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I figured it out. I wasn't spelling the things right in the command prompt (because of the hard coding)

and for those of you who helped me with the original model of this code i fixed that version...

What do you mean? I am passing a file title "uniprotFile" into the program under the command line if that is what you mean. Could you elaborate on your question more

SO this is for a homework assignment. And if you look at my previous posts you will see that I am not asking for help and I have done this work by myself. That being said I have one single error left...