int DataLoader::loadPhenotype(const std::string& pheno,
const std::string& mpheno,
const std::string& phenoName) {
this->FLAG_pheno = pheno;
this->FLAG_mpheno = mpheno;
this->FLAG_phenoName = phenoName;
// this->FLAG_imputePheno = imputePheno;
std::map<std::string, double> phenotype;
std::string label;
if (FLAG_pheno.empty()) {
logger->error("Cannot do association when phenotype is missing!");
return -1;
}
// check if alternative phenotype columns are used
if (!FLAG_mpheno.empty() && !FLAG_phenoName.empty()) {
logger->error("Please specify either --mpheno or --pheno-name");
return -1;
}
if (!FLAG_mpheno.empty()) {
label = "P" + toString(FLAG_mpheno);
int col = atoi(FLAG_mpheno);
int ret = loadPedPhenotypeByColumn(FLAG_pheno.c_str(), &phenotype, col);
if (ret < 0) {
logger->error("Loading phenotype failed!");
return -1;
}
} else if (!FLAG_phenoName.empty()) {
label = FLAG_phenoName;
int ret = loadPedPhenotypeByHeader(FLAG_pheno.c_str(), &phenotype,
FLAG_phenoName.c_str());
if (ret < 0) {
logger->error("Loading phenotype failed!");
return -1;
}
} else {
label = "P1";
int col = 1; // default use the first phenotype
int ret = loadPedPhenotypeByColumn(FLAG_pheno.c_str(), &phenotype, col);
if (ret < 0) {
logger->error("Loading phenotype failed!");
return -1;
}
}
std::vector<std::string> keys;
std::vector<double> vals;
extractMap(phenotype, &keys, &vals);
this->phenotype.appendCol(vals, label);
this->phenotype.setRowName(keys);
logger->info("Loaded [ %zu ] sample pheontypes", phenotype.size());
return 0;
}
int main(int argc, char** argv)
{
mq::MapSite::StrVec args(argv + 1, argv + argc); // "+ 1" to skip first arg. It's the name of the program
if(args.size() < 1)
{
std::cout << "[ERROR]: Not enough arguments. Type at least something to search for after the exe name.\n";
return 3;
}
std::string searchStr = args[0];
for(auto i = 1u; i < args.size(); i++)
searchStr.append(" " + args[i]);
mq::BattlezoneOneCom bz1server;
if(!bz1server.isServerGood())
{
std::cout << "[ERROR]: Cannot contact server. Exiting.\n";
return 1;
}
mq::MapSite::StrMap results = bz1server.getMaps(searchStr);
if(results.empty())
{
std::cout << "No results found for \"" << searchStr << "\"!\n";
return 0;
}
for(auto it = results.begin(); it != results.end(); it++)
{
std::cout << std::distance(results.begin(), it) << ") " << it->first << " : " << it->second << '\n';
}
bool badInput = true;
std::string input;
std::vector<unsigned int> choices(1);
while(badInput)
{
std::cout << "\nEnter the number(s) of the map to download (\"-1\" to cancel): ";
std::getline(std::cin, input);
if(input == "-1")
return 0;
std::stringstream ss(input);
badInput = false;
try
{
while(ss >> choices.back())
choices.emplace_back();
choices.erase(--choices.end()); // get rid of extra item
for(auto& c : choices)
if(c >= results.size())
throw 0;
}
catch(...)
{
badInput = true;
choices.resize(1);
std::cout << "[ERROR]: Bad input. Try again!\n";
}
}
std::string installLocation = getBZinstallDir();
if(installLocation.empty())
installLocation = getExePath();
installLocation += "addon/";
for(auto& c : choices)
{
auto choiceIter = std::next(results.begin(), c);
std::string resFileName = bz1server.downloadMap(choiceIter->second, installLocation);
if(resFileName.empty())
{
std::cout << "[ERROR]: Download failed for \"" << choiceIter->first << "\". Exiting.\n";
return 2;
}
extractMap(resFileName);
}
return 0;
}
