testSourceSeq.cpp Source File

00001 #include <iostream>
00002 #include "gn/gnSequence.h"
00003 #include <fstream>
00004 
00005 #include "gn/gnFilter.h"
00006 #include "gn/gnFASSource.h"
00007 
00008 int32 main( int32 argc, char* argv[])
00009 {
00010         argc; argv;
00011         gnSequence gps;
00012         
00013         string filename;
00014         cout << "Enter a filename to compute a base composition.\n";
00015         cin >> filename;
00016         cout << "Opening " + filename + "\n";
00017         gps.LoadSource(filename);
00018         cout << "Genome Length: " << gps.length() << " in " << gps.contigListLength() << " contigs\n";
00019         
00020         cout << "Give a file name to output composition data: ";
00021         string outfilename;
00022         cin >> outfilename;
00023         ofstream outfile(outfilename.c_str(), ios::out);
00024         outfile << "Contig_Name A_count C_count G_count T_count\n";
00025 
00026         ofstream ambig("ambigs.txt", ios::out);
00027         
00028         gnSeqI a_total = 0, c_total = 0, g_total = 0, t_total = 0, ambiguities = 0;
00029         for(int contigI=0; contigI < gps.contigListLength(); contigI++){
00030                 gnSeqI seqLength = gps.contig(contigI).length();
00031                 gnSeqC *bases = new gnSeqC[seqLength];
00032                 gps.contig(contigI).ToArray(bases, seqLength);
00033                 string contigName = gps.contigName(contigI);
00034 
00035                 gnSeqI a = 0, c = 0, g = 0, t = 0;
00036                 for(int i=0; i < seqLength; i++){
00037                         if((bases[i] == 'a')||(bases[i] == 'A'))
00038                                 a++;
00039                         else if((bases[i] == 'c')||(bases[i] == 'C'))
00040                                 c++;
00041                         else if((bases[i] == 'g')||(bases[i] == 'G'))
00042                                 g++;
00043                         else if((bases[i] == 't')||(bases[i] == 'T'))
00044                                 t++;
00045                         else{
00046                                 ambiguities++;
00047                                 ambig << bases[i];
00048                         }
00049                 }
00050                 delete[] bases;
00051                 outfile << contigName << "      " << a << "     " << c << "     " << g << "     " << t << "\n";
00052                 a_total += a; c_total += c; g_total += g; t_total += t;
00053         }
00054         outfile.close();
00055         ambig.close();
00056         cout << "Enter a file for me to write to: ";
00057         cin >> outfilename;
00058         gnFASSource::Write(gps, outfilename);
00059         cout << "A: " << a_total << "\nC: " << c_total << "\nG: " << g_total << "\nT: " << t_total << "\n";
00060         cout << "Ambiguities: " << ambiguities << "\n";
00061         cout << "For a total of: " << a_total + c_total + g_total + t_total + ambiguities << "\n";
00062         cout << "Base comp. completed.  Results are in " << outfilename << "\n";
00063         char bubba[50];
00064         cin >> bubba;
00065 }