"FGFR3": "ENSG00000068078",
"KDR": "ENSG00000128052",
"ANK2": "ENSG00000145362"
}
SERVER = "rest.ensembl.org"
ENDPOINT = "/sequence/id/"
PARAMETERS = "?content-type=application/json"
connection = http.client.HTTPConnection(SERVER)
try:
user_gene = input("Enter the gene that you want to analyze: ")
id = gene_dict[user_gene]
connection.request("GET", ENDPOINT + id + PARAMETERS)
response = connection.getresponse()
print(f"SERVER: {SERVER}")
print(f"URL: {SERVER + ENDPOINT + PARAMETERS}")
print(f"Response received!: {response.status} {response.reason} \n")
if response.status == 200:
response = json.loads(response.read().decode())
print(f"Gene: {user_gene}")
print("Description:", response["desc"])
sequence = Seq(response["seq"])
print(sequence.info())
print(f"Most frequent base: {sequence.most_frequent_base()}")
except KeyError:
print(
"The gene is not inside the data base. Choose between the following:",
list(gene_dict.keys()))
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')
termcolor.cprint(self.path, 'blue')
# IN this simple server version:
# We are NOT processing the client's request
# It is a happy server: It always returns a message saying
# that everything is ok
o = urlparse(self.path)
path_name = o.path
arguments = parse_qs(o.query)
print(f"Resources requested: {path_name}")
print(f"Parameters: {arguments}")
#print(f"Keys: {arguments.keys()}")
# Message to send back to the client
SERVER = "rest.ensembl.org"
PARAMETERS = "?content-type=application/json"
context = {}
if path_name == "/":
content_type = "text/html"
contents = read_template_html_file("./HTML_FILES/index.html").render()
# 1. GET N SPECIES OF VERTEBRATES
elif path_name == "/listSpecies":
endpoint = "/info/species"
connection = http.client.HTTPConnection(SERVER)
connection.request("GET", endpoint + PARAMETERS)
response = connection.getresponse()
vertebrates_list = []
if response.status == 200:
content_type = "text/html"
response = json.loads(response.read().decode())
context["number_species"] = len(response["species"])
if "limit" in arguments.keys():
context["limit"] = int(arguments["limit"][0])
count = 0
for n in response["species"]:
if n["division"] == "EnsemblVertebrates":
vertebrates_list.append(n["common_name"])
count += 1
if count == context["limit"]:
break
else:
context["limit"] = len(response["species"])
for i in response["species"]:
if i["division"] == "EnsemblVertebrates":
vertebrates_list.append(i["common_name"])
context["species"] = vertebrates_list
#JSON
if "json" in arguments.keys():
content_type = "application/json"
contents = str(context)
#HTML
else:
contents = read_template_html_file("./HTML_FILES/listSpecies.html").render(context=context)
# 2. GET KARYOTYPE OF A SPECIE
elif path_name == "/karyotype":
endpoint = "/info/assembly/"
specie = arguments["specie"][0]
specie = specie.replace(" ", "_")
connection = http.client.HTTPConnection(SERVER)
connection.request("GET", endpoint + specie + PARAMETERS)
response = connection.getresponse()
try:
if response.status == 200:
content_type = "text/html"
response = json.loads(response.read().decode())
context["karyotype"] = response["karyotype"]
#JSON
if "json" in arguments.keys():
content_type = "application/json"
contents = str(context)
#HTML
else:
contents = read_template_html_file("./HTML_FILES/karyotype.html").render(context=context)
except TypeError:
if "json" in arguments.keys():
content_type = "application/json"
context["karyotype"] = "ERROR, MUST ENTER A VALID SPECIES"
contents = str(context)
else:
content_type = "text/html"
contents = read_template_html_file("./HTML_FILES/Error.html").render()
#3. GET CHROMOSOME LENGTH
elif path_name == "/chromosomeLength":
endpoint = "/info/assembly/"
specie = arguments["specie"][0]
connection = http.client.HTTPConnection(SERVER)
connection.request("GET", endpoint + specie + PARAMETERS)
response = connection.getresponse()
count = 0
if response.status == 200:
response = json.loads(response.read().decode())
#JSON APPLICATION
if "json" in arguments.keys():
for chromosome in response["top_level_region"]:
if chromosome["coord_system"] == "chromosome" and chromosome["name"] == arguments["chromo"][0]:
json_chromosome = chromosome
count += 1
content_type = "application/json"
if count != 0:
contents = str(json_chromosome)
else:
context["chromosome"] = "ERROR, MUST CHECK THE NAME OF THE CHROMOSOME"
contents = str(context)
#HTML APPLICATION
else:
content_type = "text/html"
for chromosome in response["top_level_region"]:
if chromosome["coord_system"] == "chromosome" and chromosome["name"] == arguments["chromo"][0]:
context["chromosome_length"] = chromosome["length"]
count += 1
if count != 0:
contents = read_template_html_file("./HTML_FILES/chromosome_length.html").render(context=context)
else:
contents = read_template_html_file("./HTML_FILES/Error.html").render()
else:
if "json" in arguments.keys():
content_type = "application/json"
context["species"] = "ERROR, MUST CHECK THE NAME OF THE SPECIES"
contents = str(context)
else:
content_type = "text/html"
contents = read_template_html_file("./HTML_FILES/Error.html").render()
#4 GET HUMAN GENETIC SEQUENCE
elif path_name == "/geneSeq":
endpoint = "/sequence/id/"
try:
gene = arguments["gene"][0]
id = gene_dict[gene]
connection = http.client.HTTPConnection(SERVER)
connection.request("GET", endpoint + id + PARAMETERS)
response = connection.getresponse()
if response.status == 200:
response = json.loads(response.read().decode())
context["gene_name"] = gene
context["sequence"] = response["seq"]
#JSON
if "json" in arguments.keys():
content_type = "application/json"
contents = str(context)
#HTML
else:
content_type = "text/html"
contents = read_template_html_file("./HTML_FILES/gene_sequence.html").render(context=context)
except KeyError:
#JSON
if "json" in arguments.keys():
content_type = "application/json"
context["sequence"] = "ERROR, MUST ENTER A HUMAN GENE"
contents = str(context)
#HTML
else:
content_type = "text/html"
contents = read_template_html_file("./HTML_FILES/Error.html").render()
#5 GET INFO ABOUT GENETIC SEQUENCE
elif path_name == "/geneInfo":
endpoint = "/sequence/id/"
try:
gene = arguments["gene"][0]
id = gene_dict[gene]
connection = http.client.HTTPConnection(SERVER)
connection.request("GET", endpoint + id + PARAMETERS)
response = connection.getresponse()
if response.status == 200:
response = json.loads(response.read().decode())
gene_info = response["desc"]
gene_info_data = gene_info.split(":")
context["gene_name"] = gene
context["start"] = gene_info_data[3]
context["end"] = gene_info_data[4]
context["length"] = int(context["end"]) - int(context["start"])
context["id"] = id
context["chromosome_name"] = gene_info_data[2]
#JSON
if "json" in arguments.keys():
content_type = "application/json"
contents = str(context)
#HTML
else:
content_type = "text/html"
contents = read_template_html_file("./HTML_FILES/gene_info.html").render(context=context)
except KeyError:
if "json" in arguments.keys():
content_type = "application/json"
context["gene_name"] = "ERROR, INSERT THE NAME OF HUMAN GENE"
contents = str(context)
else:
content_type = "text/html"
contents = read_template_html_file("./HTML_FILES/Error.html").render()
# 6. CALCULATE GENE BASES PERCENTAGES
elif path_name == "/geneCalc":
endpoint = "/sequence/id/"
try:
gene = arguments["gene"][0]
id = gene_dict[gene]
connection = http.client.HTTPConnection(SERVER)
connection.request("GET", endpoint + id + PARAMETERS)
response = connection.getresponse()
if response.status == 200:
response = json.loads(response.read().decode())
sequence = Seq(response["seq"])
context["gene_name"] = gene
context["length"] = sequence.len()
context["percentages"] = sequence.info()
if "json" in arguments.keys():
content_type = "application/json"
context["percentages"] = context["percentages"].strip("\n")
contents = str(context)
else:
content_type = "text/html"
contents = read_template_html_file("./HTML_FILES/gene_calc.html").render(context=context)
except KeyError:
if "json" in arguments.keys():
content_type = "application/json"
context["gene_name"] = "ERROR, YOU MUST ENTER A VALID NAME FOR THE GENE"
contents = str(context)
else:
content_type = "text/html"
contents = read_template_html_file("./HTML_FILES/Error.html").render()
else:
content_type = "text/html"
contents = read_template_html_file("./HTML_FILES/Error.html").render()
#TO TEST EVERYTHING
if not "json" in arguments.keys():
#CHANGE MANUALLY THE FILE NAME TO TEST BASIC, MEDIUM
file = Path("report-medium.txt").open("a")
my_endpoint = path_name.strip("/")
if path_name != "/favicon.ico" and path_name != "/":
#my_endpoint = path_name.strip("/")
file.write(f"----> {my_endpoint} endpoint \n")
# CHANGE NUMBER OF TEST MANUALLY
file.write(f"TEST \n\n")
file.write(f"* Input: http://127.0.0.1:8080{self.path} \n"
f"\n"
f"* Output: \n\n")
file.write(contents)
file.write("\n\n"
"==================\n")
else:
pass
file.close()
# Generating the response message
self.send_response(200) # -- Status line: OK!
self.send_header('Content-Type', content_type)
if "json" in arguments.keys():
#self.send_header('Content-Type', "application/json")
self.send_header('Content-Length', len(str.encode(contents)))
else:
#self.send_header('Content-Type', "text/html")
self.send_header('Content-Length', len(contents.encode()))
# Define the content-type header:
# The header is finished
self.end_headers()
# Send the response message
self.wfile.write(contents.encode())
return
