from P1.Seq1 import Seq
GENE_FOLDER = "./PROJECT/"
gene_list = ["U5", "ADA", "FRAT1", "FXN", "RNU6_269P"]
print("-----| Practice 1, Exercise 10 |------")
for gene in gene_list:
sequence = Seq()
sequence.read_fasta(GENE_FOLDER + gene + ".txt")
print("Gene", gene, "Most frequent Base: ", sequence.frequent_base())
def do_GET(self):
"""This method is called whenever the client invokes the GET method
in the HTTP protocol request"""
# Define the type of content returned by the server
content_type = "text/html"
# Define the sequences that we are going to use in "get" and the bases for exercise 4
sequence = ["GTAGCA", "ACGTTA", "CGTAGG", "ATTGTC"]
all_bases = ["A", "C", "G", "T"]
# Print the request line
termcolor.cprint(self.requestline, 'green')
# Processing the request line
req = self.requestline.split(" ")
# Path will be: "/"
path = req[1]
# We will need to split the "?" in order to leave the msg alone
argument = path.split("?")
# We define our first argument to determine if we could continue or an error in thrown
arg0 = argument[0]
# All the information appears in "form-4.html"
if arg0 == "/":
contents = Path("form-4.html").read_text()
status = 200
elif arg0 == "/ping":
contents = """
<!DOCTYPE html>
<html lang = "en">
<head>
<meta charset = "utf-8" >
<title> ping </title >
</head >
<body>
<h2> PING ok!</h2>
<p> The SEQ2 Server in running... </p>
<a href="/">Main page</a>
</body>
</html>
"""
status = 200
elif arg0 == "/get":
# We define our second argument, the one after the "?" that we have split.
arg1 = argument[1]
# To split the "&" that is after the value
args = arg1.split("&")
# Is necessary to split the "=" after our name ("msg")
name, value = args[0].split("=")
# We define the argument n
n = int(value)
seq = sequence[n - 1]
contents = f"""
<!DOCTYPE html>
<html lang = "en">
<head>
<meta charset = "utf-8" >
<title> get </title >
</head >
<body>
<h2>Sequence number {n}</h2>
<p> {seq}</p>
<a href="/">Main page</a>
</body>
</html>
"""
status = 200
elif arg0 == "/gene":
# We define our second argument, the one after the "?" that we have split.
arg1 = argument[1]
# To split the "&" that is after the value
args = arg1.split("&")
# Is necessary to split the "=" after our name ("msg")
name, gene_name = args[0].split("=")
# Sequence of the gene
s = Seq()
s_string = str(s.read_fasta(FOLDER + gene_name))
contents = f"""
<!DOCTYPE html>
<html lang = "en">
<head>
<meta charset = "utf-8" >
<title> gene </title >
</head >
<body>
<h2>Gene {gene_name}</h2>
<textarea readonly rows="20" cols="80"> {s_string} </textarea>
<a href="/">Main page</a>
</body>
</html>
"""
status = 200
elif arg0 == "/operation":
# We define our second argument, the one after the "?" that we have split.
arg1 = argument[1]
# To split the "&" that is after the value
args = arg1.split("&")
# Name and values (=arguments)
#seq in order to create the sequence
name, seq = args[0].split("=")
#op are the different options that can be chosen after the sequence is written
name, op = args[1].split("=")
#Introduce the sequence
s = Seq(seq)
if "info" in op:
s = Seq(seq)
s_length = s.len()
list1 = []
list2 = []
for b in all_bases:
count_b = s.count_base(b)
p = round(count_b * (100 / s_length),
1) # percentage calculation with just 1 decimal
list1.append(
count_b) # list 1: where we put the total bases
list2.append(
p
) # list2 : where we put the percentage of all the bases
response = f"""
Total length: {s_length}
<p>A: {list1[0]} ({list2[0]}%)</p>
<p>C: {list1[1]} ({list2[1]}%)</p>
<p>G: {list1[2]} ({list2[2]}%)</p>
<p>G: {list1[3]} ({list2[3]}%)</p>
"""
elif "comp" in op:
response = s.complement()
elif "rev" in op:
response = s.reverse()
contents = f"""
<!DOCTYPE html>
<html lang = "en">
<head>
<meta charset = "utf-8" >
<title> operation </title >
</head >
<body>
<h2>Sequence :</h2>
<p>{seq}</p>
<h2>Operation :</h2>
<p>{op}</p>
<h2>Result :</h2>
<p>{response}</p>
<a href="/">Main page</a>
</body>
</html>
"""
status = 200
else:
# Error.html file
contents = Path("Error.html").read_text()
status = 404
# Generating the response message
self.send_response(status)
# Define the content-type header:
self.send_header('Content-Type', content_type)
self.send_header('Content-Length', len(contents.encode()))
# The header is finished
self.end_headers()
# Send the response message
self.wfile.write(contents.encode())
return
def gene(name):
s = Seq()
s.read_fasta(FOLDER + FILENAMES)
return s
from P1.Seq1 import Seq
from Client0 import Client
PRACTICE = 2
EXERCISE = 6
print(f"-----| Practice {PRACTICE}, Exercise {EXERCISE} |------")
IP = "127.0.0.1"
PORT = 8081
c = Client(IP, PORT)
s = Seq()
s.read_fasta('../P2/FRAT1.txt')
count = 0
i = 0
while i < len(s.strbases) and count < 5:
fragment = s.strbases[i:i + 10]
count += 1
i += 10
print(c.talk(fragment))
from P1.Seq1 import Seq
def print_result(i, sequence):
print("Sequence" + str(i) + ": (Length: " + str(sequence.len()),
")" + str(sequence))
print("Bases:", sequence.count())
print("Rev:", sequence.reverse())
print("Comp:", sequence.complement())
PROJECT_PATH = "../P1/PROJECT/"
print("-----| Practice 1, Exercise 9 |------")
s1 = Seq()
s1.read_fasta(PROJECT_PATH + "ADA.txt")
print_result("", s1)
print(f"-----| Practice {PRACTICE}, Exercise {EXERCISE} |------")
FOLDER = "../Session-04/"
FILENAME = "FRAT1"
# -- Parameters of the server to talk to
IP = "127.0.0.1"
PORT = 58788
c1 = Client(IP, PORT)
c2 = Client(IP, PORT + 1)
print(c1)
print(c2)
s = Seq()
s.read_fasta(FOLDER + FILENAME)
bases = str(s)
length = 10
print(f"Gene {FILENAME}: {bases}")
c1.talk(f"Sending {FILENAME} Gene to the server, in fragments of {length} bases...")
c2.talk(f"Sending {FILENAME} Gene to the server, in fragments of {length} bases...")
for index in range(0,10):
fragment = bases[index * length:(index + 1) * length]
print(f"Fragment {index + 1}: {fragment}")
if index % 2:
c2.talk(f"Fragment {index + 1}: {fragment}")
from P1.Seq1 import Seq
FOLDER = "../Session-04/"
Filename = ["U5", "ADA", "FRAT1", "FXN", "RNU6_269P"]
TypeDOC = '.txt'
bases = ['A', 'C', 'G', 'T']
print('----| Practice 1, Exercise 10| ----')
i = 0
for element in Filename:
seq = Seq()
seq.read_fasta(FOLDER + element + TypeDOC)
Dictionary_bases = seq.seq_count()
Amount_bases = list(Dictionary_bases.values())
Most_freq = max(Amount_bases)
print('Gene ', element, ': Most frequent base: ',
bases[Amount_bases.index(Most_freq)])
from P1.Seq1 import Seq
print("-----| Practice 1, Exercise 9 |------")
FOLDER = "../Session-04/"
TypeDoc = '.txt'
seq = Seq(FOLDER + 'U5' + TypeDoc)
seq.read_fasta(FOLDER + 'U5' + TypeDoc)
print("Sequence ", seq, ':', "(Length: ", seq.len(), ')', seq)
print(" Bases:", seq.seq_count())
print(' Rev: ', seq.reverse(), '\n Comp: ', seq.complement())
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')
request = self.requestline.split(' ')
raw_arg = request[1]
clean_arg = raw_arg.split('?')
argument = clean_arg[0]
if argument == '/':
contents = Path('form-4.html').read_text()
elif argument == '/ping':
contents = f"""
<!DOCTYPE html>
<html lang = "en">
<head>
<meta charset = "utf-8" >
<title> PING </title >
</head >
<body>
<h2> PING OK!</h2>
<p> The SEQ2 server is running </p>
<a href="/">Main page</a>
</body>
</html> """
elif argument == '/get':
argument1 = clean_arg[1].split('&')
name, value = argument1[0].split('=')
value = int(value)
sequence = Sequences[value]
contents = f"""
<!DOCTYPE html>
<html lang = "en">
<head>
<meta charset = "utf-8" >
<title> GET </title >
</head >
<body>
<h2> Sequence number {value}</h2>
<p> {sequence} </p>
<a href="/">Main page</a>
</body>
</html> """
elif argument == '/gene':
argument1 = clean_arg[1].split('&')
name, gene = argument1[0].split('=')
sequence = Seq()
sequence.read_fasta(FOLDER + gene + TypeDoc)
gene_str = str(sequence)
contents = f"""
<!DOCTYPE html>
<html lang = "en">
<head>
<meta charset = "utf-8" >
<title> GENE </title >
</head >
<body>
<h2> Gene: {gene}</h2>
<textarea readonly rows="20" cols="80"> {gene_str} </textarea>
<br>
<br>
<a href="/">Main page</a>
</body>
</html>"""
elif argument == '/operation':
argument1 = clean_arg[1].split('&')
name, sequence = argument1[0].split("=")
name, operation = argument1[1].split("=")
seq = Seq(sequence)
if operation == 'comp':
result = seq.complement()
elif operation == 'rev':
result = seq.reverse()
else:
length = seq.len()
num_bases = []
perc_bases = []
for element in bases:
counter_bases = seq.count_base(element)
percentage = round(
(seq.count_base(element) * 100 / seq.len()), 2)
num_bases.append(counter_bases)
perc_bases.append(percentage)
result = f"""
<p>Total length: {length}</p>
<p>A: {num_bases[0]} ({perc_bases[0]}%)</p>
<p>C: {num_bases[1]} ({perc_bases[1]}%)</p>
<p>G: {num_bases[2]} ({perc_bases[2]}%)</p>
<p>T: {num_bases[3]} ({perc_bases[3]}%)</p>"""
contents = f"""
<!DOCTYPE html>
<html lang = "en">
<head>
<meta charset = "utf-8" >
<title> OPERATION </title >
</head >
<body>
<h2>Sequence</h2>
<p>{seq}</p>
<h2>Operation</h2>
<p>{operation}</p>
<h2>Result</h2>
<p>{result}</p>
<br>
<br>
<a href="/">Main page</a>
</body>
</html>"""
else:
contents = Path('error.html').read_text()
# 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
elif cmd1 == "INFO":
seq0 = Seq(cmd2)
response = ""
termcolor.cprint("INFO", 'green')
response += f'Sequence: {cmd2}'
response += f"Total length: {seq0.len()}"
for element in bases:
resp = round(seq0.count_base(element) * (100 / seq0.len()), 2)
response += f'{element}: {seq0.count_base(element)} ( {resp}% ) \n'
elif cmd1 == "COMP":
seq0 = Seq(cmd2)
termcolor.cprint("COMP", 'green')
response = seq0.complement()
elif cmd1 == "REV":
seq0 = Seq(cmd2)
termcolor.cprint("REV", 'green')
response = seq0.reverse()
elif cmd1 == "GENE":
seq0 = Seq("")
seq0 = seq0.read_fasta(folder + cmd2 + '.txt')
termcolor.cprint("GENE", 'green')
response = seq0.reverse()
print(response)
cs.send(response.encode())
cs.close()
from P1.Seq1 import Seq
folder = "../Session-04/"
filenames = ["U5", "ADA", "FRAT1", "FXN", "RNU6_269P"]
all_bases = ["A", "C", "G", "T"]
print("-----|Practice 1 , Exercise 10 |------")
for filename in filenames:
s0 = Seq()
s0.read_fasta(folder + filename)
dictionary = s0.count()
list_values = list(dictionary.values())
maximum = max(list_values)
print(
f"Gene {filename}: Most frequent Base: {all_bases[list_values.index(maximum)]}"
)
from P1.Seq1 import Seq
def print_result(i, sequence):
print("Sequence" + str(i) + ": (Lenght: " + str(sequence.len()) + ") " + str(sequence))
print("Bases:", sequence.count())
print("Rev:", sequence.reverse())
print("Comp:", sequence.complement())
PROJECT_PATH = "../P1/PROJECT/"
print("----- | Practice 1, Exercise 9 | ------")
s1 = Seq()
s1.read_fasta(PROJECT_PATH + "U5.txt")
print_result("", s1)