Ensembl REST API – urllib2

HTTP is based on requests and responses Using urllib2 we can make http request using python and get a response from the server. Try the example below and see what it does:

In [2]:

import urllib2
request = urllib2.Request('http://rest.ensembl.org')
response = urllib2.urlopen(request)
html = response.read()
print html

---------------------------------------------------------------------------
URLError                                  Traceback (most recent call last)
<ipython-input-2-21b203025b8a> in <module>()
      1 import urllib2
      2 request = urllib2.Request('http://rest.ensembl.org')
----> 3 response = urllib2.urlopen(request)
      4 html = response.read()
      5 print html
/ext/sage/sage-8.0/local/lib/python2.7/urllib2.pyc in urlopen(url, data, timeout, cafile, capath, cadefault, context)
    152     else:
    153         opener = _opener
--> 154     return opener.open(url, data, timeout)
    155 
    156 def install_opener(opener):
/ext/sage/sage-8.0/local/lib/python2.7/urllib2.pyc in open(self, fullurl, data, timeout)
    427             req = meth(req)
    428 
--> 429         response = self._open(req, data)
    430 
    431         # post-process response
/ext/sage/sage-8.0/local/lib/python2.7/urllib2.pyc in _open(self, req, data)
    445         protocol = req.get_type()
    446         result = self._call_chain(self.handle_open, protocol, protocol +
--> 447                                   '_open', req)
    448         if result:
    449             return result
/ext/sage/sage-8.0/local/lib/python2.7/urllib2.pyc in _call_chain(self, chain, kind, meth_name, *args)
    405             func = getattr(handler, meth_name)
    406 
--> 407             result = func(*args)
    408             if result is not None:
    409                 return result
/ext/sage/sage-8.0/local/lib/python2.7/urllib2.pyc in http_open(self, req)
   1226 
   1227     def http_open(self, req):
-> 1228         return self.do_open(httplib.HTTPConnection, req)
   1229 
   1230     http_request = AbstractHTTPHandler.do_request_
/ext/sage/sage-8.0/local/lib/python2.7/urllib2.pyc in do_open(self, http_class, req, **http_conn_args)
   1196         except socket.error, err: # XXX what error?
   1197             h.close()
-> 1198             raise URLError(err)
   1199         else:
   1200             try:
URLError: <urlopen error [Errno 110] Connection timed out>

Ensembl REST API – urllib2

Use urllib2 to: - Find the Ensembl ID of P53 Print the content of the response

- Parse the response
	Store the Ensembl gene ID in a variable

- Request all transcripts of P53
	Use the Ensembl gene ID variable
	Print the content of the response

In [0]:

# Type your code here

Ensembl REST API – JSON – parsing

Try to understand the script below:

In [0]:

import json
json_string = '[{"key":"value","key_2":3.0},{"key_3":[2, 4]}]'
json_parsed = json.loads(json_string)
print "JSON_STRING =", json_string
print "JSON_PARSED =", json_parsed
print json_parsed[0]
print json_parsed[1]['key_3']

Ensembl REST API – JSON exercise

Lets download a JSON file and parse it

Use wget to store, or download via the browser: http://rest.ensembl.org/info/assembly/homo_sapiens?content-type=application/json

Read the file with Python and parse the file

Print the following information:

Assembly name and date
Name and length of the chromosomes

In [0]:

# Read the file with Python and parse the file
# Type your code here

In [0]:

# Print the following information:
# Assembly name and date
# Type your code here

In [0]:

# Name and length of the chromosomes
# Type your code here

Ensembl REST API – urllib2 and JSON

Use and try to understand the following script:

In [0]:

import urllib2
import json

server = "http://rest.ensembl.org"
endpoint = "/xrefs/symbol/homo_sapiens/BRCA2"
headers = {}
headers['Content-Type'] = 'application/json'

request = urllib2.Request(server + endpoint, headers=headers)
response = urllib2.urlopen(request)
content = response.read()
data = json.loads(content)

print data[0]['id']

Ensembl REST API – Last exercise

Use urllib2 and json to make a small tool:

Ask the user for a gene symbol (e.g. BRCA2)
Find the ensembl id of that gene
Print the gene and Ensembl ID

Request all transcripts of the gene using the Ensembl ID Print for each transcript (separated by a tab):

ID
Location = chr:start-end
Biotype

Extra - Make functions for:

Rest requests -> EnsemblRestRequest(endpoint)
Get Ensembl stable gene ID -> GetEnsemblGeneId(gene_symbol)
Get transcripts -> GetTranscripts(gene_ensembl_id)

In [0]:

# Type your code here