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#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include <iostream>
#include "libGenome/gnSequence.h"
#include <fstream>
#include "libGenome/gnFilter.h"
#include "libGenome/gnFASSource.h"
int32 main( int32 argc, char* argv[])
{
argc; argv;
gnSequence gps;
string filename;
cout << "Enter a filename to compute a base composition.\n";
cin >> filename;
cout << "Opening " + filename + "\n";
gps.LoadSource(filename);
cout << "Genome Length: " << gps.length() << " in " << gps.contigListLength() << " contigs\n";
cout << "Give a file name to output composition data: ";
string outfilename;
cin >> outfilename;
ofstream outfile(outfilename.c_str(), ios::out);
outfile << "Contig_Name A_count C_count G_count T_count\n";
ofstream ambig("ambigs.txt", ios::out);
gnSeqI a_total = 0, c_total = 0, g_total = 0, t_total = 0, ambiguities = 0;
for(int contigI=0; contigI < gps.contigListLength(); contigI++){
gnSeqI seqLength = gps.contig(contigI).length();
gnSeqC *bases = new gnSeqC[seqLength];
gps.contig(contigI).ToArray(bases, seqLength);
string contigName = gps.contigName(contigI);
gnSeqI a = 0, c = 0, g = 0, t = 0;
for(int i=0; i < seqLength; i++){
if((bases[i] == 'a')||(bases[i] == 'A'))
a++;
else if((bases[i] == 'c')||(bases[i] == 'C'))
c++;
else if((bases[i] == 'g')||(bases[i] == 'G'))
g++;
else if((bases[i] == 't')||(bases[i] == 'T'))
t++;
else{
ambiguities++;
ambig << bases[i];
}
}
delete[] bases;
outfile << contigName << " " << a << " " << c << " " << g << " " << t << "\n";
a_total += a; c_total += c; g_total += g; t_total += t;
}
outfile.close();
ambig.close();
cout << "Enter a file for me to write to: ";
cin >> outfilename;
gnFASSource::Write(gps, outfilename);
cout << "A: " << a_total << "\nC: " << c_total << "\nG: " << g_total << "\nT: " << t_total << "\n";
cout << "Ambiguities: " << ambiguities << "\n";
cout << "For a total of: " << a_total + c_total + g_total + t_total + ambiguities << "\n";
cout << "Base comp. completed. Results are in " << outfilename << "\n";
char bubba[50];
cin >> bubba;
}
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