mer_to_graph.cpp

Go to the documentation of this file.

#include <iostream>
#include <string>
#include <fstream>
#include <sstream>
#include <vector>
#include <algorithm>
#include <chrono>
#include <functional>
#include <cmath>
#include <map>
#include <tuple>
#include <cstdlib>
#include <cstdio>
#include <limits>
#include <cassert>
 
using namespace std;
 
map<string, int> vertexmap; 
uint32_t numlines;
 
 
void ParseSplint(string locline, uint32_t & vertexid, ofstream & out)
{
    string name;
        string splint;
    std::tuple<string, string, int64_t> triple; 
    
    stringstream ssline(locline);
    ssline >> name;
    assert((name == "SPLINT") || (name == "SPAN") );
    ssline >> splint;
    vector<string> contigpair(2);
    size_t pos = splint.find("<=>");
    contigpair[1] = splint.substr(pos+3);
    contigpair[0] = splint.substr(0, pos);
 
    pos = contigpair[0].find(".");
    contigpair[0] = contigpair[0].substr(0,pos);
    pos = contigpair[1].find(".");
    contigpair[1] = contigpair[1].substr(0,pos);
 
    auto ret = vertexmap.insert(make_pair(contigpair[0], vertexid));
 
    if (ret.second) // successfully inserted
        ++vertexid;
 
    get<0>(triple) = ret.first->first;
    ret = vertexmap.insert(make_pair(contigpair[1], vertexid));
    if (ret.second) ++vertexid;
        
    get<1>(triple) = ret.first->first;
    get<2>(triple) = 1; 
 
    out << get<0>(triple) << "\t" << get<1>(triple) << "\t" << get<2>(triple) << "\n";
    numlines++;
}
 
int main(int argc, char* argv[])
{
    if(argc < 4)
    {
        cout << "Usage: ./mer2gr <splint_file> <kmer_file> <span_file" << endl;
        return 0;
    }
    
    numlines = 0;
    uint32_t vertexid = 0;
    string locline;
    ofstream out("contig_graph.txt");
 
    ifstream input1(argv[1]);    
    while(getline(input1,locline))
    {
        ParseSplint(locline, vertexid, out);
    }
    input1.close();
 
    ifstream input2(argv[2]);    
    while(getline(input2,locline))
    {
        ParseSplint(locline, vertexid, out);
    }
    input2.close();
    
    ifstream input3(argv[3]);  
    while(getline(input3,locline))
    {
        ParseSplint(locline, vertexid, out);
    }
    input3.close();
 
 
    ofstream dictout("vertex_dict.txt");
    int max = 0;
    for (auto it = vertexmap.begin(); it != vertexmap.end(); ++it)
    {
    max = std::max(max, it->second);
    dictout << it ->first << endl;
    }
    cout << (max+1) << "\t" << (max+1) << "\t" << numlines << endl;
    dictout.close();
 
}