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#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libGenome/gnSourceFactory.h"
#include "libGenome/gnFASSource.h"
#include "libGenome/gnSequence.h"
#include <iostream>
#include "libGenome/gnFilter.h"
#include "libGenome/gnStringTools.h"
#include "libGenome/gnFastTranslator.h"
int main( int32 argc, char* argv[])
{
argc; argv;
try{
string filename;
cout << "Enter a filename to read bases from.\n";
cin >> filename;
cout << "Opening " + filename + "\n";
gnSequence gpseq, gnsubseq;
// string pathname = filename;
// standarizePathString( pathname );
// pathname = getPathString( pathname );
// gnSourceFactory * msf = gnSourceFactory::GetSourceFactory();
// msf->AddPath( pathname );
gpseq.LoadSource(filename);
cout << "Length " << gpseq.length() << " in " << gpseq.contigListSize() << " contigs\n";
string pretrans, posttrans, posttrans2;
const gnTranslator* dna2pro_good = gnTranslator::DNAProteinTranslator();
const gnFastTranslator* dna2pro_fast = gnFastTranslator::DNAProteinTranslator();
pretrans = gpseq.ToString();
posttrans = pretrans;
posttrans2 = pretrans;
cout << "Doing correct translation:\n";
dna2pro_good->Filter(posttrans);
cout << "done\n";
gnsubseq = posttrans;
gnFASSource::Write(gnsubseq, "profile_good.fas");
// posttrans = pretrans;
cout << "Doing fast translation:\n";
dna2pro_fast->Filter(posttrans2);
cout << "done\n";
gnsubseq = posttrans2;
gnFASSource::Write(gnsubseq, "profile_fast.fas");
cout << "base pairs 8 thru 68 are: \n";
cout << gpseq.subseq(8, 60) << "\n";
for(uint32 i=0; i < 15; i++){
try{
cout << "Contig " << i << " length " << gpseq.contig(i).length() << "\n";
}catch(gnException& gne){
cout << gne;
}
}
cout << gpseq.subseq(1000000, 10);
cin >> filename;
gnSeqI midpoint = gpseq.length() / 2;
gnSequence seqA = gpseq.subseq(1, midpoint);
gnSequence seqB = gpseq.subseq(1 + midpoint, gpseq.length() - midpoint);
cout << "Splitting " << gpseq.length() << " to " << seqA.length() << " and " << seqB.length() << "\n";
cin >> filename;
gnsubseq = gpseq.subseq(5, 10);
cout << "subseq len: " << gnsubseq.length() << "\n";
cout << "subseq: " << gnsubseq << "\n";
gnSeqC* buf = new gnSeqC[gpseq.length()];
gpseq.ToArray(buf, gpseq.length());
cout << "Give a file name to output data: ";
string outfilename;
cin >> outfilename;
gnFASSource::Write(gpseq, outfilename);
/* gnSequence new_seq = gpseq.contig(3);
cout << new_seq;
new_seq += gpseq.contig(3);
new_seq += gpseq.contig(2);
new_seq += gpseq.contig(1);
cout << new_seq;
gnFASSource::Write(new_seq, outfilename);
*/ cout << "All done. Contigs 3, 2, 1 are in " << outfilename << "\n";
char bubba[50];
cin >> bubba;
}catch(gnException& gne){
cout << gne;
string reality_bites;
cin >> reality_bites;
}
}
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