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#include <algorithm>
#include <fstream>
#include <iostream>
#include <string>
using namespace std;
// This function transforms the DNA
char replace(char c)
{
if (c == 'A') return 'T';
if (c == 'T') return 'A';
if (c == 'G') return 'C';
if (c == 'C') return 'G';
return c;
}
//This function counts how many times the string "TTTT" appears
int Count( const string & str,
const string & obj ) {
int n = 0;
ofstream outfile;
string ::size_type pos = 0;
while( (pos = obj.find( str, pos ))
!= string::npos ) {
outfile<<pos<<endl;//This should output 1st index it on the same file
n++;
pos += str.size();
outfile<<pos<<endl;//This should output last index on the same file
}
return n;
}
int main()
{
ifstream infile("dna.txt");
if (infile.fail())
{ cout<<"Error File cannot be open!"<<endl;
exit(1);
}
ofstream outfile("dna2.txt");//Output file on main function
if (outfile.fail())
{ cout<<"Error File cannot be open!"<<endl;
exit(1);
}
string dna;
size_t nPos = dna.find( "TTTT", 0 );
while (infile >> dna) {
float gc;
float content;
float gccontent;
transform(dna.begin(), dna.end(), dna.begin(), ::replace);
dna=string(dna.rbegin(), dna.rend());
outfile << dna << endl;
int n = Count( "TTTT", dna );//Where the function is declared
outfile << n << endl;//Outputs how many times the string "TTTT" appears
size_t g=count(dna.begin(), dna.end(), 'G');
size_t c=count(dna.begin(), dna.end(), 'C');
size_t t=count(dna.begin(), dna.end(), 'T');
size_t a=count(dna.begin(), dna.end(), 'A');
gc=c+g;
content=gc/dna.length();
gccontent=content*100;
outfile<<"The GC content for this strand is at "<<gccontent<<"%"<<endl;
}
system ("pause");
}
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