initial

LICENSE

+MIT License
+
+Copyright (c) 2019 Arthur Zopellaro
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

cert.pem

+-----BEGIN CERTIFICATE-----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+-----END CERTIFICATE-----

client.py

+from socket import create_connection
+from ssl import SSLContext, PROTOCOL_TLS_CLIENT
+import sys
+
+hostname='example.org'
+ip = '10.1.1.53'
+port = 3000
+context = SSLContext(PROTOCOL_TLS_CLIENT)
+context.load_verify_locations('cert.pem')
+FORMAT = 'ASCII'
+HEADER = 64
+DISCONNECT_MESSAGE = "x"
+
+#this variable is for handling entry from file or user
+TAKING_CODONS_INPUT = True
+
+#port from start args or get input
+if len(sys.argv) < 3:
+    PORT = int(input("please define the port you would like to connect to"))
+else:
+    PORT = int(sys.argv[2])
+
+#ip from start args or get input
+if len(sys.argv) < 2:
+    SERVER = input("please define the server you would like to connect to")
+else:
+    SERVER = sys.argv[1]
+
+#send by file or prompt input
+CODONS = None
+if len(sys.argv) == 4:
+    infile = open(sys.argv[3], 'r')
+    CODONS = infile.read()
+    print("here are the codons")
+    print(CODONS)
+    TAKING_CODONS_INPUT = False
+
+#handles just the sending of the codon data, no validity checking
+def send(msg, tls):
+    print("sending " + msg)
+    message = msg.encode(FORMAT)
+    msg_length = len(message)
+    #calculate length of string and send as header, instead of set START RNA message
+    send_length = str(msg_length).encode(FORMAT)
+    send_length += b' ' * (HEADER - len(send_length))
+    tls.sendall(send_length)
+    tls.sendall(message)
+    response = tls.recv(2048).decode(FORMAT)
+    if is_valid_codon(response) and msg != "x":
+        print(response)
+
+#put codons in a dictionary and use it for checking validity
+def init_codon_dict(codon_info_csv):
+    CODONS = dict()
+    f = open(codon_info_csv)
+    for line in f:
+        line = line.strip('\n')
+        (codon, protein) = line.split(",")
+        CODONS[codon] = protein
+    return CODONS
+
+VALID_CODONS = init_codon_dict("codon-aminoacid.csv")
+
+#check if the data entered is valid before sending and on receipt
+def is_valid_codon(codon):
+    print(codon)
+    valid = True
+    codons_length = len(codon)
+    print("length:", codons_length)
+    #no empties
+    if codons_length == 0:
+        valid = False
+        print("Error - length of zero")
+    if codons_length%3 != 0:
+        valid = False
+        print("Error - not divisible by 3")
+    if valid:
+        for x in range(int(codons_length/3)):
+            start = x
+            end = x+3
+            if codon[start:end] not in VALID_CODONS:
+                valid = False
+                print("error - not valid codon")
+    if valid:
+        print("passed codon check")
+        return True
+    else:
+        print("failed codon check")
+        return False
+
+
+with create_connection((ip, port)) as client:
+    with context.wrap_socket(client, server_hostname=hostname) as tls:
+        print(f'Using {tls.version()}\n')
+        while TAKING_CODONS_INPUT:
+            CODONS = input("Enter codons to optimize, or enter X to disconnect")
+            CODONS = CODONS.upper()
+            if (is_valid_codon(CODONS)):
+                send(CODONS, tls)
+            else:
+                send(DISCONNECT_MESSAGE, tls)
+                TAKING_CODONS_INPUT = False
+

codon-aminoacid.csv

+AAA,K
+AAC,N
+AAG,K
+AAT,N
+ACA,T
+ACC,T
+ACG,T
+ACT,T
+AGA,R
+AGC,S
+AGG,R
+AGT,S
+ATA,I
+ATC,I
+ATG,M
+ATT,I
+CAA,Q
+CAC,H
+CAG,Q
+CAT,H
+CCA,P
+CCC,P
+CCG,P
+CCT,P
+CGA,R
+CGC,R
+CGG,R
+CGT,R
+CTA,L
+CTC,L
+CTG,L
+CTT,L
+GAA,E
+GAC,D
+GAG,E
+GAT,D
+GCA,A
+GCC,A
+GCG,A
+GCT,A
+GGA,G
+GGC,G
+GGG,G
+GGT,G
+GTA,V
+GTC,V
+GTG,V
+GTT,V
+TAA,s
+TAC,Y
+TAG,s
+TAT,Y
+TCA,S
+TCC,S
+TCG,S
+TCT,S
+TGA,s
+TGC,C
+TGG,W
+TGT,C
+TTA,L
+TTC,F
+TTG,L
+TTT,F

key.pem

+-----BEGIN PRIVATE KEY-----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+-----END PRIVATE KEY-----

key1.pem

+-----BEGIN PRIVATE KEY-----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+-----END PRIVATE KEY-----

server.py

+from socket import socket, AF_INET, SOCK_STREAM, gethostname,  gethostbyname
+from ssl import SSLContext, PROTOCOL_TLS_SERVER
+import threading
+import sys
+
+SERVER = gethostbyname(gethostname())
+port = int(sys.argv[1])
+context = SSLContext(PROTOCOL_TLS_SERVER)
+context.load_cert_chain('cert.pem', 'key.pem')
+
+HEADER = 64
+FORMAT = "ASCII"
+
+
+
+def is_valid_codon(codon):
+    if codon in optimals:
+        print(codon + " this codon is valid")
+        return True
+    else:
+        print(codon + " this codon is NOT valid")
+        return False
+
+
+#need to score codons based on their efficiency (G or C is better)
+def score_codon(codon):
+    score = 0
+    for letter in codon:
+        if letter == "G" or letter == "C":
+            score+=1
+    return score
+
+#create a data store as a dictionary, where we can look up the codon to return
+def init_codon_dict(codon_info_csv):
+    OPTIMAL_CODONS = dict()
+    CODON_AS_KEY = dict()
+    f = open(codon_info_csv)
+    for line in f:
+        line = line.strip('\n')
+        (codon, protein) = line.split(",")
+        if protein in OPTIMAL_CODONS:
+            if score_codon(codon) > score_codon(OPTIMAL_CODONS[protein]):
+                OPTIMAL_CODONS[protein] = codon
+        else:
+            OPTIMAL_CODONS[protein] = codon
+        CODON_AS_KEY[codon] = protein
+    for codon in CODON_AS_KEY:
+        CODON_AS_KEY[codon] = OPTIMAL_CODONS[CODON_AS_KEY[codon]]
+    return CODON_AS_KEY
+
+optimals = init_codon_dict("codon-aminoacid.csv")
+
+#this is where the ip address would get validated. 
+#I have not implemented any validation, so just return true for everyone.
+
+def is_whitelisted_ip(ip_address):
+    return True
+
+def handle_client(conn, addr):
+    connected = True
+    print(f'Connected by {addr}\n')
+    print("checking IP address")
+
+    if is_whitelisted_ip(addr):
+        print("IP validated")
+    else:
+        print("Unauthorised user... disconnecting...")
+        connected = False
+
+    while connected:
+        msg_length = conn.recv(HEADER).decode(FORMAT)
+        if msg_length:
+            msg_length = int(msg_length)
+            msg = conn.recv(msg_length).decode(FORMAT)
+            print(msg)
+            if msg == "x":
+                connected = False
+            else:
+                if msg_length%3 != 0:
+                    connected = False
+                else:
+                    codons_all_valid = True
+                    msg = msg.upper()
+                    #validate codons: length of string should be multiple of three, all codons should be valid
+                    startpoint = 0
+                    endpoint = 3
+                    result = ""
+                    while endpoint <= msg_length:
+                        print(endpoint, " ? ", msg_length)
+                        checking = msg[startpoint:endpoint]
+                        if is_valid_codon(checking):
+                            print(checking)
+                            result += optimals[checking]
+                        else:
+                            connected = False
+                            codons_all_valid = False
+                            print("should exit here")
+                        
+                        startpoint+=3
+                        endpoint+=3
+                    print("finished checking all codons")
+                    if codons_all_valid:
+                        conn.send(result.encode(FORMAT))
+                    else:
+                        connected = False
+        else:
+            connected = False
+    conn.close()
+
+
+
+with socket(AF_INET, SOCK_STREAM) as server:
+    server.bind((SERVER, port))
+    server.listen()
+    with context.wrap_socket(server, server_side=True) as tls:
+        connection, address = tls.accept()
+        thread = threading.Thread(target=handle_client, args=(connection, address))
+        thread.start()
+
+
+

startClient.sh

+#!/bin/sh
+python client.py $1 $2 $3
\ No newline at end of file

startServer.sh

+#!/bin/sh
+python server.py $1
\ No newline at end of file

test.txt

+atg
\ No newline at end of file