from seq1 import Seq
# -- Create a Null sequence
seq_1 = Seq()
# -- Create a valid sequence
seq_2 = Seq("ACTGA")
# -- Create an invalid sequence
seq_3 = Seq("Invalid sequence")
print("--Practice 1, Exercise 3--")
print("sequence 1 :", seq_1)
print("sequence 2:", seq_2)
print("sequence 3:", seq_3)
from seq1 import Seq
# -- Create a Null sequence
seq_1 = Seq()
# -- Create a valid sequence
seq_2 = Seq("ACTGA")
# -- Create an invalid sequence
seq_3 = Seq("Invalid sequence")
print("Practice 1, Exercise 8")
BASES = ["A", "G", "T", "C"]
print("Sequence 1:(length: ", seq_1.len(), ")", seq_1)
print("Bases:", seq_1.count())
print("Rev:", seq_1.reverse())
print("Comp:", seq_1.complement())
print("\nSequence 2: (length:", seq_2.len(), ")", seq_2)
print("Bases:", seq_2.count())
print("Rev", seq_2.reverse())
print("Comp:", seq_2.complement())
print("\nSequence 3: (length:", seq_3.len(), ")", seq_3)
print("Bases:", seq_3.count())
print("Rev:", seq_3.reverse())
print("comp:", seq_3.complement())
from Client0 import Client
from seq1 import Seq
PRACTICE = 2
EXERCISE = 5
print(f"-----| Practice {PRACTICE}, Exercise {EXERCISE} |------")
# -- Parameters
IP = "192.168.1.41"
PORT = 8081
FOLDER = "../session-04/"
filename = FOLDER + 'U5.txt'
s = Seq()
s.read_fasta(filename)
# -- Create a client object
c = Client(IP, PORT)
c.debug_talk("Sending the U5 Gene to the server..")
c.debug_talk(s)
from seq1 import Seq
# -- Create a Null sequence
seq_1 = Seq()
# -- Create a valid sequence
seq_2 = Seq("ACTGA")
# -- Create an invalid sequence
seq_3 = Seq("Invalid sequence")
print("Practice 1, Exercise 6")
BASES = ["A", "G", "T", "C"]
print("Sequence 1:(length: ", seq_1.len(), ")", seq_1)
print("Bases:", seq_1.count())
print("\nSequence 2: (length:", seq_2.len(), ")", seq_2)
print("Bases:", seq_2.count())
print("\nSequence 3: (length:", seq_3.len(), ")", seq_3)
print("Bases:", seq_3.count())
from seq1 import Seq
print("-- Practice 1, Exercise 9 --")
folder = "../session-04/"
FILENAME =folder + "U5.txt"
# -- Create a Null sequence
s = Seq()
# -- Initialize the null seq with the given file in fasta format
s.read_fasta(FILENAME)
print(f"Sequence : (Length: {s.len()}) {s}")
print("\tBases: ", s.count())
print("\tRev: ", s.reverse())
print("\tComp:", s.complement())
from seq1 import Seq
# -- Create a Null sequence
seq_1 = Seq()
# -- Create a valid sequence
seq_2 = Seq("ACTGA")
# -- Create an invalid sequence
seq_3 = Seq("Invalid sequence")
print("Practice 1, Exercise 5")
BASES = ["A", "G", "T","C"]
print("Sequence 1:(length: ", seq_1.len(),")",seq_1)
for i in BASES:
print(i + ":", seq_1.count_base(i), end=", ")
print("\nSequence 2: (length:", seq_2.len(), ")", seq_2)
for i in BASES:
print(i + ":", seq_2.count_base(i), end= ",")
print("\nSequence 3: (length:", seq_3.len(), ")", seq_3)
for i in BASES:
print(i+ ":", seq_3.count_base(i), end=",")
from seq1 import Seq
print("--Practice 1, Exercise 1--")
SEQUENCE = Seq("ACTGA")
print("Sequence 1: (length :" , SEQUENCE.len(), ")", SEQUENCE )
from seq1 import Seq
# -- Creating a Null sequence
seq_1 = Seq()
# -- Creating a valid sequence
seq_2 = Seq("TATAC")
print("--Practice 1, Exercise 2--")
print("Sequence 1:", seq_1)
print("Sequence 2:", seq_2)
from seq1 import Seq
# -- Create a Null sequence
seq_1 = Seq()
# -- Create a valid sequence
seq_2 = Seq("ACTGA")
# -- Create an invalid sequence
seq_3 = Seq("Invalid sequence")
print("-- Practice 1, Exercise 4 --")
print("Sequence 1:(length: ", seq_1.len(), ")", seq_1)
print("Sequence 2: (length:", seq_2.len(), ")", seq_2)
print("Sequence 3; (length:", seq_3.len(), ")", seq_3)
# -- into a human-redeable string
msg = msg_raw.decode()
argument_command = msg[msg.find(" ") + 1:]
response = "ERROR"
# PING command
if "PING" in msg:
response = "OK!\n"
# GET command
elif "GET" in msg:
response = seq_list[int(argument_command)]
# INFO command
elif "INFO" in msg:
seq_info = Seq(argument_command)
count_bases_string = ""
for base, count in seq_info.count().items():
s_base = str(base) + ": " + str(count) + " (" + str(
round(count / seq_info.len() * 100, 2)) + "%)" + "\n"
count_bases_string += s_base
response = ("Sequence: " + str(seq_info) + "\n" +
"Total length: " + str(seq_info.len()) + "\n" +
count_bases_string)
elif "COMP" in msg:
seq_comp = Seq(argument_command)
response = seq_comp.complement() + "\n"
elif "REV" in msg: