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test-o-matic.cpp

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#include "gn/gnFASSource.h"
#include "gn/gnSequence.h"
#include "gn/gnTranslator.h"
#include "gn/gnStringSpec.h"
#include <fstream>
int main( int argc, char* argv[] )
{
        gnSequence erwinia_junk;
        gnSequence pruned_bush;
        string sequence_name = "mouse_small.fas";
        string output_sequence = "mouse_filt.fas";
//      cout << "Enter the name of the sequence file you want contig info on.\n";
//      cin >> sequence_name;
        try{
                erwinia_junk.LoadSource( sequence_name );
                for(uint32 contigI = 0; contigI < erwinia_junk.contigListSize(); contigI++){
                        cout << erwinia_junk.contigName( contigI ) << '\t' << erwinia_junk.contigLength( contigI ) << '\n';
                        if( erwinia_junk.contigLength( contigI ) > 1000 )
                                pruned_bush += erwinia_junk.contig( contigI );
                }
                gnFASSource::Write(pruned_bush, output_sequence);
        }catch(gnException& gne){
                cout << gne << "\n";
        }
/*
        ifstream gbk1("cpneuJ.gbk");
        ifstream gbk2("test_rc.gbk");

        uint32 badline = 0;
        char buf[30000];
        char buf2[30000];
        while(gbk1.good() && gbk2.good()){
                gbk1.getline(buf, 30000);
                gbk2.getline(buf2, 30000);
                if(strcmp(buf, buf2)){
                        cout << "mismatched line: " << badline << "\n";
                        cout << buf << endl << buf2 << endl;
                        cout << "Length 1: " << strlen(buf) << "   Length 2: " << strlen(buf2) << endl;
                        cin >> buf;
                }
                badline++;
        }
*/
/*      gnStringSpec s("");
        cout <<s.GetLength()<<endl;
        
        gnSequence t = "ACTATATA";
        if(t == string("TATATA")){
                cout << "ASDFASDFSADF";
        }*/
}
/*      // define a string to store the sequence file name
        
        string filename;
        string nseq,pseq;       
        // define a gnSequence to store the sequence
        gnSequence file_sequence;
        gnSequence prot_trans;
        
        //nseq = "BXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXX";
        //nseq = "WSTYYYBBB";
    //nseq="ATGCUXGCNGGGTATGAATEQILPFP";
        //nseq="ATGGTXAGCGGNTAR";       
        cout<<nseq<<" (original)---->  \n";
        gnSequence aSeq(nseq);
        cout<<aSeq<<" (gnSequence)----> \n";

    gnTranslator::ProteinDNAConverter->ToProtein(nseq);
    
    cout << nseq << '\n';;
  
  
  
  
  //  prot_trans.append(nseq);
        // output the first ten bases of the sequence
//      cout << prot_trans.subseq(1,10);

        return 0;
        
}

/*#include "gn/gnSequence.h"
#include <iostream>
#include <string>
#include "gn/gnTranslator.h"
#include "gn/gnFASSource.h"

int main(int argc, char* argv[]){
        gnSequence gps;
        string seq_filename;
        string out_filename;
        
        /* Get the name of the dnx file to convert to FastA /
        cout << "Debug-o-matic!\n";
        cout << "Please give the name of the fof to test: ";
        cin >> seq_filename;
        
        gps.LoadSource(seq_filename);

        cout << "Output filename: ";
        cin >> out_filename;
        gnFASSource::Write(gps, out_filename);
        
        return 0;       

}*/

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