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GPDToBED.cpp
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#include <iostream>
#include <string>
#include <sstream>
#include <fstream>
#include <vector>
#include <cstdlib>
#include <algorithm>
#include <boost/algorithm/string/split.hpp>
#include <boost/algorithm/string.hpp>
#include <boost/lexical_cast.hpp>
using namespace std;
using namespace boost;
struct GPD {
string gname;
string tname;
string chro;
string strand;
int start;
int end;
int cstart;
int cend;
int nblock;
vector<int> vec_exon_start;
vector<int> vec_exon_end;
};
void BuildGPDFromString (string &str, GPD &gpd) {
vector<string> vec_temp;
boost::split(vec_temp, str, boost::is_any_of("\t"));
gpd.gname = vec_temp[0];
gpd.tname = vec_temp[1];
int L = vec_temp[2].length();
gpd.chro = vec_temp[2];
gpd.strand = vec_temp[3];
gpd.start = lexical_cast<int>(vec_temp[4]);
gpd.end = lexical_cast<int>(vec_temp[5]);
gpd.cstart = lexical_cast<int>(vec_temp[6]);
gpd.cend = lexical_cast<int>(vec_temp[7]);
gpd.nblock = lexical_cast<int>(vec_temp[8]);
vector<string> vec1;
boost::split(vec1, vec_temp[9], boost::is_any_of(","));
for(int i = 0; i < vec1.size() - 1; ++i) (gpd.vec_exon_start).push_back(lexical_cast<int>(vec1[i]));
vector<string> vec2;
boost::split(vec2, vec_temp[10], boost::is_any_of(","));
for(int i = 0; i < vec2.size() - 1; ++i) (gpd.vec_exon_end).push_back(lexical_cast<int>(vec2[i]));
}
void DisplayGPD (GPD gpd) {
cout << gpd.gname << endl;
cout << gpd.tname << endl;
cout << gpd.chro << endl;
cout << gpd.strand << endl;
cout << gpd.start << endl;
cout << gpd.end << endl;
cout << gpd.cstart << endl;
cout << gpd.cend << endl;
cout << gpd.nblock << endl;
for(int i = 0; i < gpd.vec_exon_start.size(); ++i) cout << gpd.vec_exon_start[i] << '\t';
cout << endl;
for(int i = 0; i < gpd.vec_exon_end.size(); ++i) cout << gpd.vec_exon_end[i] << '\t';
cout << endl;
}
void ChangeToBEDExon (ofstream &ouf, GPD gpd) {
for(int i = 0; i < gpd.nblock; ++i){
int left = gpd.vec_exon_start[i] - 100 * (i == 0);
if(left < 1) left = 1;
int right = gpd.vec_exon_end[i] + 100 * (i == gpd.nblock - 1);
ouf << gpd.chro << '\t' << left << '\t' << right << '\t' << gpd.tname << "_exon_" << i + 1 << "\t0\t" << gpd.strand << endl;
}
}
/*void ChangeToBEDIntron (ofstream &ouf, GPD gpd) {
if(gpd.nblock > 1){
for(int i = 1; i < gpd.nblock; ++i){
ouf << gpd.chro << '\t' << gpd.vec_exon_end[i - 1] + 1 << '\t' << gpd.vec_exon_start[i] - 1 << '\t' << gpd.tname << "_intron_" << i << "\t0\t" << gpd.strand << endl;
}
}
}*/
int main (int argc, char **argv) {
ifstream inf(argv[1]);
ofstream exon_ouf(argv[2], ios::trunc);
//ofstream intron_ouf(argv[3], ios::trunc);
while(inf){
string strInput;
getline(inf, strInput);
if(strInput.length() > 0){
GPD gpd;
BuildGPDFromString(strInput, gpd);
ChangeToBEDExon(exon_ouf, gpd);
//ChangeToBEDIntron(intron_ouf, gpd);
}
}
inf.close(); exon_ouf.close(); //intron_ouf.close();
return 0;
}