def gene(cs, argument):
GENE_FOLDER = "./SEQUENCES/"
print_colored("GENE", "green")
seq = Seq()
response = seq.read_fasta(GENE_FOLDER + argument + ".txt")
print(response)
cs.send(str(response).encode())
def comp(cs, list_sequences, argument):
print_colored("COMP", "green")
seq = Seq(list_sequences[int(argument)])
response = seq.complement()
response = "COMP " + str(seq) + "\n" + response
print(response)
cs.send(response.encode())
def rev(cs, list_sequences, argument):
print_colored("REV", "green")
seq = Seq(list_sequences[int(argument)])
response = seq.reverse()
response = "REV " + str(seq) + "\n" + response
print(response)
cs.send(response.encode())
def info(cs, list_sequences, argument):
print_colored("INFO", "green")
seq = Seq(list_sequences[int(argument)])
print(seq)
number_dict = seq.count()
len1 = len(str(seq))
percentage_dict = seq.percentage(seq.count_bases(), len1)
response = "Sequence: " + list_sequences[int(
argument)] + "\nTotal length: " + str(len1) + "\n"
for key in number_dict:
response += (str(key) + ": " + str(number_dict[key]) + " (" +
str(percentage_dict[key], ) + "%)\n")
print(response)
cs.send(response.encode())
def lengthSeq(gene, genes_dict):
SERVER = "rest.ensembl.org"
ENDPOINT = "/sequence/id/"
PARAMS = "?content-type=application/json"
ID = genes_dict[gene]
connection = http.client.HTTPConnection(SERVER)
connection.request("GET", ENDPOINT + ID + PARAMS)
response = connection.getresponse()
print(response.status, response.reason)
answer_decoded = response.read().decode()
dict_response = json.loads(answer_decoded)
sequence = Seq(dict_response["seq"])
length = sequence.len()
context = {"length": length, "gene": gene}
content = su.read_template_html_file("HTML/lengthCalc.html").render(
context=context)
return content
def percentageSeq(gene, genes_dict):
SERVER = "rest.ensembl.org"
ENDPOINT = "/sequence/id/"
PARAMS = "?content-type=application/json"
ID = genes_dict[gene]
connection = http.client.HTTPConnection(SERVER)
connection.request("GET", ENDPOINT + ID + PARAMS)
response = connection.getresponse()
print(response.status, response.reason)
answer_decoded = response.read().decode()
dict_response = json.loads(answer_decoded)
sequence = Seq(dict_response["seq"])
lenght = sequence.len()
a, c, g, t = sequence.percentage(sequence.count_bases(), lenght)
context = {"A": a, "C": c, "G": g, "T": t, "gene": gene}
content = su.read_template_html_file("HTML/percentageCalc.html").render(
context=context)
return content
from client0 import Client
from pathlib import Path
from Seq02 import Seq
PRACTICE = 2
EXERCISE = 6
print(f"-----| Practice {PRACTICE}, Exercise {EXERCISE} |------")
# -- Parameters of the server to talk to
IP = "192.168.1.12"
PORT = 12000
# -- Create a client object
c = Client(IP, PORT)
s = Seq()
s.read_fasta("FRAT1.txt")
count = 0
for i in range(0, len(s.strbases), 10):
fragment = s.strbases[i:i + 10]
print(fragment)
count = count + 1
if count == 5:
break
print("Fragment", count, ":", fragment)
print(c.talk(fragment))
"FGFR3": "ENSG00000068078",
"KDR": "ENSG00000128052",
"ANK2": "ENSG00000145362"
}
SERVER = "rest.ensembl.org"
ENDPOINT = "/sequence/id/"
PARAMETERS = "?content-type=application/json"
connection = http.client.HTTPConnection(SERVER)
try:
for key, ID in genes_dict.items():
connection.request("GET", ENDPOINT + ID + PARAMETERS)
response = connection.getresponse()
if response.status == 200:
response_dict = json.loads(response.read().decode())
#response = json.dumps(response_dict, indent=4, sort_keys=True
sequence = Seq(response_dict["seq"])
s_length = sequence.len()
percentages = sequence.percentage()
most_frequent_base = sequence.frequent_base(sequence.count())
print_colored("Gene: ", key, "yellow")
print_colored("Description: ", response_dict['desc'], "yellow")
print_colored("Total length: ", s_length, "yellow")
for key, value in percentages.items():
print_colored(key, value, "blue")
print_colored("Most frequent base: ", most_frequent_base, "yellow")
except KeyError:
print(
"The gene is not inside our dictionary. Choose one of the following: ",
list(genes_dict.keys()))
from Seq02 import Seq
print('-----| Exercise 1 |------')
seq_list = Seq('ACTGA')
print('Sequence: 1 , (Lenght : ' + str(seq_list.len()) + " ) " + str(seq_list))
from Seq02 import Seq
print("-----| Practice 1, Exercise 4 |------")
s1 = Seq('NULL')
s2 = Seq("ACTGA")
s3 = Seq("ERROR")
print("Sequence 1: (Length : ", s1.len(), ")", s1)
print("Sequence 1: (Length : ", s2.len(), ")", s2)
print("Sequence 1: (Length : ", s3.len(), ")", s3)
from client0 import Client
from pathlib import Path
from Seq02 import Seq
PRACTICE = 2
EXERCISE = 1
print(f"-----| Practice {2}, Exercise {7} |------")
IP = "192.168.1.12"
PORT = 12000
PORT_2 = 12002
c = Client(IP, PORT)
c_2 = Client(IP, PORT_2)
s = Seq()
s.read_fasta('../P0/FRAT1.txt')
i = 0
count = 0
while i < len(s.strbases) and count < 10:
fragment = s.strbases[i:i + 10]
count += 1
i += 10
fragment_text = "Fragment " + str(count) + ": " + fragment
print(fragment_text)
if count % 2 == 0:
print(c_2.debug_talk(fragment_text))
else:
print(c.debug_talk(fragment_text))
from Seq02 import Seq
print('-----| Practice 1, Exercise 10 |------')
bases = ["A", "C", "T", "G"]
list_of_genes = ["U5", "ADA", "FRAT1", "FXN", "RNU6_269P" ]
txt = ".txt"
FOLDER = "../SEQUENCES/"
for e in list_of_genes:
s0 = Seq('')
val = 0
base = ''
s0 = s0.read_fasta(FOLDER+e+txt)
dict1 = s0.count()
for i, t in dict1.items():
while t > val:
val = t
base = i
print("Gene ", e, " : Most frequent base: ", base)
from Seq02 import Seq
print("-----| Practice 1, Exercise 6 |------")
s1 = Seq()
s2 = Seq("ACTGA")
s3 = Seq("Invalid sequence")
print("Sequence 1: (Length : ", s1.len(), ")", s1)
print("Bases:", s1.count())
print("Sequence 2: (Length : ", s2.len(), ")", s2)
print("Bases:", s2.count())
print("Sequence 3: (Length : ", s3.len(), ")", s3)
print("Bases:", s3.count())
}
SERVER = "rest.ensembl.org"
ENDPOINT = "/sequence/id/"
PARAMETERS = "?content-type=application/json"
connection = http.client.HTTPConnection(SERVER)
try:
user_gene = input("Enter the gene you want to analise: ")
ID = genes_dict[user_gene]
connection.request("GET", ENDPOINT + ID + PARAMETERS)
response = connection.getresponse()
if response.status == 200:
response_dict = json.loads(response.read().decode())
#print(json.dumps(response_dict, indent=4, sort_keys=True))
sequence = Seq(response_dict["seq"])
s_length = sequence.len()
a, c, g, t = sequence.percentage(sequence.count_bases(), s_length)
most_frequent_base = sequence.frequent_base(sequence.count())
print_colored("Gene: ", user_gene, "yellow")
print_colored("Total length: ", s_length, "yellow")
print(a)
print(c)
print(t)
print(g)
print(most_frequent_base)
except KeyError:
print("The gene is not inside our dictionary. Choose one of the following: ", list(genes_dict.keys()))
from Seq02 import Seq
print("-----| Practice 1, Exercise 3 |------")
s1 = Seq('NULL')
s2 = Seq("ACTGA")
s3 = Seq("ERROR")
print("Sequence 1: ", s1)
print("Sequence 2: ", s2)
print("Sequence 3: ", s3)
from Seq02 import Seq
print('-----| Practice 1, Exercise 9 |------')
FOLDER = "../SEQUENCES/"
file_name = FOLDER + "U5.txt"
s0 = Seq('')
s0 = s0.read_fasta(file_name)
print(f"Sequence : (Length: {s0.len()}) {s0}")
print(f"Bases: {s0.count()}")
print(f"Rev: {s0.reverse(s0)}")
print(f"Comp: {s0.complement(s0)}")
from Seq02 import Seq
print("-----| Practice 1, Exercise 8 |------")
s1 = Seq('NULL')
s2 = Seq("ACTGA")
s3 = Seq("Invalid sequence")
print("Sequence", 1, ": (Length:", s1.len(), ")", s1)
print(f"Bases: {s1.count()}")
print(f"Rev: {s1.reverse(s1)}")
print(f"Comp: {s1.complement(s1)}")
print("Sequence", 2, ": (Length:", s2.len(), ")", s2)
print(f"Bases: {s2.count()}")
print(f"Rev: {s2.reverse(s2)}")
print(f"Comp: {s2.complement(s2)}")
print("Sequence", 3, ": (Length:", s3.len(), ")", s3)
print(f"Bases: {s3.count()}")
print(f"Rev: {s3.reverse(s3)}")
print(f"Comp: {s3.complement(s3)}")
from Seq02 import Seq
print('-----| Practice 1, Exercise 2 |------')
s1 =Seq('NULL')
s2 =Seq("ACTGA")
print('Sequence 1', s1)
print('Sequence 2', s2)
