get_common_consensus.cpp

#include<iostream>
#include<iterator>
#include<sstream>
#include<vector>
#include<fstream>

const uint32_t MAX_SIZE = 100000;

bool check_if_equal(char** n, int n_size, std::ifstream *f){
  if(*n[0] == '\n' || *n[0] == '\0' || *n[0]==EOF || f[0].eof())
    return false;
  for(int i = 1; i < n_size;i++){
    if(*n[i] != *n[0] || *n[i] == '\0' || *n[i] == '\n' || *n[0]==EOF || f[i].eof())
      return false;
  }
  return true;
}

int compare_consensus(char** f, int n_string, std::string out){
  std::ifstream *cns = new std::ifstream[n_string];
  std::ofstream o(out+".fa");
  o << ">Common_Consensus" << std::endl;
  int i, j;
  char** l = new char*[n_string];
  for(i = 0; i < n_string;i++){
    std::cout << f[i+1] << std::endl;
    l[i] = new char;
    cns[i].open(f[i + 1]);
    cns[i].read(l[i], 1);
    if(*l[i]!='>'){
      std::cout << "Error " << f[i] << " is not a fasta file." << std::endl;
      return 0;
    }
    while(*l[i] !='\n'){
      cns[i].read(l[i], 1);
    }
    cns[i].read(l[i], 1);   // Read next character after \n
  }
  // Get to beginning of matching substring
  while(!check_if_equal(l, n_string, cns)){
    for(j = 0; j<n_string;j++){
      cns[j].read(l[j], 1);
    }
  }
  for(j = 0; j < n_string; j++)
    if(*l[j] == EOF){
      std::cout << "Warning: No common regions between consensus sequences" << std::endl;
      return 0;
    }
  while(check_if_equal(l, n_string, cns)){
    o << *l[0];
    for(j = 0; j<n_string;j++){
      cns[j].read(l[j], 1);
    }
  }
  for(i = 0; i < n_string; i++){
    cns[i].close();
  }
  o.close();
  delete[] cns;
  delete[] l;
  return 0;
}

int main(int argv, char** argc){
  compare_consensus(argc, argv - 1, "test");
}