dna_sequencing.py

"""A cell's genetic composition determines what it does or the structure it has. An activated gene produces
a messenger RNA which in turn is converted to a peptide in the ribosomal complex. The nucleotide sequence on the gene
 can allow us to predict the sequence of amino acid in peptides that is obtained from that gene.
 The Template or antisense is the strand that gets transcribed i.e complimentary to mRNA
 while the coding and sense refer to the strand that is NOT transcribed i.e similar to mRNA"""

"""This program help to determine the amino acid sequence in a gene whether the user has mRNA, sense DNA
 or antisense DNA sequence. Moreover, it can also help in determining the portion of the gene that proteins are obtained
 """

peptide_dict = { 
        'AUA':'Ile', 'AUC':'Ile', 'AUU':'Ile', 'AUG':'Met', 
        'ACA':'Thr', 'ACC':'Thr', 'ACG':'Thr', 'ACU':'Thr', 
        'AAC':'Asn', 'AAU':'Asn', 'AAA':'Lys', 'AAG':'Lys', 
        'AGC':'Ser', 'AGU':'Ser', 'AGA':'Arg', 'AGG':'Arg',                  
        'CUA':'Leu', 'CUC':'Leu', 'CUG':'Leu', 'CUU':'Leu', 
        'CCA':'Pro', 'CCC':'Pro', 'CCG':'Pro', 'CCU':'Pro', 
        'CAC':'His', 'CAU':'His', 'CAA':'Gln', 'CAG':'Gln', 
        'CGA':'Arg', 'CGC':'Arg', 'CGG':'Arg', 'CGU':'Arg', 
        'GUA':'Val', 'GUC':'Val', 'GUG':'Val', 'GUU':'Val', 
        'GCA':'Ala', 'GCC':'Ala', 'GCG':'Ala', 'GCU':'Ala', 
        'GAC':'Asp', 'GAU':'Asp', 'GAA':'Glu', 'GAG':'Glu', 
        'GGA':'Gly', 'GGC':'Gly', 'GGG':'Gly', 'GGU':'Gly', 
        'UCA':'Ser', 'UCC':'Ser', 'UCG':'Ser', 'UCU':'Ser', 
        'UUC':'Phe', 'UUU':'Phe', 'UUA':'Leu', 'UUG':'Leu', 
        'UAC':'Tyr', 'UAU':'Tyr', 'UAA':'*', 'UAG':'*', 
        'UGC':'Cys', 'UGU':'Cys', 'UGA':'*', 'UGG':'Trp', 
    } 

def main():
    print(mrna_to_amino_acid("AUGACUAAGUAA"))
    enter1 = int(input("Please enter 1 if you have the Coding or Sense DNA sequence. \n"
                       "Enter 2 for the Template or Antisense DNA sequence. \n"
                       "Enter 3 for Messenger RNA sequence: "))
    if enter1 == 1:
        c_dna_to_mrna()
    elif enter1 == 2:
        t_dna_to_c_dna()
    elif enter1 == 3:
        mrna_to_peptide()
    else:
        print("Please enter the appropriate number")


def t_dna_to_c_dna():
    """
       This coverts the DNA base to the corresponding RNA base
       T -> P -> A
       A -> Q -> T
       C -> R -> G
       G -> S -> C
    """

    t_dna = str(input("Please enter the Template DNA sequence: "))
    t_dna = t_dna.upper()
      
    c_dna = ""

    for i in t_dna:
        if (i == 'A'):
            c_dna = c_dna + 'T'
        elif (i == 'T'):
            c_dna = c_dna + 'A'
        elif (i == 'C'):
            c_dna = c_dna + 'G'
        elif (i == 'G'):
            c_dna = c_dna + 'C'
    
    return c_dna


def c_dna_to_mrna():
    """ This program converts coding DNA sequence to messenger RNA sequence """
    c_dna = str(input("Please enter the Coding DNA sequence: "))
    c_dna = c_dna.upper()
    mrna = dna_to_mrna(c_dna)
    print("The messenger RNA sequence is " + str(mrna) + ".")
    mrna_to_amino_acid(mrna)
    # print("The Peptide sequence is " + str(amino_acid) + ".")


def dna_to_mrna(c_dna):
    """
    This coverts the DNA base to the corresponding RNA base
    T -> A
    A -> U
    C -> G
    G -> C
    """
    
    mrna = ""

    for i in c_dna:
        if (i == 'A'):
            mrna = mrna + 'U'
        elif (i == 'T'):
            mrna = mrna + 'A'
        elif (i == 'C'):
            mrna = mrna + 'G'
        elif (i == 'G'):
            mrna = mrna + 'C'
    
    return mrna


def mrna_to_peptide():
    """ This program converts to messenger RNA sequence to the corresponding peptide"""
    merna = str(input("Please enter the Messenger RNA sequence: "))
    mrna = merna.upper()
    mrna_to_amino_acid(mrna)


def mrna_to_amino_acid(mrna):

    # i = 0
    # while 
    # codone = mran[current 3]
    # if codone is start === start recording
    # if codone is stop and recording is ongoing, stop and print the recorded amino acid
    # if codone is not start and stop
    # else continue looping and increment i by 3
    # if at end of mran exit the loop and print amino acid

    # AUGACUAAGUAA
    i: int = 0
    continueLooping = True
    record = "" # our current amino acid/peptide
    recording = False # to track if we've hit a start codone
    mranLength = len(mrna) # the length of the mran

    while continueLooping == True:
        if (i + 3 <= mranLength): # check to see if we're at the end of the mran
            condone = mrna[i: i + 3] # pick the current mran by selecting 3 characters from the index, i

            if (condone == "AUG"): # if codone is a start codone
                recording = True  # we set the recording state to true
                record = peptide_dict[condone] # get amino acid from dictionary using codone as the key, then add to the record
            elif (peptide_dict[condone] == "*" and recording == True): # if codone is a stop codone and we are in recording state
                recording = False # set the recording state to False (because we are no longer recording)
                print("Peptide sequence recorded: " + record) # print our current recorded amino acid
                record = "" # clear our record for new amino acids to be encountered
            else: # if codone is neither start nor stop
                if (recording): # have we encountered a start codone? if yes,
                    record = record + "-" + peptide_dict[condone] # get amino acid from dictionary using codone as the key, then add to the record

            i = i + 3 # increment our index by 3
        else: # we are at the end of the mrna
            if (recording == True): # if we are still recording at this time
                print(record) # print whatever we have recorded
            break # then we exit the loop

if __name__ == '__main__':
    main()