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PolishGPD.cpp
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PolishGPD.cpp
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#include <iostream>
#include <string>
#include <sstream>
#include <fstream>
#include <vector>
#include <map>
#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;
//string cstart;
//string 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 DisplayGPDInLine (GPD gpd) {
cout << gpd.gname << '\t';
cout << gpd.tname << '\t';
cout << gpd.chro << '\t';
cout << gpd.strand << '\t';
cout << gpd.start << '\t';
cout << gpd.end << '\t';
cout << "*" << '\t';
cout << "*" << '\t';
cout << gpd.nblock << '\t';
for(int i = 0; i < gpd.vec_exon_start.size(); ++i) cout << gpd.vec_exon_start[i] << ',';
cout << '\t';
for(int i = 0; i < gpd.vec_exon_end.size(); ++i) cout << gpd.vec_exon_end[i] << ',';
cout << endl;
}
map<string,GPD> BuildGPDMap (ifstream &inf) {
map<string,GPD> gpd_map;
while(inf){
string strInput;
getline(inf, strInput);
if(strInput.length() > 0){
GPD gpd;
BuildGPDFromString(strInput, gpd);
gpd_map[gpd.tname] = gpd;
}
}
return gpd_map;
}
int main (int argc, char **argv) {
ifstream gpdinf(argv[1]);
ifstream inf(argv[2]);
map<string,GPD> gpd_map = BuildGPDMap(gpdinf);
map<string,GPD>::iterator it;
while(inf){
string strInput;
getline(inf, strInput);
if(strInput.length() > 0){
vector<string> vec;
split(vec, strInput, is_any_of("\t"));
string read_name = vec[0];
int tss = lexical_cast<int>(vec[5]);
int polya = lexical_cast<int>(vec[7]);
it = gpd_map.find(read_name);
if(it == gpd_map.end()){
cout << "Alert" << endl;
continue;
}
if((it->second).strand == "+"){
(it->second).vec_exon_start[0] = tss;
(it->second).vec_exon_end[(it->second).nblock-1] = polya;
}
else{
(it->second).vec_exon_start[0] = polya;
(it->second).vec_exon_end[(it->second).nblock-1] = tss;
}
DisplayGPDInLine(it->second);
}
}
gpdinf.close(); inf.close();
return 0;
}