TestRevComp.cpp Source File

00001 #include "gn/gnSourceFactory.h"
00002 #include "gn/gnFASSource.h"
00003 #include "gn/gnDNXSource.h"
00004 #include "gn/gnSEQSource.h"
00005 #include "gn/gnSequence.h"
00006 #include <iostream>
00007 #include <fstream>
00008 
00009 #include "gn/gnFilter.h"
00010 
00011 int main( int32 argc, char* argv[])
00012 {
00013 
00014         argc; argv;
00015 
00016         string filename;
00017         cout << "Enter a filename to read bases from.\n";
00018         cin >> filename;
00019         cout << "Opening " + filename + "\n";
00020         gnSequence gnseq, smallseq;
00021         if(gnseq.LoadSource(filename))
00022                 cout << "Sequence has " << gnseq.length() << " base pairs.\n";
00023         
00024         smallseq = gnseq.subseq(3836480, 10);
00025         cout << smallseq;
00026         string dump;
00027         cin >> dump;
00028 
00029         cout << "Give a file name to output reverse complement data: ";
00030         string outfilename;
00031         cin >> outfilename;
00032         cout << "Bases are:\n";
00033 //      cout << gpseq;
00034         cout << "\nComplement Bases are:\n";
00035         gnBaseSpec* gpbs = gnseq.GetSpec();
00036         gpbs->SetReverseComplement(true);
00037 //      cout << gpseq << "\n";
00038         
00039         gnFASSource::Write(gnseq, outfilename);
00040 //      gnGBKSource::Write(gpbs, "testfile.seq");
00041 //      gnDNXSource::Write(gpbs, "testfile.dnx");
00042         
00043         cout << "All done.  RevComp is in " << outfilename << "\n";
00044         char bubba[50];
00045         cin >> bubba;
00046 }