def info(seq):
s1 = Seq(seq)
count_bases = s1.count_bases()
nucleotides = ("A", "C", "G", "T")
percentage = s1.percentage_base(count_bases, s1.len())
i = 0
percentage_bases = ""
for i in range(0, len(count_bases)):
percentage_bases += nucleotides[i] + ": " + str(
count_bases[i]) + " (" + percentage[i] + ")\n"
i += 1
context = {"result": [str(s1.len()), percentage_bases]}
print(context)
return context
def info(cs, seq):
print_colored("INFO", "yellow")
s1 = Seq(seq)
count_bases = s1.count_bases()
nucleotides = ("A", "C", "G", "T")
percentage = s1.percentage_base(count_bases, s1.len())
response1 = "Sequence: " + str(s1) + "\nTotal length: " + str(
s1.len()) + "\n"
print(response1)
i = 0
response2 = ""
for i in range(0, len(count_bases)):
response2 += nucleotides[i] + ": " + str(
count_bases[i]) + " (" + percentage[i] + ")\n"
i += 1
print(response2)
cs.send((response1 + response2).encode())
def do_GET(self):
global contents
termcolor.cprint(self.requestline, 'green')
termcolor.cprint(self.path, 'blue')
o = urlparse(self.path)
path_name = o.path
arguments = parse_qs(o.query)
print("Resource requested: ", path_name)
print("Parameters: ", arguments)
# 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
context = {}
# Message to send back to the client
PARAMETERS = '?content-type=application/json'
SERVER = "rest.ensembl.org"
connection = http.client.HTTPConnection(SERVER)
if path_name == '/':
contents = Path('./html/index.html').read_text()
elif path_name == "/listSpecies":
try:
ENDPOINT = '/info/species'
connection.request('GET', ENDPOINT + PARAMETERS)
response = connection.getresponse()
final_response = json.loads(response.read().decode())
species_list = final_response['species']
names_list = []
for elem in species_list:
s1 = elem['name']
lists = [s1]
names_list = names_list + lists
if 'limit' in arguments:
limit = int(arguments['limit'][0])
final_list = names_list[:limit]
if limit <= len(final_list):
context['length'] = len(names_list)
context['final_list'] = final_list
context['limit'] = limit
contents = su.read_template_html_file(
'./html/limit_name_list.html').render(
context=context)
else:
contents = su.read_template_html_file(
'./html/error.html').render(context=context)
elif 'limit' not in arguments:
context['length'] = len(names_list)
context['final_list'] = names_list
contents = su.read_template_html_file(
'./html/full_name_list.html').render(context=context)
except KeyError:
contents = su.read_template_html_file(
'./html/error.html').render(context=context)
elif path_name == "/karyotype":
try:
species_name = arguments['species_name'][0]
ENDPOINT = '/info/assembly/'
connection.request('GET', ENDPOINT + species_name + PARAMETERS)
response = connection.getresponse()
final_response = json.loads(response.read().decode())
karyotype = final_response['karyotype']
context['karyotype'] = karyotype
contents = su.read_template_html_file(
'./html/karyotype.html').render(context=context)
except KeyError:
contents = su.read_template_html_file(
'./html/error.html').render(context=context)
elif path_name == "/chromosomeLength":
try:
if 'species_name' not in arguments:
contents = su.read_template_html_file(
'./html basic/ERROR.html').render()
elif 'chromosome_name' not in arguments:
contents = su.read_template_html_file(
'./html basic/ERROR.html').render()
else:
global chromosome_length
species_name = arguments['species_name'][0]
chromosome_name = arguments['chromosome_name'][0]
ENDPOINT = '/info/assembly/'
connection.request('GET',
ENDPOINT + species_name + PARAMETERS)
response = connection.getresponse()
final_response = json.loads(response.read().decode())
list_dict = final_response['top_level_region']
for elem in list_dict:
if (elem['name']
== chromosome_name) and (elem['coord_system']
== 'chromosome'):
chromosome_length = elem['length']
else:
contents = su.read_template_html_file(
'./html/error.html').render(context=context)
context['chromosome_length'] = chromosome_length
contents = su.read_template_html_file(
'./html/chromosome_length.html').render(
context=context)
except KeyError:
contents = su.read_template_html_file(
'./html/error.html').render(context=context)
elif path_name == "/geneSeq":
try:
gene = arguments['gene'][0]
GENE_ID = genes_dict[gene]
ENDPOINT = '/sequence/id/'
connection.request('GET', ENDPOINT + GENE_ID + PARAMETERS)
response = connection.getresponse()
final_response = json.loads(response.read().decode())
sequence = final_response['seq']
context['sequence'] = sequence
contents = su.read_template_html_file(
'./html/Seq.html').render(context=context)
except KeyError:
contents = su.read_template_html_file(
'./html/error.html').render(context=context)
elif path_name == "/geneInfo":
try:
gene = arguments['gene'][0]
GENE_ID = genes_dict[gene]
ENDPOINT = '/sequence/id/'
connection.request('GET', ENDPOINT + GENE_ID + PARAMETERS)
response = connection.getresponse()
final_response = json.loads(response.read().decode())
info_list = final_response['desc'].split(':')
context['genname'] = gene
context['start'] = info_list[3]
context['end'] = info_list[4]
context['length'] = int(info_list[4]) - int(info_list[3])
context['id'] = GENE_ID
context['chromoname'] = info_list[1]
contents = su.read_template_html_file(
'./html/Info.html').render(context=context)
except KeyError:
contents = su.read_template_html_file(
'./html/error.html').render(context=context)
elif path_name == '/geneCalc':
try:
gene = arguments['gene'][0]
GENE_ID = genes_dict[gene]
ENDPOINT = '/sequence/id/'
connection.request('GET', ENDPOINT + GENE_ID + PARAMETERS)
response = connection.getresponse()
final_response = json.loads(response.read().decode())
sequence = final_response['seq']
s = Seq(sequence)
context['length'] = s.len()
context['percentageA'] = s.percentage_base('A')
context['percentageC'] = s.percentage_base('C')
context['percentageG'] = s.percentage_base('G')
context['percentageT'] = s.percentage_base('T')
contents = su.read_template_html_file(
'./html/Calc.html').render(context=context)
except KeyError:
contents = su.read_template_html_file(
'./html/error.html').render(context=context)
else:
pass
self.send_response(200) # -- Status line: OK!
# Define the content-type header:
self.send_header('Content-Type', 'text/html')
content_length = len(str.encode(contents))
self.send_header('Content-Length', content_length)
# The header is finished
self.end_headers()
# Send the response message
self.wfile.write(contents.encode())
return
