To automate transfer, you need SSH keys setup without any username/passphrase.
And if your transferring between Linux machines disregard all puttygen instructions. That's for putty on Windows.
You say you "received a text file which looks like a key file", which suggests you communicating with someone who administers the remote server?
I'd suggest you communicate with that person, explaining that you want to automate the file transfer and need an SSH key pair setup without any passphrase.
If you have a shell account on the remote server (that gives you write-access to the location where the files are to be stored) then you could set it up yourself, but I think you should first have a chat with whoever is on the other end
