'''
According to the central dogma in molecular biology, genetic information in 
biological systems flows from DNA to RNA to protein. To make an mRNA, a part of a 
DNA strand is transcribed. The resulting mRNA has nucleotides complementary to 
the DNA template (note: RNA contains uracil instead of thymine). To produce 
a protein, ribosomes then use codons (sets of 3 nucleotides) on mRNA, which are 
matched with their complementary anticodones on aminoacid-carrying tRNAs. 

Let's go through the process of a) transcription, b) translation, and c) checking 
for mutations in GFP, everyone's favourite marker protein.
'''

'''
Exercise: Pseudocode

For each of the exercises below, start by writing 
pseudocode on a piece of paper. Only once you're done with pseudocode should 
you start working on Python code in VS Code.
'''

'''
Exercise A: GFP transcription

Write a for loop that will take the string GFP_DNA and convert it to the 
complementary RNA sequence. Put it into a string called GFP_RNA.
You do not have to worry about reversing the order.
You may assume the input is all capital letters and contains only A, T, C, 
and G. Return the GFP_RNA string as capital letters as well.
'''

GFP_DNA = "TATTTACGATGAGCAAAGGCGAAGAACTGTTTACCGGCGTGGTGCCGATTCTGGTGGAACTGGATGGC\
    GATGTGAACGGCCATAAATTTAGCGTGAGCGGCGAAGGCGAAGGCGATGCGACCTATGGC\
    AAACTGACCCTGAAATTTATTTGCACCACCGGCAAACTGCCGGTGCCGATGCCGACCCTG\
    GTGACCACCTTTAGCTATGGCGTGCAGTGCTTTAGCCGCTATCCGGATCATGCGAAACAG\
    CATGATTTTTTTAAAAGCGCGATGCCGGAAGGCTATGTGCAGGAACGCACCATTTTTTTT\
    AAAGATGATGGCAACTATAAAACCCGCGCGGAAGTGAAATTTGAAGGCGATACCCTGGTG\
    AACCGCATTGAACTGAAAGGCATTGATTTTAAAGAAGATGGCAACATTCTGGGCCATAAA\
    CTGGAATATAACTATAACAGCCATAACGTGTATATTATGGCGGATAAACTGAAAAACGGC\
    ATTAAAGTGAACTTTAAAATTCGCCATAACATTGAAGATGGCAGCGTGCAGCTGGCGGAT\
    CATTATCAGCAGAACACCCCGATTGGCGATGGCCCGGTGCTGCTGCCGGATAACCATTAT\
    CTGAGCACCCAGAGCGCGCTGAGCAAAGATCCGAACGAAAAACGCGATCATATGGTGCTG\
    CTGGAATTTGTGACCGCGGCGGGCATTACCCATGGCATGGATGAACTGATTAAA"

# Your code here


'''
Exercise B: GFP translation

Write a for loop that will take the output string GFP_RNA from Exercise A and
return the protein code GFP_protein (as capitalized one letter amino acid codes).
You *cannot* assume that the coding sequence is aligned with the start of your 
sequence (i.e., there may be nucleotides in the RNA sequence before the start codon).

Use standard RNA codon table from:
https://en.wikipedia.org/wiki/DNA_and_RNA_codon_tables
'''

# Your code here


'''
Exercise C: GFP mutations

After trying to grow the cells with the protein you just translated, the cells 
were yellow. Turns out the colleagues who gave us the GFP actually gave us a 
GFP variant.

Write a code that gives a list of the amino acid mutations written as XNY, 
where X is the original amino acid, N is the position of the mutation, and 
Y is the new amino acid.
Example: Mutation of K to G at position 55 is written as: K55G 

As input you have:
* GFP_protein - your sequence from the previous section
* GFP_reference - a reference sequence

You may assume the sequences are the same length.
'''

GFP_reference = "MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTL\
    VTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLV\
    NRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLAD\
    HYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK"

# Your code here