def info_send(cs, argument):
termcolor.cprint('INFO', 'green')
s = Seq(argument)
info_dict = s.info_seq()
response1 = 'Total length: ' + str(len(argument)) + '\n'
cs.send(response1.encode())
response2 = 'A: ' + str(info_dict['A'][0]) + ' ' + str(info_dict['A'][1]) + '%' + '\n'
cs.send(response2.encode())
response3 = 'C: ' + str(info_dict['C'][0]) + ' ' + str(info_dict['C'][1]) + '%' + '\n'
cs.send(response3.encode())
response4 = 'G: ' + str(info_dict['G'][0]) + ' ' + str(info_dict['G'][1]) + '%' + '\n'
cs.send(response4.encode())
response5 = 'T: ' + str(info_dict['T'][0]) + ' ' + str(info_dict['T'][1]) + '%' + '\n'
cs.send(response5.encode())
print(response1, response2, response3, response4, response5)
def info(sequence):
s = Seq(sequence)
info_dict = s.info_seq()
response = f"""Total length {len(sequence)}
A: {info_dict['A'][0]} ({info_dict['A'][1]}%)
C: {info_dict['C'][0]} ({info_dict['C'][1]}%)
G: {info_dict['A'][0]} ({info_dict['G'][1]}%)
T: {info_dict['T'][0]} ({info_dict['T'][1]}%)"""
context = {
'sequence': sequence,
'information': response,
'operation': 'Info'
}
contents = read_template_html_file('operation.html').render(
context=context)
return contents
def obtain_info_list(dict_info):
input_seq = dict_info['seq']
sequence_seq = Seq(input_seq)
seq_length = []
length = sequence_seq.len()
seq_length.append(length)
info_dict = sequence_seq.info_seq()
A_list = info_dict['A']
C_list = info_dict['C']
G_list = info_dict['G']
T_list = info_dict['T']
info_list = []
info_list.append(A_list)
info_list.append(C_list)
info_list.append(G_list)
info_list.append(T_list)
info_list.append(seq_length)
return info_list
def get_list_info(dict_info):
sequence_asked = dict_info['seq']
seq_seq = Seq(sequence_asked)
length_seq = []
length = seq_seq.len()
length_seq.append(length)
info_dict = seq_seq.info_seq()
list_A = info_dict['A']
list_C = info_dict['C']
list_G = info_dict['G']
list_T = info_dict['T']
lists_info = []
lists_info.append(list_A)
lists_info.append(list_C)
lists_info.append(list_G)
lists_info.append(list_T)
lists_info.append(length_seq)
return lists_info
connection = http.client.HTTPConnection(SERVER)
for g in GENES_LIST:
try:
ID = DICT_GENES[g]
connection.request("GET", ENDPOINT + ID + PARAMETERS)
response = connection.getresponse()
print("\nSERVER: ", SERVER)
print("URL: ", SERVER + ENDPOINT + ID + PARAMETERS)
print("Response received:", response.status, response.reason, "\n")
if response.status == 200:
response_dict = json.loads(response.read().decode())
# print(json.dumps(response_dict, indent=4, sort_keys=True))
print_colored("GENE: ", g, "yellow")
print_colored("Description: ", response_dict["desc"], "yellow")
sequence = Seq(response_dict["seq"])
seq_length = sequence.len()
count_dict = sequence.count_bases()
# most_frequent_base = sequence.most_frequent_base(count_dict)
info_dict = sequence.info_seq()
A = info_dict['A']
G = info_dict['G']
C = info_dict['C']
T = info_dict['T']
bases_dict = {'G': G[0], 'A': A[0], 'C': C[0], 'T': T[0]}
max_value = max(bases_dict, key=bases_dict.get)
print(colored("Total length:", "yellow"), seq_length, "\n", colored(f"""A: {A[0]} ({round(A[1], 1)}%)
C: {C[0]} ({round(C[1], 1)}%)
G: {G[0]} ({round(G[1], 1)}%)
T: {T[0]} ({round(T[1], 1)}%)""", "blue"), "\n", colored("Most frequent base:", "yellow"), max_value)
except KeyError:
print("The gene is not inside our database. Choose one of the following", list(DICT_GENES.keys()))
