def do_GET(self):
"""This method is called whenever the client invokes the GET method
in the HTTP protocol request"""
# Print the request line
termcolor.cprint(self.requestline, 'green')
# Message to send back to the client
#We start here to program the code of the medium level starting with the code that will give back the index, which is our main page
if self.path == '/' or self.path == '/index.html':
filename = 'index.html'
with open(filename, 'r') as f:
contents = f.read()
elif '/listSpecies' in self.path:
try:
if 'limit=' in self.path:
limit = self.path.split('limit=')[1]
print(limit)
conn = http.client.HTTPConnection('rest.ensembl.org')
conn.request("GET", "/info/species?content-type=application/json")
# -- Wait for the server's response
r1 = conn.getresponse()
# -- Print the status
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
# -- Read the response's body and close
# -- the connection
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
species_l = resp['species']
conn.close()
contents = """
<html>
<body style="background-color: D7B7BC;"><FONT FACE="monospace" SIZE = 5 COLOR = 'white'><h3>List of the chosen limited species </h3></FONT>
<ol>"""
limit = int(limit)
counter = 0
for specie in species_l:
contents = contents + "<li>" + specie['display_name'] + "</li>"
counter = counter + 1
if counter == limit:
break
contents = contents + """</ol>
</body>
</html>
"""
else:
conn = http.client.HTTPConnection('rest.ensembl.org')
conn.request("GET", "/info/species?content-type=application/json")
# -- Wait for the server's response
r1 = conn.getresponse()
# -- Print the status
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
# -- Read the response's body and close
# -- the connection
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
species_l = resp['species']
contents = """
<html>
<body style="background-color: D7B7BC;"><FONT FACE="monospace" SIZE = 5 COLOR = 'white'><h3>List of all the species </h3></FONT>
<ol>"""
for specie in species_l:
contents = contents + "<li>" + specie['display_name'] + "</li>"
contents = contents + """</ol>
</body>
</html>
"""
except IndexError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except ValueError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except KeyError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except TypeError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
elif '/karyotype' in self.path:
try:
specie = self.path.split('=')[1]
conn = http.client.HTTPConnection('rest.ensembl.org')
conn.request("GET", "/info/assembly/"+specie+"?content-type=application/json")
r1 = conn.getresponse()
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
karyotype_l = resp['karyotype']
print(karyotype_l)
contents = """
<html>
<body style="background-color: D7B7BC;"><FONT FACE="monospace" SIZE = 5 COLOR = 'white'><h3>Chromosomes of the chosen specie: </h3></FONT>
<ul>"""
for elem in karyotype_l:
contents = contents + "<li>" + elem + "</li>"
contents = contents + """</ul>
</body>
</html>
"""
except IndexError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except TypeError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except ValueError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except KeyError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
elif '/chromosomeLength' in self.path:
try:
slice = self.path.split('&')[1]
chromo = slice.split('=')[1]
slice2 = self.path.split('&')[0]
specie = slice2.split('=')[1]
print("The chromosome number to study its length is: ", chromo)
print("The specie to study is: ", specie)
conn = http.client.HTTPConnection('rest.ensembl.org')
conn.request("GET", "/info/assembly/" + specie + "?content-type=application/json")
r1 = conn.getresponse()
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
info = resp['top_level_region']
length = 0
for elem in info:
if elem['name'] == chromo:
length = str(elem['length'])
print(length)
contents = """
<html>
<body style="background-color: D7B7BC;"><FONT FACE="monospace" SIZE = 5 COLOR = 'white'><h3>The length of the chromosome of the chosen specie is: </h3></FONT>
<ul>"""
contents = contents + "<li>" + length + "</li>"
"""</ul>
</body>
</html>
"""
except IndexError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except ValueError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except KeyError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except TypeError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
elif '/geneSeq' in self.path:
try:
gene = self.path.split('=')[1]
conn = http.client.HTTPConnection('rest.ensembl.org')
conn.request("GET", "/homology/symbol/human/" + gene + "?content-type=application/json")
r1 = conn.getresponse()
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
id = resp['data'][0]['id']
print(id)
conn.request("GET", "/sequence/id/" + id + "?content-type=application/json")
r1 = conn.getresponse()
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
#print(resp)
sequence = resp['seq']
print(sequence)
contents = """
<html>
<body style="background-color: D7B7BC;"><FONT FACE="monospace" SIZE = 5 COLOR = 'white'><h3>The sequence of the given human gene is: </h3></FONT>
<ul>"""
contents = contents + "<li>" + sequence + "</li>"
"""</ul>
</body>
</html>
"""
except IndexError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except ValueError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except KeyError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except TypeError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
elif '/geneInfo' in self.path:
try:
gene = self.path.split('=')[1]
conn = http.client.HTTPConnection('rest.ensembl.org')
conn.request("GET", "/homology/symbol/human/" + gene + "?content-type=application/json")
r1 = conn.getresponse()
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
id = resp['data'][0]['id']
print(id)
conn.request("GET", "/overlap/id/" + id + "?feature=gene;content-type=application/json")
r1 = conn.getresponse()
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
start = resp[0]['start']
end = resp[0]['end']
length = end-start
chromo_name = resp[0]['assembly_name']
contents = """
<html>
<body style="background-color: D7B7BC;"><FONT FACE="monospace" SIZE = 5 COLOR = 'white'><h3>The information asked of the given human gene is: </h3></FONT>
<ul>"""
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The start of the sequence is: </h5></FONT>""" + str(start) + "</li>"
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The end of the sequence is: </h5></FONT>""" + str(end) + "</li>"
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The length of the sequence is: </h5></FONT>""" + str(length) + "</li>"
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The name of the gene is: </h5></FONT>""" + str(chromo_name) + "</li>"
"""</ul>
</body>
</html>
"""
except IndexError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except ValueError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except KeyError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except TypeError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
elif '/geneCalc' in self.path:
try:
gene = self.path.split('=')[1]
conn = http.client.HTTPConnection('rest.ensembl.org')
conn.request("GET", "/homology/symbol/human/" + gene + "?content-type=application/json")
r1 = conn.getresponse()
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
id = resp['data'][0]['id']
print(id)
conn.request("GET", "/sequence/id/" + id + "?content-type=application/json")
r1 = conn.getresponse()
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
# print(resp)
sequence = resp['seq']
print(sequence)
s1 = Seq(sequence)
total_length = len(sequence)
pa = s1.perc('A')
pt = s1.perc('T')
pc = s1.perc('C')
pg = s1.perc('G')
contents = """
<html>
<body style="background-color: D7B7BC;"><FONT FACE="monospace" SIZE = 5 COLOR = 'white'><h3>The calculations asked of the given sequence is: </h3></FONT>
<ul>"""
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The total lenght of the sequence is: </h5></FONT>""" + str(total_length) + "</li>"
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The percentage of A's in the sequence is: </h5></FONT>""" + str(pa) + "</li>"
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The percentage of T's in the sequence is: </h5></FONT>""" + str(pt) + "</li>"
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The percentage of C's in the sequence is: </h5></FONT>""" + str(pc) + "</li>"
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The percentage of G's in the sequence is: </h5></FONT>""" + str(pg) + "</li>"
"""</ul>
</body>
</html>
"""
except IndexError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except ValueError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except KeyError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except TypeError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
elif '/geneList' in self.path:
try:
slice = self.path.split('&')[1]
start = slice.split('=')[1]
slice2 = self.path.split('&')[0]
chromo = slice2.split('=')[1]
slice3 = self.path.split('&')[2]
end = slice3.split('=')[1]
print('The number of chromosome is: ', chromo)
print('The start point is: ', start)
print('The end point is: ', end)
conn = http.client.HTTPConnection('rest.ensembl.org')
conn.request("GET", "/overlap/region/human/" + str(chromo) + ":" + str(start) + "-" + str(end) + "?content-type=application/json;feature=gene;feature=transcript;feature=cds;feature=exon")
r1 = conn.getresponse()
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
contents = """
<html>
<body style="background-color: D7B7BC;"><FONT FACE="monospace" SIZE = 5 COLOR = 'white'><h3>The names of the genes located in the chromosome asked from the start to end positions are: </h3></FONT>
<ul>"""
for elem in resp:
position1 = elem['feature_type']
if position1 == "gene":
position2 = elem['id']
print(position2)
contents = contents + "<li>" + 'The name of the chromosome is: ' + str(position2) + "</li>"
"""</ul>
</body>
</html>
"""
except IndexError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except ValueError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except KeyError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except TypeError:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
else:
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
# Generating the response message
self.send_response(200) # -- Status line: OK!
# Define the content-type header:
self.send_header('Content-Type', 'text/html')
self.send_header('Content-Length', len(str.encode(contents)))
# The header is finished
self.end_headers()
# Send the response message
self.wfile.write(str.encode(contents))
return
def do_GET(self):
"""This method is called whenever the client invokes the GET method
in the HTTP protocol request"""
json_response = False
answer_value = 200
# Print the request line
termcolor.cprint(self.requestline, 'green')
# Message to send back to the client
#The main programming code appears below, and it starts with the index page (principal page)
if self.path == '/' or self.path == '/index.html':
json_response = False
filename = 'index.html'
with open(filename, 'r') as f:
contents = f.read()
#we program now the code for the path list species
elif '/listSpecies' in self.path:
try:
arguments = self.main(self.path)
if 'limit' in arguments:
try:
limit = int(arguments['limit'])
except Exception:
limit = 0
else:
limit = 0
print(limit)
conn = http.client.HTTPConnection('rest.ensembl.org')
conn.request("GET", "/info/species?content-type=application/json")
# -- Wait for the server's response
r1 = conn.getresponse()
# -- Print the status
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
# -- Read the response's body and close
# -- the connection
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
species_l = resp['species']
if type(limit) != int:
answer_value = 400
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
elif limit == 0:
limit = len(species_l)
conn.close()
#As this is the advance level of the practice the user can choose to select the json option, so if json is in arguments the program give back the contents in json format
if 'json' in arguments:
json_response = True
species = []
counter = 0
for specie in species_l:
specie_f = specie['display_name']
species.append(specie_f)
counter = counter + 1
if counter == limit:
break
contents = json.dumps(species)
else:
json_response = False
contents = """
<html>
<body style="background-color: D7B7BC;"><FONT FACE="monospace" SIZE = 5 COLOR = 'white'><h3>List of the chosen limited species </h3></FONT>
<ol>"""
counter = 0
for specie in species_l:
contents = contents + "<li>" + specie['display_name'] + "</li>"
counter = counter + 1
if counter == limit:
break
contents = contents + """</ol>
</body>
</html>
"""
except ValueError:
answer_value = 400
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except KeyError:
answer_value = 400
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except TypeError:
answer_value = 404
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
elif '/karyotype' in self.path:
try:
arguments = self.main(self.path)
if 'specie' in arguments and arguments['specie'] != "":
specie = arguments['specie']
conn = http.client.HTTPConnection('rest.ensembl.org')
conn.request("GET", "/info/assembly/"+specie+"?content-type=application/json")
r1 = conn.getresponse()
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
karyotype_l = resp['karyotype']
print(karyotype_l)
if 'json' in arguments:
json_response = True
contents = json.dumps(karyotype_l)
else:
json_response = False
contents = """
<html>
<body style="background-color: D7B7BC;"><FONT FACE="monospace" SIZE = 5 COLOR = 'white'><h3>Chromosomes of the chosen specie: </h3></FONT>
<ul>"""
for elem in karyotype_l:
contents = contents + "<li>" + elem + "</li>"
contents = contents + """</ul>
</body>
</html>
"""
else:
answer_value = 404
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except KeyError:
answer_value = 400
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
elif '/chromosomeLength' in self.path:
try:
arguments = self.main(self.path)
if ('specie') in arguments and ('chromo') in arguments:
specie = arguments['specie']
chromo = arguments['chromo']
print("The chromosome number to study its length is: ", chromo)
print("The specie to study is: ", specie)
conn = http.client.HTTPConnection('rest.ensembl.org')
conn.request("GET", "/info/assembly/" + specie + "?content-type=application/json")
r1 = conn.getresponse()
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
if 'top_level_region' in resp:
info = resp['top_level_region']
length = 0
for elem in info:
if elem['name'] == chromo:
length = str(elem['length'])
print(length)
if 'json' in arguments:
json_response = True
resp_ ={'Length' : length}
contents = json.dumps(resp_)
else:
json_response = False
contents = """
<html>
<body style="background-color: D7B7BC;"><FONT FACE="monospace" SIZE = 5 COLOR = 'white'><h3>The length of the chromosome of the chosen specie is: </h3></FONT>
<ul>"""
contents = contents + "<li>" + str(length) + "</li>"
"""</ul>
</body>
</html>
"""
else:
answer_value = 404
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
else:
answer_value = 404
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except KeyError:
answer_value = 400
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except TypeError:
answer_value = 400
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
elif '/geneSeq' in self.path:
try:
arguments = self.main(self.path)
if 'gene' in arguments:
gene = arguments['gene']
conn = http.client.HTTPConnection('rest.ensembl.org')
conn.request("GET", "/homology/symbol/human/" + gene + "?content-type=application/json")
r1 = conn.getresponse()
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
id = resp['data'][0]['id']
print(id)
conn.request("GET", "/sequence/id/" + id + "?content-type=application/json")
r1 = conn.getresponse()
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
sequence = resp['seq']
print(sequence)
if 'json' in arguments:
json_response = True
resp_ = {'Sequence': sequence}
contents = json.dumps(resp_)
else:
json_response = False
contents = """
<html>
<body style="background-color: D7B7BC;"><FONT FACE="monospace" SIZE = 5 COLOR = 'white'><h3>The sequence of the given human gene is: </h3></FONT>
<ul>"""
contents = contents + "<li>" + sequence + "</li>"
"""</ul>
</body>
</html>
"""
else:
answer_value = 400
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except KeyError:
answer_value = 400
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except TypeError:
answer_value = 400
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
elif '/geneInfo' in self.path:
try:
arguments = self.main(self.path)
gene = arguments['gene']
conn = http.client.HTTPConnection('rest.ensembl.org')
conn.request("GET", "/homology/symbol/human/" + gene + "?content-type=application/json")
r1 = conn.getresponse()
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
id = resp['data'][0]['id']
print(id)
conn.request("GET", "/overlap/id/" + id + "?feature=gene;content-type=application/json")
r1 = conn.getresponse()
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
id = resp[0]['id']
start = resp[0]['start']
end = resp[0]['end']
length = (end-start)+1
chromo = resp[0]['seq_region_name']
if 'json' in arguments:
json_response = True
resp_ = {'Id': id,'Chromo-name': chromo, 'Start': start, 'End': end, 'Length': length }
contents = json.dumps(resp_)
else:
json_response = False
contents = """
<html>
<body style="background-color: D7B7BC;"><FONT FACE="monospace" SIZE = 5 COLOR = 'white'><h3>The information asked of the given human gene is: </h3></FONT>
<ul>"""
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The id of the sequence is: </h5></FONT>""" + str(id) + "</li>"
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The start of the sequence is: </h5></FONT>""" + str(start) + "</li>"
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The end of the sequence is: </h5></FONT>""" + str(end) + "</li>"
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The length of the sequence is: </h5></FONT>""" + str(length) + "</li>"
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The name of the gene is: </h5></FONT>""" + str(chromo) + "</li>"
"""</ul>
</body>
</html>
"""
except KeyError:
answer_value = 400
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except TypeError:
answer_value = 400
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
elif '/geneCalc' in self.path:
try:
arguments = self.main(self.path)
gene = arguments['gene']
conn = http.client.HTTPConnection('rest.ensembl.org')
conn.request("GET", "/homology/symbol/human/" + gene + "?content-type=application/json")
r1 = conn.getresponse()
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
id = resp['data'][0]['id']
print(id)
conn.request("GET", "/sequence/id/" + id + "?content-type=application/json")
r1 = conn.getresponse()
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
# print(resp)
sequence = resp['seq']
print(sequence)
s1 = Seq(sequence)
total_length = len(sequence)
pa = s1.perc('A')
pt = s1.perc('T')
pc = s1.perc('C')
pg = s1.perc('G')
if 'json' in arguments:
json_response = True
s1 = Seq(sequence)
total_length = len(sequence)
resp_ = {'Sequence': sequence, 'Length': total_length, 'PercA': pa, 'PercT': pt, 'PercC': pc, 'PercG': pg}
print(type(resp_))
contents = json.dumps(resp_)
else:
json_response = False
contents = """
<html>
<body style="background-color: D7B7BC;"><FONT FACE="monospace" SIZE = 5 COLOR = 'white'><h3>The calculations asked of the given sequence is: </h3></FONT>
<ul>"""
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The total lenght of the sequence is: </h5></FONT>""" + str(total_length) + "</li>"
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The percentage of A's in the sequence is: </h5></FONT>""" + str(pa) + "</li>"
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The percentage of T's in the sequence is: </h5></FONT>""" + str(pt) + "</li>"
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The percentage of C's in the sequence is: </h5></FONT>""" + str(pc) + "</li>"
contents = contents + "<li>" + """<FONT FACE="monospace" SIZE = 5 COLOR = 'darkslategray'><h5>The percentage of G's in the sequence is: </h5></FONT>""" + str(pg) + "</li>"
"""</ul>
</body>
</html>
"""
except KeyError:
answer_value = 400
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except TypeError:
answer_value = 400
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
elif '/geneList' in self.path:
try:
arguments = self.main(self.path)
start = arguments['start']
chromo = arguments['chromo']
end = arguments['end']
print('The number of chromosome is: ', chromo)
print('The start point is: ', start)
print('The end point is: ', end)
conn = http.client.HTTPConnection('rest.ensembl.org')
conn.request("GET", "/overlap/region/human/" + str(chromo) + ":" + str(start) + "-" + str(end) + "?content-type=application/json;feature=gene;feature=transcript;feature=cds;feature=exon")
r1 = conn.getresponse()
print()
print("Response received: ", end='')
print(r1.status, r1.reason)
text_json = r1.read().decode("utf-8")
resp = json.loads(text_json)
if 'json' in arguments:
try:
json_response = True
id_l = []
for elem in resp:
position1 = elem['feature_type']
if position1 == "gene":
position2 = elem['id']
id_l.append(str(position2))
contents = json.dumps(id_l)
except TypeError:
resp_ = 'None'
contents = json.dumps(resp_)
else:
json_response = False
contents = """
<html>
<body style="background-color: D7B7BC;"><FONT FACE="monospace" SIZE = 5 COLOR = 'white'><h3>The names of the genes located in the chromosome asked from the start to end positions are: </h3></FONT>
<ul>"""
for elem in resp:
#print(elem)
position1 = elem['feature_type']
if position1 == "gene":
position2 = elem['id']
print(position2)
contents = contents + "<li>" + 'The name of the chromosome is: ' + str(position2) + "</li>"
"""</ul>
</body>
</html>
"""
except KeyError:
answer_value = 404
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
except TypeError:
answer_value = 404
filename = 'error.html'
with open(filename, 'r') as f:
contents = f.read()
else:
answer_value = 404
filename = 'error.html'
print('prueba')
with open(filename, 'r') as f:
contents = f.read()
# Generating the response message
self.send_response(answer_value) # -- Status line: OK!
if (json_response == True) :
self.send_header('Content-Type', 'application/json')
else:
self.send_header('Content-Type', 'text/html')
# Define the content-type header:
self.send_header('Content-Length', len(str.encode(contents)))
# The header is finished
self.end_headers()
# Send the response message
self.wfile.write(str.encode(contents))
return