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//
// input file to DNA original array
// send array to function to make uppercase
// make a compliment of DNA
// change
// (T -> A, A -> T, G -> C, C -> G)
// send compliment to to fucntion transcrition
// change
// (T -> A, A -> U, G -> C, C -> G)
// send transcription to function translation
// use if else to check for start codon
// compare array triplets to codons and change them
// break when stop codon is reached
// output to file
#include <iostream>
#include <fstream>
#include <cstring>
#include <cmath>
using namespace std;
void uppercase(char original[], int& length);
void DNAcompliment(char original[], char compliment[], int& length);
void transcription(char compliment[], char mRNA[], int& length);
bool translation(char mRNA[], char codons[], int& length);
int main(int argc, char *argv[]){
ifstream in_stream;
bool debug = true;
const int N = 82;
int length = 0, nlength = 0;
char DNA_original[N] = {'\0'}, compliment[N] = {'\0'}, mRNA[N] = {'\0'}, amino_acid[N] = {'\0'};
in_stream.open(argv[1]);
if (in_stream.fail())
cout << "File failed to open. \n";
ofstream out_stream(argv[2]);
while (in_stream >> DNA_original) {
length = strlen(DNA_original);
uppercase(DNA_original, length);
if (debug) { cout << "original= " << DNA_original << endl; }
DNAcompliment(DNA_original, compliment, length);
if (debug) { cout << "DNAcompliment= " << DNAcompliment << endl; }
transcription(compliment, mRNA, length);
if (debug) { cout << "Transcription= " << transcription << endl; }
translation(mRNA, amino_acid, length);
if (debug) { cout << "Translation= " << translation << endl; }
out_stream << "strand DNA=" << DNA_original;
out_stream << ", strand mRNA=";
for (int i = 0; i < length; i++){
out_stream << mRNA[i];
}
out_stream << ", amino_acid=";
nlength = strlen(amino_acid);
for (int i = 0; i < nlength; i++){
out_stream << amino_acid[i];
}
out_stream << endl;
DNA_original[N] = '\0';
compliment[N] = '\0';
amino_acid[N] = '\0';
mRNA[N] = '\0';
}
in_stream.close();
out_stream.close();
return 0;
}
void uppercase(char original[], int& length){
for (int i = 0; i < length; i++) {
original[i] = toupper(original[i]);
}
}
void DNAcompliment(char original[], char compliment[], int& length){
for (int i = 0; i < length; i++)
switch (original[i]){
case 'T': compliment[i] = 'A'; break;
case 'A': compliment[i] = 'T'; break;
case 'G': compliment[i] = 'C'; break;
case 'C': compliment[i] = 'G'; break;
default: compliment[i] = '?';
}
}
void transcription(char compliment[], char mRNA[], int& length){
for (int i = 0; i < length; i++)
switch (compliment[i]){
case 'T': compliment[i] = 'A'; break;
case 'A': compliment[i] = 'U'; break;
case 'G': compliment[i] = 'C'; break;
case 'C': compliment[i] = 'G'; break;
default: compliment[i] = '?';
}
}
bool translation(char mRNA[], char amino_acid[], int& length){
bool var = true;
for (int i = 0; i < length; i++){
if (mRNA[i] == 'A' && mRNA[i+1] == 'U' && mRNA[i+2] == 'G'){
for (int i = 3, account = 0; i < length; i+=3, account++){
if (mRNA[i] == 'G' && mRNA[i+1] == 'C' && mRNA[i+2] == 'U'){
amino_acid[account] = 'A';
}
else if (mRNA[i] == 'C' && mRNA[i+1] == 'A' && mRNA[i+2] == 'U'){
amino_acid[account] = 'H';
}
else if (mRNA[i] == 'A' && mRNA[i+1] == 'A' && mRNA[i+2] == 'U'){
amino_acid[account] = 'I';
}
else if (mRNA[i] == 'C' && mRNA[i+1] == 'C' && mRNA[i+2] == 'U'){
amino_acid[account] = 'P';
}
else if (mRNA[i] == 'G' && mRNA[i+1] == 'A' && mRNA[i+2] == 'U'){
amino_acid[account] = 'D';
}
else if (mRNA[i] == 'A' && mRNA[i+1] == 'A' && mRNA[i+2] == 'U'){
amino_acid[account] = 'N';
}
else if (mRNA[i] == 'G' && mRNA[i+1] == 'A' && mRNA[i+2] == 'A'){
amino_acid[account] = 'E';
}
else if (mRNA[i] == 'U' && mRNA[i+1] == 'C' && mRNA[i+2] == 'U'){
amino_acid[account] = 'S';
}
else if (mRNA[i] == 'U' && mRNA[i+1] == 'G' && mRNA[i+2] == 'U'){
amino_acid[account] = 'S';
}
else if (mRNA[i] == 'U' && mRNA[i+1] == 'G' && mRNA[i+2] == 'A'){
break;
}
else cout << '?';
}
break;
}
}
return (true);
}
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