EDIT_1_HW_BioInfa

import random
from termcolor import colored


def makeDNA(countAT, countCG):
    countA = int(countAT / 2)
    countT = int(countAT / 2)
    countC = int(countCG / 2)
    countG = int(countCG / 2)
    strA = ''.join(random.choice("A") for _ in range(countA))
    strT = ''.join(random.choice("T") for _ in range(countT))
    strC = ''.join(random.choice("C") for _ in range(countC))
    strG = ''.join(random.choice("G") for _ in range(countG))
    listDNA = list(strA + strT + strC + strG)
    random.shuffle(listDNA)
    DNA = ''.join(listDNA)
    return DNA


def reverseDNA(strDNA):
    rDNA = ""
    for i in strDNA:
        if i == "A":
            rDNA = rDNA + "T"
        elif i == "T":
            rDNA = rDNA + "A"
        if i == "G":
            rDNA = rDNA + "C"
        elif i == "C":
            rDNA = rDNA + "G"
    return rDNA[::-1]


def orf_it_up(strDNA, k):
    listORF = []
    listAmino = []
    start_codon = "ATG"
    stop_codons = ["TAA", "TAG", "TGA"]

    gencode = {
        'ATA': 'I', 'ATC': 'I', 'ATT': 'I', 'ATG': 'M',
        'ACA': 'T', 'ACC': 'T', 'ACG': 'T', 'ACT': 'T',
        'AAC': 'N', 'AAT': 'N', 'AAA': 'K', 'AAG': 'K',
        'AGC': 'S', 'AGT': 'S', 'AGA': 'R', 'AGG': 'R',
        'CTA': 'L', 'CTC': 'L', 'CTG': 'L', 'CTT': 'L',
        'CCA': 'P', 'CCC': 'P', 'CCG': 'P', 'CCT': 'P',
        'CAC': 'H', 'CAT': 'H', 'CAA': 'Q', 'CAG': 'Q',
        'CGA': 'R', 'CGC': 'R', 'CGG': 'R', 'CGT': 'R',
        'GTA': 'V', 'GTC': 'V', 'GTG': 'V', 'GTT': 'V',
        'GCA': 'A', 'GCC': 'A', 'GCG': 'A', 'GCT': 'A',
        'GAC': 'D', 'GAT': 'D', 'GAA': 'E', 'GAG': 'E',
        'GGA': 'G', 'GGC': 'G', 'GGG': 'G', 'GGT': 'G',
        'TCA': 'S', 'TCC': 'S', 'TCG': 'S', 'TCT': 'S',
        'TTC': 'F', 'TTT': 'F', 'TTA': 'L', 'TTG': 'L',
        'TAC': 'Y', 'TAT': 'Y', 'TAA': '*', 'TAG': '*',
        'TGC': 'C', 'TGT': 'C', 'TGA': '*', 'TGG': 'W'}

    position = 0
    orf = ""
    aas = ""
    while position < len(strDNA) - 2:
        current_codon = strDNA[position:position + 3]

        if current_codon == start_codon:

            while not (current_codon in stop_codons) and (current_codon in gencode):
                orf += current_codon
                aas += gencode[current_codon]
                position += 3
                current_codon = strDNA[position:position + 3]
            orf += current_codon
            if current_codon in stop_codons:
                aas += '*'

            if len(orf) >= 30 and len(orf) % 3 == 0:
                listORF.append(orf)
                listAmino.append(aas)

            orf = ""
            aas = ""

        position += 3
    if listORF:
        strDNA1  = strDNA
        maxL = max(listORF, key=len)
        print(maxL)
        print(strDNA1.rindex(maxL)+k, '-', strDNA1.index(maxL)+len(maxL)+k-1)
        print(max(listAmino, key=len))
    else:
        print(colored('Nothing', 'red'))


if __name__ == '__main__':
    print("Enter length of DNA dnaSize=")
    dnaSize = int(input())
    print("Enter content percentage of CG percentCG= ")
    percentGC = int(input())
    percentAT = 100 - percentGC
    countGC = int((dnaSize * percentGC) / 100)
    countAT = int((dnaSize * percentAT) / 100)
    strDNA = makeDNA(countAT, countGC)
    print('DNA=', strDNA)
    rDNA = reverseDNA(strDNA)
    print('rDNA=', rDNA)
    phi_genome = strDNA
    phi_genome_plus1 = strDNA[1:]
    phi_genome_plus2 = strDNA[2:]
    phi_genome_reversed = rDNA  # reversed string
    phi_genome_reversed_plus1 = rDNA[1:]
    phi_genome_reversed_plus2 = rDNA[2:]

    all_genomes = [phi_genome, phi_genome_plus1, phi_genome_plus2, phi_genome_reversed, phi_genome_reversed_plus1,
                   phi_genome_reversed_plus2]

    print(colored('On direct stand', 'blue'))
    print(colored('On 1st frame', 'green'))
    orf_it_up(all_genomes[0], 1 )
    print(colored('On 2nd frame', 'green'))
    orf_it_up(all_genomes[1], 2)
    print(colored('On 3rd frame', 'green'))
    orf_it_up(all_genomes[2], 3)
    print(colored('On reverse stand', 'blue'))
    print(colored('On 1st frame', 'green'))
    orf_it_up(all_genomes[3], 1)
    print(colored('On 2nd frame', 'green'))
    orf_it_up(all_genomes[4], 2)
    print(colored('On 3rd frame', 'green'))
    orf_it_up(all_genomes[5], 3)