I need help on how to read a string sequence(genetic sequence) frame by frame in C++. I have found all the start codons(ATG) and stop codons(TAG, TGA, TAA) all in ascending order. Next step is to find a start(ATG) that ends with either (TAG, TGA, TAA) and use substr to get the potential gene. I have some code started on doing the frames but I am not sure on how to continue. The frames basically follows this:

int main()

{

string fileName;

cout

cin >> fileName;

fstream fileStream(fileName, ios::in);

if (fileStream.fail())

{

cout

exit(1);

}

cout

char dummyChar = '>';

fileStream >> dummyChar;

string dummyString;

getline(fileStream, dummyString);

cout

cout

string genome,fasta;

int length;

float cTotal, gTotal, gcTotal, gcPercent;

while (!fileStream.eof())

{

getline(fileStream,genome); // Saves the line in genome.

fasta += genome;//appending each line to string fasta

}

length = fasta.length();

cTotal = countGenes(fasta, 'C'); // Acquires total amount of "C" genes

gTotal = countGenes(fasta, 'G'); // Acquires total amount of "G" genes

gcTotal = (gTotal + cTotal); // Total amount of both "C" and "G" genes

gcPercent = ((gcTotal / fasta.size()) * 100); // Total percentage of both "C" and "G" genes out of all genes

cout

vector startCodonPositions;

startCodon(fasta, startCodonPositions, "ATG");

cout

vector stopCodonPositions;

startCodon(fasta, stopCodonPositions, "TAG");

startCodon(fasta, stopCodonPositions, "TGA");

startCodon(fasta, stopCodonPositions, "TAA");

cout

// sorting the stop codons by acending order

sort(stopCodonPositions.begin(), stopCodonPositions.end(), sortAcend);

// printing the stop codons in ascending order

// for (int i : stopCodonPositions)

// {

// cout

// }

//string currentGene = fasta.substr(startCodonPositions + 3, stopCodonPositions - (startCodonPositions + 3));

// Frame 1

int pos = 0;

while (2 + pos

{

if(startCodonPositions[0], startCodonPositions[1], startCodonPositions[2])

{

pos += 3;

}

++pos;

}

// Frame 2

pos = 1;

while ( 2 + pos

{

if(startCodonPositions[0], startCodonPositions[1], startCodonPositions[2])

{

//is ATG ...

pos += 3;

}

++pos;

}

// Frame 3

pos = 2;

while ( 2 + pos

{

if(startCodonPositions[0], startCodonPositions[1], startCodonPositions[2])

{

//is ATG ...

pos += 3;

}

++pos;

}

fileStream.close();

//NC_003988_1.fna

return 0;

}

My gene.cpp

int countGenes(string str, char gene)

{

int count = 0, length = 7374; // Counter and string length

for (unsigned i = 0; i

{

if (str[i] == gene)

count++;

}

// See how many times the character repeats

int geneRepetition = length / str.size();

count = (count * geneRepetition);

/* If the length is not a multiple of the string size

check for the remaining repeating characters. */

for (unsigned i = 0; i

{

if (str[i] == gene)

count++;

}

return count;

}

void startCodon(string str, vector& vec, string codon)

{

size_t start = 0;

bool search = true;

while (search)

{

start = str.find(codon, start);

if (start == string::npos)

break;

vec.push_back(start);

start++;

}

}

bool sortAcend(int i, int j)

{

return i

}

Part of the csv file:

>NC_003988.1 Simian enterovirus A, complete genome GAGTGTTCCCACCCAACAGGCCCACTGGGTGTTGTACTCTGGTATTACGGTACCTTTGTACGCCTATTTT ATTTCCCCCCCCTTTTTGAAACTTAGAAGTTAATAATAAACACGCTCACTAGGTGCACTACATCCAGTAG TGTAATGAGCAAGCACTTCTGTCTYCCCCGGGAGGGATATATGGTACGCTGTGCAAACGGCGGAAATTAA TCCTACCGTTAACCGCCCACCTACTCCGAGAAGCCTAGTACCTAATTGGATTTATCAATGGAGTTGCGCT CAGCAGGTGACCCTGACCTGCCAGCTCCGGCTGATGGACCTGGGCTTTCCCCACAGGCGACTGTGGCCCA GGTCGCGTGGCGGCCGGCCCACCCCCCTGGGTGGGACGCCTTGATAATGACAAGGTGGGAAGAGCCTATT GGGCTAGCTGGTTTCCTCCGGCCTCCTGAATGCGGCTAACCTTAACCCCAGAGCATATGGTAGCAACCCA GCTACTAGTATGTCATAATGCGTAAGTCTGGGATGGGACCGACTACTTTGGAGAGTCCGTGTTTCTATTG TTTCTTTAATCAATCTTATGGTGACAATTTATAGTGCCCTGAGTATTGATTGGTTGTTGCTTTTGACAAT TATTGAGACATCACATAGACATAATGGGAGCTCAAGTAAGCAGGCAAACGTCTGGTGCGCATGACACCCG GATACGGGCTGAACAGGGCGCAAACATTCATTATACTAATATCAATTATTATAGAGATGCAGCTAGCAAT GCAGCAAGCAAAATGGACTATTCCCAGGATCCGGACAAGTTCACGAAACCAGTACTTGATGCTATAACTG AACCATTACCCACGCTGAAGTCCCCTAGTGCTGAGGCATGTGGGTACAGCGACCGAGTTGCACAACTGAC AATTGGCAATTCCACTATCACTACTCAGGAAGCCGCCAATGTGGTGGTCGCATATGGACAATGGCCTGAA TATTTAGATTCGAAGGATGCAACTGCCGTGGATAAGCCCACACAGCCCGATGTAGCCTCAAATAGATTTT ACACTCTTAAGACAGTGTCTTGGGAGAAGAGTTCAACTGGCTGGTATTGGAAATTCTCGGATTGTCTGGC TTCTGTTGGATTATTTGGACAGAATGTACAGTATCATTATTTAGGCCGTTATGGGTTAGCGGTTCATGTG CAATGTAATGCTTCAAAATTTCATCAGGGCACTCTACTGGTCTTAGCAATACCAGAATGGGAGATTGGGG TGTCTAATGCTGATAGGGCATCCTTTAATCTAACAAACCCCGATAAGAACGGGCATACTATGACTGGTCA AGAAGCTTATTGCTTACATAATGGGACTAACATCCATTCTTCACTGGTATTTCCACATCAATTCATCAAT CTTAGGACAAACAATTGTGCTACGTTAGTCTTGCCCTATGTGGGAGCAACACCACTGGACACACCGATCA AGCATAATGTTTGGTCATTGGTAGTAATACCGGTGGTCCCGTTGGATTACACCACTGGTGCAACTACACA AGTGCCTATAACAATAACAATGGCTCCAATGGCGTGCGAGTTTAACGGACTGCGCAATGCCATCACCCAA GGGCTGCCAGTACTCAATACACCCGGCTCTGGGCAGTTTGTGACTACAGATAATTTCCAATCACCAAACT TGATTCCAAATTTTGATGTGACACAAGTCTTTAATAGTCCAGGTGAAATTATTAATTTACAGCAGTATGT CCAGATTGAGGGCATTATGGAAATCAATAATGTAGCAAGTGCAAATAATTTGGAGAGAATTCGCATTCCA ATATCAGTCCAGAGTGGAATTGATGAGATGTTATTTGCAATCAACTGCAACCCAGGAACAGCCCAGGAGT TTAGACGCACACCCCTGGGAGATGTGTGTAGGTATTATACACAGTGGTCAGGTAGCATACAAATTACATT TACATTTTGTGGTTCATTTATGACAACAGGAAAATTATTAATTTGCTACACCCCTCCGGGTGGTCGAGTA CCACAAAATAGAGAGGAGGCAATGCTAGGGACTAATGTGATCTGGGATTTTGGTTTACAATCCAGCGTTA CGCTGAACATACCGTGGATAAGTGGAGCCCATTTTAGAAACACTTCTGTTAATGTCGATGGTTTTGATAA CACAGGGTATGTATCTGCTTGGTTTCAAACGAACATGGTAGTTCCTCCCGATGCTCCAACGACTGCTTAT ATATTGGCTTTTACATCAGCCAAGGATGATTTCTCGATGCGCTTGTTGCGGGATACAGCAGAGATTTCGC AAGACGGATTTCTGCAAGGACCAATAGATCAAGCAATAGAAAAAGTAATCACTGATGTAGTGTCTGACAC GCGTGAGTCTAGTAGTGACTTTAGCATTGGGGCTGTTCCAGCATTGAATGCGGTGGAAACTGGAGCCACT TCGCAAGCTAGTGTTGAGTCCACCATTGAGACGCGGGCCGTGCAGAATCGTCATCGCACTTCTGAGATGA GCGTGGAAAGCTTTTTGGGCCGCTCTAGTTTAGTAACTCGCTTTACCATTAATAATGGAGGAACAAATAA TGCCACGAAGTTTCGTAACTGGAAAATAAACTTAAAGGAAGTGGTGCAGCTGCGGCGTAAATTAGAAATG TTTACTTACGTGCGCTTTGATCTTGAGGTGACTATAGTGGCTGTGAATTTGACTGGAAATGGAGGAGTGC GTTACATGTACCAAGCAATGTACTGCCCCCCAGGTGCCCCCCTCCCCACCAATGCTGATCAATATCTGTG GCAATCCTCGACAAATCCCTCCATAATCGGAGCAGTTGGTGAAGTCCCAGGCAGAGTATCAGTGCCTTTT GTGTCAAATGCTAATATGTATGCCACCTTTTATGATGGATATCCATCCTTTGGAAGCATAAATGGACAGG GAAATGGCTCTGATTACGGTGCATTCATACCAAATGATATGGGTACATTGTGTTTCCGATTACTCAATAT CTTTAATAATGGTCCACAAATTCAATTTAGAGTGTTCATGAAACCCAAGCATGTACGAGTATGGTGCCCA

Thank you.

GTALGA CA A LAJ GA A A Frame 1 STOP bin GTAJGACAAJ ATG A A A Frame 2 GTATGACA ATALGA A A Frame 3 Mec STOP Start codon's position ensures that this frame is chosen GTALGA CA A LAJ GA A A Frame 1 STOP bin GTAJGACAAJ ATG A A A Frame 2 GTATGACA ATALGA A A Frame 3 Mec STOP Start codon's position ensures that this frame is chosen