def gene(cs, argument):
print_colored("GENE", "yellow")
gene = Seq()
folder = "../P0/Sequences/"
gene.read_fasta(folder + argument + ".txt")
cs.send(str(gene).encode())
return gene
def rev(argument, cs):
print_colored("REV", "yellow")
argument = Seq(argument.replace('"', ""))
rev_seq = str(Seq.seq_reverse(argument))
response = f"""Initial sequence: {argument}
Reverse sequence: {rev_seq}"""
cs.send(response.encode())
print(response)
def comp(argument, cs):
print_colored("COMP", "yellow")
argument = Seq(argument.replace('"', ""))
comp_seq = str(Seq.seq_complement(argument))
response = f"""Initial sequence: {argument}
Complement sequence: {comp_seq}"""
cs.send(response.encode())
print(response)
def gene(seq_name):
PATH = "./Sequences/" + seq_name + ".txt"
s1 = Seq()
# s1.read_fasta(PATH)
context = {"gene_name": seq_name, "gene_contents": s1.read_fasta(PATH)}
contents = read_template_html_file("./html/gene.html").render(
context=context)
return contents
def gene(argument, cs):
print_colored("GENE", "yellow")
sequence = Seq(Seq.seq_read_fasta_2("./Sequences/" + argument.replace('"', "") + ".txt"))
comp_seq = str(Seq.seq_complement(sequence))
rev_seq = str(Seq.seq_reverse(sequence))
colored_response = f"""Initial sequence: {termcolor.colored(sequence, "red")}
Complement sequence: {termcolor.colored(comp_seq, "green")}
Reverse sequence: {termcolor.colored(rev_seq, "blue")}"""
response = f"""Initial sequence: {sequence}
Complement sequence: {comp_seq}
Reverse sequence: {rev_seq}"""
cs.send(response.encode())
print(response)
def info(argument, cs):
print_colored("INFO", "yellow")
list_bases = ["A", "C", "T", "G"]
argument = Seq(argument.replace('"', ""))
t_l = Seq.len(argument)
count_list = []
percentage_list = []
for base in list_bases:
count_list.append(argument.count_base_1(base))
for i in range(0, len(count_list)):
percentage_list.append(count_list[i] * 100 / t_l)
response = f"""Sequence: {argument}
Total length: {t_l}
A: {count_list[0]} ({percentage_list[0]}%)
C: {count_list[1]} ({percentage_list[0]}%)
G: {count_list[2]} ({percentage_list[0]}%)
T: {count_list[3]} ({percentage_list[0]}%)"""
cs.send(response.encode())
print(response)
def info(argument):
sequence = Seq(argument)
seq_len = sequence.len()
bases_count = list(sequence.count().values())
bases_percent = list(sequence.base_percentage().values())
bases = list(sequence.count().keys())
msg = f"Sequence: {sequence}\n" \
f"Total length: {seq_len}\n"
for i in range(len(bases)):
msg += f"{bases[i]}: {bases_count[i]} ({bases_percent[i]}%)\n"
return msg
def info(cs, argument):
print_colored("INFO", "yellow")
sequence = Seq(argument)
seq_len = sequence.len()
bases_count = list(sequence.count().values())
bases_percent = list(sequence.base_percentage().values())
bases = list(sequence.count().keys())
msg = f"Sequence: {sequence}\n" \
f"Total length: {seq_len}\n"
for i in range(len(bases)):
msg += f"{bases[i]}: {bases_count[i]} ({bases_percent[i]}%)\n"
cs.send(str(msg).encode())
return msg
def rev(cs, argument):
print_colored("REV", "yellow")
sequence = Seq(argument)
rev = sequence.reverse()
cs.send(str(rev).encode())
return rev
def comp(cs, argument):
print_colored("COMP", "yellow")
sequence = Seq(argument)
comp = sequence.complement()
cs.send(str(comp).encode())
return comp
def process_client(cs):
# reading the message from the client
msg = cs.recv(2048).decode("utf-8")
msg = msg.split('\n')
se = Seq(msg[0])
response = ""
ac = "ACTG"
if msg[0] == "asdf":
response += "EMPTY"
cs.send(str.encode(response))
nmbr = 0
for n in msg[0].upper():
if n in ac:
nmbr += 1
if nmbr == len(msg[0]):
response += "OK!"
response += "\n"
elif nmbr != len(msg[0]):
response += "ERROR"
cs.send(str.encode(response))
for i in msg[1:]:
if i == 'len':
response += se.len()
elif i == 'complement':
response += se.complement().strbases
elif i == 'reverse':
response += se.reversed().strbases
elif i == 'countA':
response += se.counting('A')
elif i == 'countC':
response += se.counting('C')
elif i == 'countT':
response += se.counting('T')
elif i == 'countG':
response += se.counting('G')
elif i == 'percA':
response += se.percentage('A')
elif i == 'percC':
response += se.percentage('C')
elif i == 'percT':
response += se.percentage('T')
elif i == 'percG':
response += se.percentage('G')
# Sending the message back to the client
# because we are an eco server
cs.send(str.encode(response))
cs.close()
def rev(argument):
sequence = Seq(argument)
rev = sequence.reverse()
return rev
def comp(argument):
sequence = Seq(argument)
comp = sequence.complement()
return comp