COSC540-Project Socket Programming Solved

In this assignment, you will be converting input virus RNA to an optimised form that is likely to create a better vaccine. Your task is to use TCP sockets to create a client process that sends unoptimised RNA to a server, which replies with optimised RNA. The protocol that your solution must implement is described below.

Background Information
It is strongly recommended you read Bert Hubert's post Reverse Engineering the source code of the BioNTech/Pfizer SARS-CoV-2 Vaccine for relevant background information.

The basic idea is that vaccines can be developed by slightly modifying some RNA from a virus. Nature groups three nucleotides into a codon which can be represented as a group of three G, C, A, or T characters. Thus, there are 64=43 possible codons. Each codon is converted into an amino acid when processed by a cell to fold into a protein. But there are only 20 different amino acids. This means a given amino acid may be able to be encoded by multiple different codons.

For this assignment, you must implement a set of optimisation rules that take a string of RNA as input and return an optimised version.

Optimisation Rules
To determine your optimisation rules, you can use details of how RNA from the COVID-19 virus S protein has been modified to create the extremely efficient BioNTech/Pfizer SARS-CoV-2 Vaccine S protein.

It is not acceptable to simply return the input RNA as the output. Your rules must make some attempt to optimise the input while ensuring that the associated amino acids for each codon are identical in the output. For this purpose, you are provided with codonaminoacid.csv which specifies the amino acid associated with each codon.

As a starting point, it is generally the case that a higher number of G and/or C characters improves the efficiency of an mRNA vaccine. So one approach would be to consider the amino acid generated by a given codon and replace it with the codon with the most G and/or C characters that produces the same amino acid. Please do not feel that you must limit your approach to this guideline.

Protocol
Each message in the protocol consists of a string of ASCII characters followed by the line feed character (ASCII code 10). All messages from the client should be case insensitive. All messages from the server should be uppercase.

An interaction begins with the client sending a START RNA message to the server.

The client then sends a message consisting of G, C, A, and/or T characters to represent codons.

The server then responds with a message consisting of G, C, A, and/or T characters to represent optimised codons.

The client can then either send a new START RNA message (in which case the process repeats) or send a DISCONNECT message.

Once the client has sent a DISCONNECT message, it should exit. Once the server has recieved a DISCONNECT message, it should close the socket and wait for a new connection.

Any other message sent to or from the client is considered an error, and should result in the receiving party dropping the connection. In particular, any RNA string that includes characters outside of G, C, A, or T, or has a length that is not a multiple of three, must be considered an error.

Interface
Your client must be able to be invoked by taking either two or three command line arguments. The first argument is the host name of the server to connect to. The second argument is the port number of the server to connect to. The third, optional, argument is a filename.

If the filename is specified, your client must read the contents of the first line of the file and determine if it is a valid RNA string. If it is not valid, the client should display an appropriate error message and exit. If it is valid, your client must send a START RNA message to the server, followed by the RNA string from the file. The client must then print out the response from the server before sending a DISCONNECT message and exiting.

If no filename is specified, the client should present a menu to the user, allowing them to either send RNA, or to exit.

In the case the user chooses to send RNA, your client must prompt the user to type it in. If the resulting input is not valid, the client should display an appropriate error message. If the input is valid, the client should send this to the server (after a START RNA message) and output the response for the user. In either case, your program must then display the menu again to allow the user to make a new choice.

In the case the user chooses to exit, the client should send a DISCONNECT message to the server if it has sent at least one START RNA message in the session. The client should then exit.

Example
These examples show the protocol only. This is not how interactions with the program should look to the end user (see the Interface section above for these details). Note, also, that the protocol does not include the "Client: " or "Server: " strings - they are just included to make these examples clearer.

Example 1
Client: DISCONNECT
Note that the server drops the connection after an error.

Example 2
Client: START RNA 

Client: atg Server: AUG
Note that the client drops the connection after an error.

Example 3
Client: START RNA 

Client: ATGTTT 

Server: ATGTTC Client: ATGTTT
Note that the server drops the connection after an error.

Example 4
p

Client: START RNA Client: ATGTT
Note that the server drops the connection after an error.

Example 5
Client: START RNA Client: ATGTTT 

Server: ATGTTC 

Client: DISCONNECT
Both client and server complete normally.

Example 6
Client: START RNA 

Client: ATGTTT 

Server: ATGTTC 

Client: START RNA 

Client: TTTATG 

Server: TTCATG 

Client: DISCONNECT
Both client and server complete normally.