTGTTTAAATTTTTTTTTTTTTTTTTCAAAAAAAATATAAATAATTTCTATTTCTATCTTTTTTTTTTTACATTTTCTCTCTTTTCATATTGTTATTTATCTATATATTATTTTTATAAATTATTTAGAAAAAAATTTTTTTCCTATTTTAAAAAAATTTTTTTTTTTTTTTTGCTAATATTTTTTATATATTTATGAGTTATACAGGAAGAAAATAATATAAATGAAAAAGAAACAAAGTTAGAAACGGAAAAAGCAATTAATATTGGAAATATCTTACTTAATGCTATGCAAAAGCGACGACTTCTAATGCATTTTGGTTAA
  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/sequence/id/WBGene00221255?';
  10. my $response = $http->get($server.$ext, {
  11.   headers => { 'Content-type' => 'text/plain' }
  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/sequence/id/WBGene00221255?"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/plain", "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/sequence/id/WBGene00221255?"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/plain", "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/sequence/id/WBGene00221255?'
  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/plain'})
  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/sequence/id/WBGene00221255?";
  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/plain");
  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/sequence/id/WBGene00221255?' -H 'Content-type:text/plain'
  3.  
  1. wget -q --header='Content-type:text/plain' 'https://parasite.wormbase.org/rest-19/sequence/id/WBGene00221255?'  -O -
  2.  

/rest-19/sequence/id/Bm4789.1?type=cdna;content-type=text/x-fasta;object_type=transcript


 >Bm4789.1.
AAAAATCCTACATTAAAACGAAATTGGGTTCCAACGGGTCGATGTCTTCAAAAAATGCCC
GGACGGACCCACAATGGGTAACACCTTCTTCTAATCAGGATGTACCACCGGATTATGAAA
CGATTGGTACCATATTTGGTTATGCACTTCTAGTGCTTTCATGGATTCTAATCATAATTA
CCTTTCCATTTTCTATGTGTGTTTGCTTAAAAGTCATCAAAGAGTACGAAAGGGTAGTAA
TATTTCGAATTGGTCGGCTTGTTTTTGGTGGCGCTCGTGGACCAGGAATGATATTTGTCA
TACCGTGCATCGATACATACAGGAAAATTGATCTTAGGGTTGTGTCATATGCTGTGCCTC
CGCAAGAAATTCTTTCAAAAGATTCAGTAACGGTATCTGTTGATGCCGTGGTCTATTTTC
GTACTTCTGATCCGATTGCATCTGTGAATAACGTTGACGATGCTATATACTCGACAAAAT
TGCTCGCTCAAACAACTTTGCGTAACGCACTTGGCATGAAAACTTTAACCGAGATGTTAA
CGGAACGTGAAGCTATTGCGCAACTTTGTGAAACAATTTTGGATGAAGGAACCGAACATT
GGGGTGTTAAGGTGGAACGAGTAGAAGTCAAAGATATTAGATTACCTCAACAGTTAACAC
GTGCAATGGCGGCAGAAGCTGAAGCTGCACGTGAAGCACGTGCTAAAGTTGTCGCAGCGG
AAGGTGAACAGAAGGCATCTCGAGCTCTTAAAGAAGCCGCCGATGTAATTCAATCTAATC
CGGTAGCCTTACAGTTACGACATCTTCAAGCATTAAATAGCATCGCAGCGGAGCACAATT
CAACAATCGTATTTCCGGTACCAGTGGAAATGTTTGGGGCATTTATGAAGAAAGATAATT
AA

  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/sequence/id/Bm4789.1?object_type=transcript;type=cdna';
  10. my $response = $http->get($server.$ext, {
  11.   headers => { 'Content-type' => 'text/x-fasta' }
  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/sequence/id/Bm4789.1?object_type=transcript;type=cdna"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-fasta", "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/sequence/id/Bm4789.1?object_type=transcript;type=cdna"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-fasta", "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/sequence/id/Bm4789.1?object_type=transcript;type=cdna'
  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-fasta'})
  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/sequence/id/Bm4789.1?object_type=transcript;type=cdna";
  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-fasta");
  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/sequence/id/Bm4789.1?object_type=transcript;type=cdna' -H 'Content-type:text/x-fasta'
  3.  
  1. wget -q --header='Content-type:text/x-fasta' 'https://parasite.wormbase.org/rest-19/sequence/id/Bm4789.1?object_type=transcript;type=cdna'  -O -
  2.  

/rest-19/sequence/id/Bm4789.1?type=cds;content-type=text/x-fasta;object_type=transcript


 >Bm4789.1.
ATGTCTTCAAAAAATGCCCGGACGGACCCACAATGGGTAACACCTTCTTCTAATCAGGAT
GTACCACCGGATTATGAAACGATTGGTACCATATTTGGTTATGCACTTCTAGTGCTTTCA
TGGATTCTAATCATAATTACCTTTCCATTTTCTATGTGTGTTTGCTTAAAAGTCATCAAA
GAGTACGAAAGGGTAGTAATATTTCGAATTGGTCGGCTTGTTTTTGGTGGCGCTCGTGGA
CCAGGAATGATATTTGTCATACCGTGCATCGATACATACAGGAAAATTGATCTTAGGGTT
GTGTCATATGCTGTGCCTCCGCAAGAAATTCTTTCAAAAGATTCAGTAACGGTATCTGTT
GATGCCGTGGTCTATTTTCGTACTTCTGATCCGATTGCATCTGTGAATAACGTTGACGAT
GCTATATACTCGACAAAATTGCTCGCTCAAACAACTTTGCGTAACGCACTTGGCATGAAA
ACTTTAACCGAGATGTTAACGGAACGTGAAGCTATTGCGCAACTTTGTGAAACAATTTTG
GATGAAGGAACCGAACATTGGGGTGTTAAGGTGGAACGAGTAGAAGTCAAAGATATTAGA
TTACCTCAACAGTTAACACGTGCAATGGCGGCAGAAGCTGAAGCTGCACGTGAAGCACGT
GCTAAAGTTGTCGCAGCGGAAGGTGAACAGAAGGCATCTCGAGCTCTTAAAGAAGCCGCC
GATGTAATTCAATCTAATCCGGTAGCCTTACAGTTACGACATCTTCAAGCATTAAATAGC
ATCGCAGCGGAGCACAATTCAACAATCGTATTTCCGGTACCAGTGGAAATGTTTGGGGCA
TTTATGAAGAAAGATAATTAA

  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/sequence/id/Bm4789.1?type=cds;object_type=transcript';
  10. my $response = $http->get($server.$ext, {
  11.   headers => { 'Content-type' => 'text/x-fasta' }
  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/sequence/id/Bm4789.1?type=cds;object_type=transcript"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-fasta", "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/sequence/id/Bm4789.1?type=cds;object_type=transcript"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-fasta", "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/sequence/id/Bm4789.1?type=cds;object_type=transcript'
  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-fasta'})
  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/sequence/id/Bm4789.1?type=cds;object_type=transcript";
  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-fasta");
  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/sequence/id/Bm4789.1?type=cds;object_type=transcript' -H 'Content-type:text/x-fasta'
  3.  
  1. wget -q --header='Content-type:text/x-fasta' 'https://parasite.wormbase.org/rest-19/sequence/id/Bm4789.1?type=cds;object_type=transcript'  -O -
  2.  

/rest-19/sequence/id/WBGene00221255?content-type=text/x-fasta;type=genomic


 >WBGene00221255.1 supercontig:Bmal-4.0:Bm_007:479867:484217:-1
AGTATCCAATTCAACAATAGATGGAGCTACAATTTTCTCAATTGTGAATTCCACATGATG
ATTTGCAGTGTCCACCAGGGTTCACGTTCACCAGGTGGTCCAACTGGTTCATTAGGTTCT
GGTTCGTCTCGTTTACCTGGTGGTCCGGTTGGTCCCTTGAAAGTCAGACATAGAAAATAT
TGAATTACAGAAAGGTATGTAAGAAAAGATGCAAAATGCTCTTAGACAATTCGTTTTGCA
TTTAAATTAAAAAAAAAAAATTGTTTTTCATTTAAATTTAAATTAATTATAAACCTAAAA
TGAAGTATAGAATAAATGGCTTCTTAGTGTTATAAAAGGGTTTAATTCAAATATTTTACA
ATTTTTAATGCAGTTACAATAGTTAGGGAAAAAATGAAATATGCCAAGCAACCATTTCAC
CAGGAGATGCTGGTGGCCCGAAATTGCTAGATGGAATCATATCTGGTCCTGGTGAACCTT
TGGGTCCACGAAGCCCTTGTGATCTTGGTGGCCCGAAATTGCTAGATGGAATCCTATCTG
GTCCTGGCGAACCTTTGGATCCACGAGGTCCTTGTGATCCTGGTGGCCCGAAATTGCTAG
ATGGAATCCTATCTGGTCCTGGTGAACCTTTGGATCCACGAAGTCCTTGTGATCCTGGTG
GCCCGAAATTGCTAGATGGAATCCTATCTGGTCCTGGTGAACCTTTGGATCCACGAAGTC
CTTGTGATCCTGGTGGCCCGAAATTGCTAGATGGAATCCTATCTGGTCCTGGCGAACCTT
TGGATCCACGAGGTCCTTGTGATCCTGGTGGCCCGAAATTGCTAGATGGAATCATATCTG
GTCCTGATGAACCTTTGGATCCATCAGGTCCTTGTGATCCTGGTAGACCTTTGATTCCTC
TTCCACGATTGTATCATCACCAGGTAGACTCATAATATATAAGTAATAACTTAATGACTT
TACTTTACTTTTTTTTTTAATTTACAAATATGCATTATATTGTTCGGTAGTGCATCGATC
TCTTCGTATTATTTATTTTCCACTACGATTTTTATTTCTTTGTGGTTCTTATTGTTTAAT
TGTGCCAGCAAAAATTTCTTTCTAACTTTTTATTAATTTGTATTTTATTTAGTTTCATTC
CAACATTATCACTGATCTGATTATAATCCAATTGCAGTATTTTATAGCTAAGTAAAGATT
AAAAAAAAAAATTAAAACTTAATCTTTGTCCTTTCAGACATCAATCAAATTACTTTTTAT
TTTTTTTTTATAGCAGAATGAAATGTACCTTAATGCTAGGCTCACCTTCCTCATCAGAAA
AGTCCAGGTGCTTCGGAATCGCCTATCCTACCTCCTTTACCTGGTCTTCCAGGTATGCCG
TGATGATCTGGTTCACCAGGTATCCTGGTTCTCCTTTTTCTCCTCTATTTCCTGGTGGTC
CTGCAGGATAAATCATGCTTGAAATTCCTTTTTTAATTTGATGCACTACATTTTGCAACA
AAGTAGATAAAATCAAAAGAAAAAAAATGATTTAAATGATTTATTTAAATATTAAATATT
AAAAAAATTAAATTATAAAAAATTCTTGTGTGAACCAAATTCTGGTTCCAATGAAATATC
TAAGTTTGCATTTTCCCTAAATTTATCATTTAATTCTTAATTTATTTCTAATAGATCTAC
TATGACTTGATGGAAGCTTAGAATTGTTGTCATAAAATGGTTTATAAATAATAATAATAC
ATTGATTATCAGTTAAATTCTCTTAGCATATATTAATTATTTAAAAATTTTTGTCTGAAA
CCTTTCAGTATTAGAAGTGTTTTTTGAACATATAAGCAAAATTTTAATTTTTTTTAAGAA
GAAATTCAAACAATTATAAAACTTTATGCAAATTTGAAATTTGATATTTAAATAAATTAA
AAAAAAAAAAAGTTTCATGGTTATTTTGTTTAACTATTACAATAGGAAACGGTAATTTGT
GTCTTTACCATATGAAATAAGCAAAAGGTTTAATTAAATGTTATTAGCAAAAAATTTTTG
AAAAAATGAATAAAAAATGAAGAAATAATATTGCTATTACAATTATAATAGGAAATTTGA
TTATTGATTATTTATATTTGGAACTTATAGTAGGAAATTTGATTATTTATTATATATTTG
AAACTTATAATAGGAAATTTTGATTATTGATTATCTATATTTGGAACTTATAATAAGAAA
TTTGATTGTTGATTATCTATATTTGGAACTTATAATAGGAAATTTGATTATTGATTATCT
ATATTTGGAACTTATAATAGGAAATTTGATTATTGATTATCTATATCTTATAATAGGAAT
TTTGATTATTGATTATCTATATTTGGAACTTATAATGAGAAATTTGATTGTTGATTATCT
ATATTTGGAATTATAATAAGAAATTTGATTATTGATTATCTATATTTGGAACTTATAATA
GGAAATTTGATTATTGATTATCTATATTTGGAACTTATAATAGGAAATTTGATTATTGAT
TATCTATATCTTATAATAGGAATTTTGATTATTGATTATCTATATTTGGAACTTATAATG
AGAAATTTGATTGTTGATTATCTATATTTGGAACTTATAATAGAAATTTTGATTATTGAT
TATCACTAAAACTTTATAATTGTCACCAGATACTACTACAATATTTGGAACTTATATAAG
AAATTGTAATAGGAAATCTGATTATTGATTATCACTAAAGTTTTATAATTGTCTAGGAAT
TTTGATTATTGATTATCTATATTTGGAACTTATAATGAGAAATTTGATTGTTGATTATCT
ATATTTGGAATTATAATAAGAAATTTGATTATTGATTATCTATATTTGGAACTTATAATA
GGAAATTTGATTATTGATTATCTATATTTGGAACTTATAATAGGAAATTTGATTATTGAT
TATCTATATCTTATAATAGGAATTTTGATTATTGATTATCTATATTTGGAACTTATAATG
AGAAATTTGATTGTTGATTATCTATATTTGGAACTTATAATAGAAATTTTGATTATTGAT
TATCACTAAAACTTTATAATTGTCACCAGATACTACTACAATATTTGGAACTTATATAAG
AAATTGTAATAGGAAATCTGATTATTGATTATCACTAAAGTTTTATAATTGTTACCAAAA
CAAGAAGAAAAAGGAAGGAAAAAAAGAAAAAATTTTTTCAGTAATATAATCATTGGAATT
GATACTACTTCAAAAATATTACCATATTTTCTGCTCATATTCCGTGTCTTTCCGGATAAC
AGGATTAAAATATTCCGGTTATGCAGAAACAGGTCAAAGGGCAACAACACGTCAATGAAT
TACTTCCATCAGTGATACAACAGGAAGATCCAACAAACGATTCACTGTCACCGTTGTCAT
CTGCTCGTTGCACTGATCAATATCAAAGTGATAAACTGTTAGCTGTAAGTGTTAATGTGT
TAACTTTCGAGAAATACTAGTGATAAGGAAGCAATTTGAATATGCCACTTTAAAATGACT
GATAAGCAAACTATCAGCTTATCATACACTAGTAAATTAGAAATAATAATGATAAGTTGA
ATTTTTTTTTTTAATTTTTTCATTTGTTAAAATAATCAGTGCAATTAGTGATATATGATA
GTTACAGTATGTTAATAATTCTTCAAAATAACTTTGCAGAATTATTCTCTTCTAGAAAAG
CATACTTTTAAAGCGTTGATGGCGTAATCTGACGTAAAAAAAACGTAATCTGACGTAAAA
AAAAAGAAAAAAACTATGAAAGAGAAATTTTTACATAGTAAGAAAAAAAATTTTTAAAAC
AAAAACAAGAAAAAAACTAGCAATTTTAAATTAAATAAATTAAAAAAATTATCATAAAAT
ACTTTAACTGTTGTAGGAGATTCGTAATGGAGTACAATTGCGCCACGTAATACCAAATGA
TCATAAACAATGCGCTAAAATGCTTTATGATAAAGCATGCGAGAAAAAAGTAATCATTTT
GATAAATTTGTTTAAATTTTTTTTTTTTTTTTTCAAAAAAAATATAAATAATTTCTATTT
CTATCTTTTTTTTTTTACATTTTCTCTCTTTTCATATTGTTATTTATCTATATATTATTT
TTATAAATTATTTAGAAAAAAATTTTTTTCCTATTTTAAAAAAATTTTTTTTTTTTTTTT
GCTAATATTTTTTATATATTTATGAGTTATACAGGAAGAAAATAATATAAATGAAAAAGA
AACAAAGTTAGAAACGGAAAAAGCAATTAATATTGGAAATATCTTACTTAATGCTATGCA
AAAGCGACGACTTCTAATGCATTTTGGTTAA

  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/sequence/id/WBGene00221255?type=genomic';
  10. my $response = $http->get($server.$ext, {
  11.   headers => { 'Content-type' => 'text/x-fasta' }
  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/sequence/id/WBGene00221255?type=genomic"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-fasta", "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/sequence/id/WBGene00221255?type=genomic"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-fasta", "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/sequence/id/WBGene00221255?type=genomic'
  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-fasta'})
  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/sequence/id/WBGene00221255?type=genomic";
  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-fasta");
  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/sequence/id/WBGene00221255?type=genomic' -H 'Content-type:text/x-fasta'
  3.  
  1. wget -q --header='Content-type:text/x-fasta' 'https://parasite.wormbase.org/rest-19/sequence/id/WBGene00221255?type=genomic'  -O -
  2.  

/rest-19/sequence/id/WBGene00221255?expand_5prime=10;content-type=text/x-fasta;type=genomic


 >WBGene00221255.1 supercontig:Bmal-4.0:Bm_007:479867:484227:-1
TCAGAACATAAGTATCCAATTCAACAATAGATGGAGCTACAATTTTCTCAATTGTGAATT
CCACATGATGATTTGCAGTGTCCACCAGGGTTCACGTTCACCAGGTGGTCCAACTGGTTC
ATTAGGTTCTGGTTCGTCTCGTTTACCTGGTGGTCCGGTTGGTCCCTTGAAAGTCAGACA
TAGAAAATATTGAATTACAGAAAGGTATGTAAGAAAAGATGCAAAATGCTCTTAGACAAT
TCGTTTTGCATTTAAATTAAAAAAAAAAAATTGTTTTTCATTTAAATTTAAATTAATTAT
AAACCTAAAATGAAGTATAGAATAAATGGCTTCTTAGTGTTATAAAAGGGTTTAATTCAA
ATATTTTACAATTTTTAATGCAGTTACAATAGTTAGGGAAAAAATGAAATATGCCAAGCA
ACCATTTCACCAGGAGATGCTGGTGGCCCGAAATTGCTAGATGGAATCATATCTGGTCCT
GGTGAACCTTTGGGTCCACGAAGCCCTTGTGATCTTGGTGGCCCGAAATTGCTAGATGGA
ATCCTATCTGGTCCTGGCGAACCTTTGGATCCACGAGGTCCTTGTGATCCTGGTGGCCCG
AAATTGCTAGATGGAATCCTATCTGGTCCTGGTGAACCTTTGGATCCACGAAGTCCTTGT
GATCCTGGTGGCCCGAAATTGCTAGATGGAATCCTATCTGGTCCTGGTGAACCTTTGGAT
CCACGAAGTCCTTGTGATCCTGGTGGCCCGAAATTGCTAGATGGAATCCTATCTGGTCCT
GGCGAACCTTTGGATCCACGAGGTCCTTGTGATCCTGGTGGCCCGAAATTGCTAGATGGA
ATCATATCTGGTCCTGATGAACCTTTGGATCCATCAGGTCCTTGTGATCCTGGTAGACCT
TTGATTCCTCTTCCACGATTGTATCATCACCAGGTAGACTCATAATATATAAGTAATAAC
TTAATGACTTTACTTTACTTTTTTTTTTAATTTACAAATATGCATTATATTGTTCGGTAG
TGCATCGATCTCTTCGTATTATTTATTTTCCACTACGATTTTTATTTCTTTGTGGTTCTT
ATTGTTTAATTGTGCCAGCAAAAATTTCTTTCTAACTTTTTATTAATTTGTATTTTATTT
AGTTTCATTCCAACATTATCACTGATCTGATTATAATCCAATTGCAGTATTTTATAGCTA
AGTAAAGATTAAAAAAAAAAATTAAAACTTAATCTTTGTCCTTTCAGACATCAATCAAAT
TACTTTTTATTTTTTTTTTATAGCAGAATGAAATGTACCTTAATGCTAGGCTCACCTTCC
TCATCAGAAAAGTCCAGGTGCTTCGGAATCGCCTATCCTACCTCCTTTACCTGGTCTTCC
AGGTATGCCGTGATGATCTGGTTCACCAGGTATCCTGGTTCTCCTTTTTCTCCTCTATTT
CCTGGTGGTCCTGCAGGATAAATCATGCTTGAAATTCCTTTTTTAATTTGATGCACTACA
TTTTGCAACAAAGTAGATAAAATCAAAAGAAAAAAAATGATTTAAATGATTTATTTAAAT
ATTAAATATTAAAAAAATTAAATTATAAAAAATTCTTGTGTGAACCAAATTCTGGTTCCA
ATGAAATATCTAAGTTTGCATTTTCCCTAAATTTATCATTTAATTCTTAATTTATTTCTA
ATAGATCTACTATGACTTGATGGAAGCTTAGAATTGTTGTCATAAAATGGTTTATAAATA
ATAATAATACATTGATTATCAGTTAAATTCTCTTAGCATATATTAATTATTTAAAAATTT
TTGTCTGAAACCTTTCAGTATTAGAAGTGTTTTTTGAACATATAAGCAAAATTTTAATTT
TTTTTAAGAAGAAATTCAAACAATTATAAAACTTTATGCAAATTTGAAATTTGATATTTA
AATAAATTAAAAAAAAAAAAAGTTTCATGGTTATTTTGTTTAACTATTACAATAGGAAAC
GGTAATTTGTGTCTTTACCATATGAAATAAGCAAAAGGTTTAATTAAATGTTATTAGCAA
AAAATTTTTGAAAAAATGAATAAAAAATGAAGAAATAATATTGCTATTACAATTATAATA
GGAAATTTGATTATTGATTATTTATATTTGGAACTTATAGTAGGAAATTTGATTATTTAT
TATATATTTGAAACTTATAATAGGAAATTTTGATTATTGATTATCTATATTTGGAACTTA
TAATAAGAAATTTGATTGTTGATTATCTATATTTGGAACTTATAATAGGAAATTTGATTA
TTGATTATCTATATTTGGAACTTATAATAGGAAATTTGATTATTGATTATCTATATCTTA
TAATAGGAATTTTGATTATTGATTATCTATATTTGGAACTTATAATGAGAAATTTGATTG
TTGATTATCTATATTTGGAATTATAATAAGAAATTTGATTATTGATTATCTATATTTGGA
ACTTATAATAGGAAATTTGATTATTGATTATCTATATTTGGAACTTATAATAGGAAATTT
GATTATTGATTATCTATATCTTATAATAGGAATTTTGATTATTGATTATCTATATTTGGA
ACTTATAATGAGAAATTTGATTGTTGATTATCTATATTTGGAACTTATAATAGAAATTTT
GATTATTGATTATCACTAAAACTTTATAATTGTCACCAGATACTACTACAATATTTGGAA
CTTATATAAGAAATTGTAATAGGAAATCTGATTATTGATTATCACTAAAGTTTTATAATT
GTCTAGGAATTTTGATTATTGATTATCTATATTTGGAACTTATAATGAGAAATTTGATTG
TTGATTATCTATATTTGGAATTATAATAAGAAATTTGATTATTGATTATCTATATTTGGA
ACTTATAATAGGAAATTTGATTATTGATTATCTATATTTGGAACTTATAATAGGAAATTT
GATTATTGATTATCTATATCTTATAATAGGAATTTTGATTATTGATTATCTATATTTGGA
ACTTATAATGAGAAATTTGATTGTTGATTATCTATATTTGGAACTTATAATAGAAATTTT
GATTATTGATTATCACTAAAACTTTATAATTGTCACCAGATACTACTACAATATTTGGAA
CTTATATAAGAAATTGTAATAGGAAATCTGATTATTGATTATCACTAAAGTTTTATAATT
GTTACCAAAACAAGAAGAAAAAGGAAGGAAAAAAAGAAAAAATTTTTTCAGTAATATAAT
CATTGGAATTGATACTACTTCAAAAATATTACCATATTTTCTGCTCATATTCCGTGTCTT
TCCGGATAACAGGATTAAAATATTCCGGTTATGCAGAAACAGGTCAAAGGGCAACAACAC
GTCAATGAATTACTTCCATCAGTGATACAACAGGAAGATCCAACAAACGATTCACTGTCA
CCGTTGTCATCTGCTCGTTGCACTGATCAATATCAAAGTGATAAACTGTTAGCTGTAAGT
GTTAATGTGTTAACTTTCGAGAAATACTAGTGATAAGGAAGCAATTTGAATATGCCACTT
TAAAATGACTGATAAGCAAACTATCAGCTTATCATACACTAGTAAATTAGAAATAATAAT
GATAAGTTGAATTTTTTTTTTTAATTTTTTCATTTGTTAAAATAATCAGTGCAATTAGTG
ATATATGATAGTTACAGTATGTTAATAATTCTTCAAAATAACTTTGCAGAATTATTCTCT
TCTAGAAAAGCATACTTTTAAAGCGTTGATGGCGTAATCTGACGTAAAAAAAACGTAATC
TGACGTAAAAAAAAAGAAAAAAACTATGAAAGAGAAATTTTTACATAGTAAGAAAAAAAA
TTTTTAAAACAAAAACAAGAAAAAAACTAGCAATTTTAAATTAAATAAATTAAAAAAATT
ATCATAAAATACTTTAACTGTTGTAGGAGATTCGTAATGGAGTACAATTGCGCCACGTAA
TACCAAATGATCATAAACAATGCGCTAAAATGCTTTATGATAAAGCATGCGAGAAAAAAG
TAATCATTTTGATAAATTTGTTTAAATTTTTTTTTTTTTTTTTCAAAAAAAATATAAATA
ATTTCTATTTCTATCTTTTTTTTTTTACATTTTCTCTCTTTTCATATTGTTATTTATCTA
TATATTATTTTTATAAATTATTTAGAAAAAAATTTTTTTCCTATTTTAAAAAAATTTTTT
TTTTTTTTTTGCTAATATTTTTTATATATTTATGAGTTATACAGGAAGAAAATAATATAA
ATGAAAAAGAAACAAAGTTAGAAACGGAAAAAGCAATTAATATTGGAAATATCTTACTTA
ATGCTATGCAAAAGCGACGACTTCTAATGCATTTTGGTTAA

  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/sequence/id/WBGene00221255?type=genomic;expand_5prime=10';
  10. my $response = $http->get($server.$ext, {
  11.   headers => { 'Content-type' => 'text/x-fasta' }
  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/sequence/id/WBGene00221255?type=genomic;expand_5prime=10"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-fasta", "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/sequence/id/WBGene00221255?type=genomic;expand_5prime=10"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-fasta", "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/sequence/id/WBGene00221255?type=genomic;expand_5prime=10'
  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-fasta'})
  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/sequence/id/WBGene00221255?type=genomic;expand_5prime=10";
  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-fasta");
  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/sequence/id/WBGene00221255?type=genomic;expand_5prime=10' -H 'Content-type:text/x-fasta'
  3.  
  1. wget -q --header='Content-type:text/x-fasta' 'https://parasite.wormbase.org/rest-19/sequence/id/WBGene00221255?type=genomic;expand_5prime=10'  -O -
  2.  

/rest-19/sequence/id/WBGene00221255?multiple_sequences=1;content-type=text/x-seqxml%2Bxml;type=protein


  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/sequence/id/WBGene00221255?multiple_sequences=1;type=protein';
  10. my $response = $http->get($server.$ext, {
  11.   headers => { 'Content-type' => 'text/x-seqxml+xml' }
  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/sequence/id/WBGene00221255?multiple_sequences=1;type=protein"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-seqxml+xml", "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/sequence/id/WBGene00221255?multiple_sequences=1;type=protein"
  5.  
  6. r = requests.get(server+ext, headers={ "Content-Type" : "text/x-seqxml+xml", "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/sequence/id/WBGene00221255?multiple_sequences=1;type=protein'
  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-seqxml+xml'})
  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/sequence/id/WBGene00221255?multiple_sequences=1;type=protein";
  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-seqxml+xml");
  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/sequence/id/WBGene00221255?multiple_sequences=1;type=protein' -H 'Content-type:text/x-seqxml+xml'
  3.  
  1. wget -q --header='Content-type:text/x-seqxml+xml' 'https://parasite.wormbase.org/rest-19/sequence/id/WBGene00221255?multiple_sequences=1;type=protein'  -O -
  2.  

/rest-19/sequence/id/Bm4789.1?content-type=application/json


 {
  "id": "Bm4789.1",
  "desc": "supercontig:Bmal-4.0:Bm_v4_ChrX_scaffold_001:13581797:13588425:-1",
  "query": "Bm4789.1",
  "seq": "AAAAATCCTACATTAAAACGAAATTGGGTTCCAACGGGTCGATGTCTTCAAAAAATGCCCGGACGGACCCACAATGGGTAACACCTTCTTCTAATCAGGTAAGTGTAAATTTTTTTAATTTCTTTTCTCTTTCTCTAGATATTATAATAAGCAGTATTATGCAATGTTACGGTGTACCTTTTATTAGATCCCAAAAAAATGCTTTTAATCACAACCAATGATAATCTTAGGATATGTTATTGGTTTTTCAGAATAAATGAAAACTTTCGAAATTTTCTTTTTAACAATATCTAACTGTTTACTTCTCCTTTTCCGTAATACTATTAAAATGGATTTCAGGATGTACCACCGGATTATGAAACGATTGGTACCATATTTGGTTATGCACTTCTAGTGCTTTCATGGATTCTAATCATAATTACCTTTCCATTTTCTATGTGTGTTTGCTTAAAAGTAAATGTGTTAATTTTTTTCTCATAGACTTTATTTCATACTGATTAGCAGTTCATTTAATTATTGTTTAACAATAATTAATAACAATTAAAATTTAAATTTGATATTGGAAAAATTCCTTCAAACTTTGTCATTTGAATTCTTTCTAGTGACATTTATTAGATCAACAGAAAATAAGTGAGGATAGTTTTTAAAGAACTAAGTTGAAAATAATTACATGAAATGAATTATTTAATAATTAAAATAGTTCTATAGGTCATCAAAGAGTACGAAAGGGTAGTAATATTTCGAATTGGTCGGCTTGTTTTTGGTGGCGCTCGTGGACCAGGAATGATATTTGTCATACCGTGCATCGATACATACAGGAAAATTGATCTTAGGTTAGTTTTTTAATCATTTTCCATACTACTATCGTACAACATTAATAGGAATAGTAACAAGAAGACATTATTACGGTAGCAGTTCATAGTAGTTCTACTTCAATCCATTTGAATTTTCAAGTACTTATTATTGTAGCTTTCATCATCTTCAATAGTTATAGTTTTAAAATATCAATGAATTTATTATGAAACAGATTGTAAATATGAAATAAGCACTATTCCTTATTATTTAATTCAAATTTGATACATCAAGAAATGTTCAAATTTTTCATGTCTATATATATCTGAATGATAAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAAAATAATAAAAAAATAATAAAATAAAATAATAAAAAATAATAATAAAATAATAATAATAATAATAATAATAATAATATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATTAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAAAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATATAATAATAATATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATATAATAATAATAATAATAATAATATAATAATAATAATAATAATAATAATATAATAATAATATAATAATAATAAAAAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATATAATAATAATAATAATAATAAATAATAATAATAATAATAATAATAATAATAATAATAATAAAATAATAATAATAATAATATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATATAATAATAAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAAAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAACAATAAATAAATAACAAGTAAATAAATAATAAATAACAATAATAATAACAATAGTAATACGTTCAATTGTTTAATCTTTTCATATTGACATGTGCCAATTTTTAAGTTAGAATTTAAACCCTCTTTCTCTTCCTCTCTTTTCCTCCCTCTTTTGCTAAAAGACAAATTTCAACTATTTCAGTACTTTTAGTATTAAGCTTTGAAGCATTCCATGTTTTTATGATTAAATTTATTAATATTCGCATGGAAATTTTTATCAGTTTGAGAAATTGGGCAAAATTTTTTAAGAAATAAATTTCACTGCGAGAAAAAAAAAGAAAAAGGAAAGAAACAGACGCATACAGTAGTATTTACTAAAAAAAAAAAAAACATGAAAATAAATACAAATCTTCCAAACAAATGTAATCAAATTGAAAAGCTTGAAATTTCGTTTCCTCGGATGGAAAAGTAATGCAATGCGAAAAATGCATGAAAAAAAAAAAAAGCATTGTTCATCTAATCATACTTTATTTTTTCTCTCCCTTCTTTCACTTTTCCTTCTCTCTTTGTCATCTATTTTTTATCTCTTCAAATTCATTTTTGTTTTTGTTTTTTTCTTTTTATTTTTCATCTTTAGTAAAAATAAAATCACGAATTATTCTTTTCTGTATTTGTGATTTAAATGATAGATTAACACTAATTGATTTCACTACATTGCATAGTTAATTTTTCAGAAGAAAATGATCATACTTTTTACTTCCGATTTTTTCTCCTTGTTTACTTCTTTAGATATTCAATAATTTTTAATTTCAAGTAAACGAAAGTTGATAAATTTCAACTATATTATTATTTAAACTAAATGAATTTATTATTATCATCATCATTTGAAATAAAGCTATCAGTTTTAAATTATAATTTAGTCTTTAACATTTTATCGCATTTTATCGCATTAATCAATGGTAGTTATATAATACTATTATCGAAAAACTTTTTGCAAATATTTCAACAAATTTTTTTTTTTCGAATTATCTTTTTACGATTGAATAAGCAAGCAAGCAATTCTCATATGCATTGCATACTGAAATGATTACTTCAAAGATTCGTTGTTTGAAATAAGAAAATGCTGACGTCTTTTCTTTTTTTTTTTCGTTTTCTTTATTTTATCTTTACTTTTTTTTTCACCAAATTATTGCTATTTATGAAAATTTAAACAAGCTTTCGTCTTTTTCTTTCTTTCTTTCTTTCATTCTTGCGTTTTTCCCCCTTCTTTCTGTGAATTGAAATGAAATTGAAGTATTGTTCACTTTTATAGACGATATCAATTTTTTAAGTATCATTATGCAAAATTGAAAATGGAAGAACAAATATTTTTCCAATAATATGTCACATTATTACCACCTAATACTTCAAAGGTTATAATAACTTTAGCGAAAGGCTATGTCAATTTTTTTGTTTTCTTATAAATGTAAAAAAAAAAGAAAAAAAAAAGACATAAAAAATATATTTTGTCATCCAATGAAAAGAAAGAAAAGAAAAGAAATAAAATAAAAAGAATTTATCAAAAAGGCAAATAAAAAAAAAATTTTACCATCAAAATATTTGCAATGTTTTTTGATTAATTAATTAAATGAAAAAAGAAAAAAACTTTTTTAAAGGGTTGTGTCATATGCTGTGCCTCCGCAAGAAATTCTTTCAAAAGATTCAGTAACGGTATCTGTTGATGCCGTGGTCTATTTTCGTACTTCTGATCCGATTGCATCTGTGAATAACGTTGACGATGCTATATACTCGACAAAATTGCTCGCTCAAACAACTTTGCGTAACGCACTTGGTAATTCAATTATTTATTATTATGATTTAGTTGAATTAAATAATTTTTTTAAAACTAAATAACTTTTTTTTTGATAATTTTAAATTTCAAAATTATTTGGATAACAGAATATGCAGTTATATAATTTTGAATAAAGACAGAAAAGATATATTAGAAAATTTATCACAAAAACAAAATAAAGTTGAAATTAAATTTTGGAATTTATAAATTTAATCATATTTATTATTCAGTGGATAGCAGATAAGATTGGTTAATTTAACAAACGATAAAAATTAAACAATTATTGAAATGGCGCTATACATTATCGTTTTTTTTTTTTTCATTTCTTTTAGAAGGAGATAGCAAATCTTTCATTACATTAATTTAACTTTTTATCGCTTATTCTAGTAAAAAGTTTGGTTTGTATTTGATAGGAAGAAATTAAATTTTGAAAAAAGGAGAAAAAAAACGATGATATGTATTACTTTTTACAGCTAAGTTTTTCATTATTGATGTTACTCTTTAAAAAAATGCCAGAATGGACTTATCTTAAAATTAGAATTGTATAATAAGACTTAAACCTTACTTTAATAAGAGCTATGTAACATATTAAGTGTTAGAAAGAAAATCCTAGGCCATTTTTTATTTAGGCATGAAAACTTTAACCGAGATGTTAACGGAACGTGAAGCTATTGCGCAACTTTGTGAAACAATTTTGGATGAAGGAACCGAACATTGGGGTGTTAAGGTTTAACTTCTCTTTTTATTTTACTTTTTAATTTTTCTTTTTCTTTTTTTTTGATTCTATTAGAAATTTTTAAACATTTTAATCTTTTACTACATATATGCTAATACTGGTAAAGAAAATTATTGAAAAGTCCGGAAATCCCGAGTGATACCATTAGTTATTACCAATAGAATGTTTTTCATTTAATGCTTTACTATTGAAAGTAAATTATCTATAAATTATAGGTACTATGGTTAATAACAGTAAATTACAGGTGGAACGAGTAGAAGTCAAAGATATTAGATTACCTCAACAGTTAACACGTGCAATGGCGGCAGAAGCTGAAGCTGCACGTGAAGCACGTGCTAAAGTTGTCGCAGCGGAAGGTGAACAGAAGGTAAGTGATTTTCACACTTTTTTTTTTTTCAATCTCTTATCATGAAATTAAAATTATCATAAAATTAAACAAAAAACAAATCATATCTCTTCTCCAGTTTTTCAGTCATTTAATTTATTTTAATAAAAATTCAAATTTATTTAAATATTTCTGAGTGCTTTTACTGAATTAAAAAAAATGTTTTTTACAATATATTTTCTTTGGAATTTATTTCATTAAGTAATAAGAATTAAATTTCTAATCATAGGAATTAAATTTTAACTAAAATAATAATTCTTTTTTGGTAGAATTATGCAAAATATATGGATTGAAAGATTAAAATGTTTATCCAAAATATAAAAATATAAGAAGGGGAAAAAAAACAAAGAAAAATGATTCATATAACATTTGTTCTAGTTCAATTTTTTTCGCAAAATTTCAATTTTACTAAATTTTGTATTAATTTAAATGTTAATTTATTTATGTTCGTAATATTTAACAAAAATTGAAGGCATCTCGAGCTCTTAAAGAAGCCGCCGATGTAATTCAATCTAATCCGGTAGCCTTACAGTTACGACATCTTCAAGCATTAAATAGCATCGCGTATAATTCTTTCTCTTTTTTTCACTAGTAAGAAAAAAATTGTTAATTTGAAAACTATTTAAAAAGAGCAAATTCAAAAAAAAAAAGGAAGAAATTATTAGAGTATTAATTTAAAATTTGATAATTATTCCATGCGTAAGAAGATAAACAAACATATTTGATCACTCGATAAAGCATATTATCTTGCATTTAACTAATTCAAATATTATGAAAAAATTTTGCTCACTCTCCTGATATATGTATTTTCAAATAGTGAAGTAATGATTTATAGTGATAATGGTGGTAATAAGTGCTATAAATGATTATATTATCATTTATAAGTAACAGCAAGTGGTGCATGTTATAACTAATGATAAAAGATGATAAATCGTTTTAAAATTATATATTTTATAGAGCGGAGCACAATTCAACAATCGTATTTCCGGTACCAGTGGAAATGTTTGGGGCATTTATGAAGAAAGATAATTAA",
  "molecule": "dna",
  "version": null
}
  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/sequence/id/Bm4789.1?';
  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/sequence/id/Bm4789.1?"
  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/sequence/id/Bm4789.1?"
  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/sequence/id/Bm4789.1?'
  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/sequence/id/Bm4789.1?";
  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/sequence/id/Bm4789.1?' -H 'Content-type:application/json'
  3.  
  1. wget -q --header='Content-type:application/json' 'https://parasite.wormbase.org/rest-19/sequence/id/Bm4789.1?'  -O -
  2.  

Resource Information

MethodsGET
Response formatsfasta
json
text
yaml
jsonp
Slice length1e7