def info_func(s):
s = Seq(s)
l = s.length()
ac = s.count_base("A")
tc = s.count_base("T")
cc = s.count_base("C")
gc = s.count_base("G")
resp = f"""Sequence: {s}
Total length: {l}
A: {ac} ({round((ac/l)*100)})%
C: {cc} ({round((cc/l)*100)})%
T: {tc} ({round((tc/l)*100)})%
G: {gc} ({round((gc/l)*100)})%"""
return resp
r1 = conn.getresponse()
print(f"Response received!: {r1.status} {r1.reason}\n")
data1 = r1.read().decode()
gene = json.loads(data1)
termcolor.cprint(f"Gene: ", "yellow", end="")
print(f"{namegene}")
termcolor.cprint("Description: ", "yellow", end="")
print(f"{gene['desc']}"
) #see esembl page for desc and seq (especial functions)
sequence = gene['seq']
s = Seq(sequence)
l = s.length()
ac = s.count_base("A")
tc = s.count_base("T")
cc = s.count_base("C")
gc = s.count_base("G")
termcolor.cprint("Total length: ", "yellow", end="")
print(l)
resp = f"""
A: {ac} ({round((ac / l) * 100)})%
C: {cc} ({round((cc / l) * 100)})%
T: {tc} ({round((tc / l) * 100)})%
G: {gc} ({round((gc / l) * 100)})%"""
print(resp)
dictionary = s.count()
listvalues = list(dictionary.values())
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')
# Analize the request line
req_line = self.requestline.split(' ')
# Get the path. It always start with the / symbol
path = req_line[1]
# Read the arguments
arguments = path.split('?')
# Get the verb. It is the first argument
verb = arguments[0]
# -- Content type header
# -- Both, the error and the main page are in HTML
contents = Path('Error.html').read_text()
error_code = 404
if verb == "/":
# Open the form1.html file
# Read the index from the file
contents = Path('form-4.html').read_text()
error_code = 200
elif verb == "/ping":
contents ="""
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>PING</title>
</head>
<body style="background-color: lightblue;">
<h1> PING OK! </h1>
<p> The SEQ 2 server is running </p>
<hr>
<a href="/">MAIN PAGE</a>
</body>
</html>
"""
error_code = 200
elif verb == "/get":
# -- Get the argument to the right of the ? symbol
pair = arguments[1]
# -- Get all the pairs name = value
pairs = pair.split('&')
# -- Get the two elements: name and value
name, value = pairs[0].split("=")
n_v = int(value)
seq = sequences[n_v]
# -- Generate the html code
contents = f"""
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>GET</title>
</head>
<body style="background-color: lightyellow;">
<h2>Sequence number {n_v}</h2>
<p> {seq} </p>
<a href="/">Main page</a>
</body>
</html>
"""
error_code = 200
elif verb == "/gene":
# -- Get the argument to the right of the ? symbol
pair = arguments[1]
# -- Get all the pairs name = value
pairs = pair.split('&')
# -- Get the two elements: name and value
name, gene = pairs[0].split("=")
s = Seq()
s1 = Seq(s.read_fasta(folder + gene + txt))
gene_info = str(s1)
# -- Generate the html code
contents = f"""
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>GENE</title>
</head>
<body style="background-color: magenta;">
<h2>Gene: {gene}</h2>
<textarea readdonly rows = "20" cols = "60"> {gene_info}</textarea>
<br>
<a href="/">Main page</a>
</body>
</html>
"""
error_code = 200
elif verb == "/operate":
# -- Get the argument to the right of the ? symbol
pair = arguments[1]
# -- Get all the pairs name = value
pairs = pair.split('&')
# -- Get the two elements: name and value
name, sequence = pairs[0].split("=")
name, operation = pairs[1].split("=")
s = Seq(sequence)
if operation == "info":
l = s.length()
ac = s.count_base("A")
tc = s.count_base("T")
cc = s.count_base("C")
gc = s.count_base("G")
resp = f"""
<p>Total length: {l}</p>
<p>A: {ac} ({round((ac / l) * 100)})%</p>
<p>C: {cc} ({round((cc / l) * 100)})%</p>
<p>T: {tc} ({round((tc / l) * 100)})%</p>
<p>G: {gc} ({round((gc / l) * 100)})%</p>"""
elif operation == "rev":
resp = s.seq_reverse()
else:
resp = s.seq_complement()
contents = f"""
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>OPERATION</title>
</head>
<body style="background-color: lightgreen;">
<h2>Sequence:</h2>
<p> {sequence} </p>
<h2> Operation: </h2>
<p> {operation}</p>
<h2> Result: </h2>
<p> {resp} </p>
<br>
<a href="/">Main page</a>
</body>
</html>
"""
error_code = 200
# Generating the response message
self.send_response(error_code) # -- 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