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testgpSequence.cpp

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#include "gn/gnSourceFactory.h"
#include "gn/gnFASSource.h"
#include "gn/gnSequence.h"

#include <iostream>

#include "gn/gnFilter.h"
#include "gn/gnStringTools.h"
#include "gn/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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