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From page 34 of the textbook:

Modify your program so it is more flexible, allowing the input sequences to contain either lowercase or uppercase letters by simply converting all input sequences to uppercase.

From Dr. Miller's feedback, I also need to test how the program handles template strands.

We need to be able to handle DNA sequences in all four states (coding/template and 3'/5'). This has to be something we can handle through the commandline interface using argparse.

From page 34 of the textbook:

This program could just as well be used to compare two DNA sequences. Modify it so the user can choose whether to compare the DNA sequences directly, translate them before comparing, or both.

From page 34 of the textbook:

Modify your program so that stop codons are included in your codon table (if you haven't already included them). Then devise a way to represent a stop when you translate your DNA sequences and to show this nonsense mutation in your mutation list. Test your program with mutation A from the Test Your Understanding section.

Dr. Miller says "[t]here is no point in comparing" these two sequences.

From Dr. Miller's email:

You have just shown that Mary is not a CF carrier. Perhaps your translation is wrong but maybe it will work better if you remember that Mary’s alleles are NOT in 3’ order.

Here's the command:

christopher@ArcticThunder:~/Mutation-Detector$ python Mutation_Detector.py ~/Downloads/Homework\ 2\ Test\ Data/mutantA.fasta ~/Downloads/Homework\ 2\ Test\ Data/mutantB.fasta

And the traceback:

Traceback (most recent call last):
  File "Mutation_Detector.py", line 56, in <module>
    sequence_comparison.compare_amino_1letter(aminoseq1, aminoseq2, args.outfile)
  File "/home/christopher/Mutation-Detector/sequence_comparison.py", line 28, in compare_amino_1letter
    if seq1[i] != seq2[i]:
IndexError: string index out of range

All test runs need to be repeated for the second submission, since the output has now changed with the addition of nonsense mutation support.

From page 34 of the textbook:

Write a program in the language used in your course to implement the above pseudocode. Test your program initially with the short wild-type sequence from the Test Your Understanding section and a missense mutant version of this sequence. You can also test it with the mutant B sequence from Test Your Understanding. Be sure you know the expected results for these test sequences before you run this program. Then test it with your wild-type CTFR sequence and Mary's alleles (not Tom's - this is discussed in the On Your Own Project that follows) from the Web Exploration section.

my_fastaA.fasta and my_fastaB.fasta both contain uracil, despite being 5' coding DNA sequences. Re-run the tests on these sequences.

From page 34 of the textbook:

Allow the user to input either the template or nontemplate strand of DNA or an mRNA sequence, in either 5'→3' or 3'→5' orientation. Request input form the user to identify the sequences, and then manipulate them as necessary to produce an mRNA sequence before translating. Use the short sequence in Test Your Understanding to generate test sequences for your program.