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#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libGenome/gnFASSource.h"
#include "libGenome/gnSequence.h"
#include "libGenome/gnTranslator.h"
#include "libGenome/gnStringSpec.h"
#include <fstream>
int main( int argc, char* argv[] )
{
gnSequence seq_a, seq_b;
string seq_a_name="styphi.fas";
string seq_b_name="typhi.gbk";
try{
seq_a.LoadSource( seq_a_name );
cout << seq_a_name << '\t' << seq_a.length() << " bp\n";
seq_b.LoadSource( seq_b_name );
cout << seq_b_name << '\t' << seq_b.length() << " bp\n";
}catch(gnException& gne){
cout << gne << "\n";
}
uint len = 50;
uint increment = 1027;
const gnCompare* dna_comp = gnCompare::DNASeqCompare();
for( uint seqI = 1; seqI <= 200000; seqI+= increment ){
string str_a, str_b;
str_a = seq_a.ToString( len, seqI );
str_b = seq_b.ToString( len, seqI );
if( !dna_comp->Contains( str_a, str_b ) ){
cout << str_a << endl << str_b << endl;
seqI -= increment;
}
}
gnSequence seq_in;
string seq_name = "sequin.gbk";
string out_seq = "seqout.gbk";
try{
seq_in.LoadSource( seq_name );
cout << seq_name << '\t' << seq_in.length() << " bp\n";
gnFASSource::Write( seq_in, out_seq );
}catch(gnException& gne){
cout << gne << "\n";
}
/*
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 "libGenome/gnSequence.h"
#include <iostream>
#include <string>
#include "libGenome/gnTranslator.h"
#include "libGenome/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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