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
00034 cout <<
"\nComplement Bases are:\n";
00035
gnBaseSpec* gpbs = gnseq.
GetSpec();
00036 gpbs->
SetReverseComplement(
true);
00037
00038
00039
gnFASSource::Write(gnseq, outfilename);
00040
00041
00042
00043 cout <<
"All done. RevComp is in " << outfilename <<
"\n";
00044
char bubba[50];
00045 cin >> bubba;
00046 }