bool dataframesAreEqual(Rcpp::DataFrame &a, Rcpp::DataFrame &b) { Rcpp::NumericVector a1 = a["a"]; Rcpp::CharacterVector b1 = a["b"]; Rcpp::DoubleVector c1 = a["c"]; Rcpp::NumericVector a2 = b["a"]; Rcpp::CharacterVector b2 = b["b"]; Rcpp::DoubleVector c2 = b["c"]; if(a.size() != b.size()) { DLOG(INFO) << "sizes different"; return false; } for(int i = 0; i < a1.size(); i++) { if(a1[i] != a2[i]) { DLOG(INFO) << a1[i] << " vs " << a2[i]; return false; } if(b1[i] != b2[i]) { DLOG(INFO) << b1[i] << " vs " << b2[i]; return false; } if(c1[i] != c2[i]) { DLOG(INFO) << c1[i] << " vs " << c2[i]; return false; } } return true; }
Interaction::Interaction(vector<double> const& instance,vector<bool> const& factor, Rcpp::DataFrame const& class_data,double epsilon_cont,double epsilon_cat,int p_depth,int nb_class,double p_radius){ vector<InteractionItem> new_items(class_data.size()); Rcpp::CharacterVector names = class_data.names(); for(int i=0;i<class_data.size();++i){ vector<double> attr_data = Rcpp::as<vector<double> >(class_data[i]); string name = Rcpp::as<string>(names[i]); if(factor[i]){ InteractionItem item(name,instance[i],i,epsilon_cat,factor[i],attr_data); new_items[i] = item; } else{ InteractionItem item(name,instance[i],i,epsilon_cont,factor[i],attr_data); new_items[i] = item; } } items = new_items; depth = p_depth; sims_valid = false; vector<double> new_sims(nb_class); sims = new_sims; radius = p_radius; }
vector<double> random_instance(Rcpp::DataFrame const& x, Generator& prng){ // Select random row number int row = prng(); vector<double> instance(x.size()); for(int i=0;i<x.size();++i){ vector<double> col = Rcpp::as<vector<double> >(x[i]); instance[i] = col[row]; } return instance; }
Rcpp::StringMatrix DataFrame_to_StringMatrix( Rcpp::DataFrame df ){ Rcpp::StringVector sv = df(0); Rcpp::StringMatrix sm(sv.size(), df.size()); sm.attr("col.names") = df.attr("col.names"); sm.attr("row.names") = df.attr("row.names"); for(int i=0; i < df.size(); i++){ sv = df(i); for(int j=0; j < sv.size(); j++){ sm(j, i) = sv(j); } } return sm; }
void helper(const std::string& url, const bool dropCaches, const std::string& objType) { if(dropCaches) { LOG(INFO) << "Dropping caches ..."; int res, res2; if ((res = system ("sync")) == -1) { throw std::runtime_error("Error running sync"); } if ((res2 = system ("sudo sh -c 'echo 3 > /proc/sys/vm/drop_caches'")) == -1) { throw std::runtime_error("Error dropping caches"); } } //std::string extension = base::utils::getExtension(url); std::string protocol = base::utils::getProtocol(url); std::string filename = base::utils::stripProtocol(url); base::IFilePtr file = hdfsutils::FileFactory::makeFile(protocol, filename); if( hdfsutils::isHdfs(protocol)) { hdfsutils::HdfsFile *p = (hdfsutils::HdfsFile *)file.get(); base::ConfigurationMap hdfsconf; hdfsconf["hdfsConfigurationFile"] = std::string("../ddc/test/data/server.conf"); p->configure(hdfsconf); } base::FileStatus status = file->stat(); base::ConfigurationMap conf; std::string schema = "000:int64," "001:int64,002:int64,003:int64,004:int64,005:int64,006:int64,007:int64,008:int64," "009:int64,010:int64,011:int64,012:int64,013:int64,014:int64,015:int64,016:int64," "017:int64,018:int64,019:int64,020:int64,021:int64,022:int64,023:int64,024:int64," "025:int64,026:int64,027:int64,028:int64,029:int64,030:int64,031:int64,032:int64," "033:int64,034:int64,035:int64,036:int64,037:int64,038:int64,039:int64,040:int64," "041:int64,042:int64,043:int64,044:int64,045:int64,046:int64,047:int64,048:int64," "049:int64,050:int64,051:int64,052:int64,053:int64,054:int64,055:int64,056:int64," "057:int64,058:int64,059:int64,060:int64,061:int64,062:int64,063:int64,064:int64," "065:int64,066:int64,067:int64,068:int64,069:int64,070:int64,071:int64,072:int64," "073:int64,074:int64,075:int64,076:int64,077:int64,078:int64,079:int64,080:int64," "081:int64,082:int64,083:int64,084:int64,085:int64,086:int64,087:int64,088:int64," "089:int64,090:int64,091:int64,092:int64,093:int64,094:int64,095:int64,096:int64," "097:int64,098:int64,099:int64,100:int64,101:int64,102:int64,103:int64,104:int64," "105:int64,106:int64,107:int64,108:int64,109:int64,110:int64,111:int64,112:int64," "113:int64,114:int64,115:int64,116:int64,117:int64,118:int64,119:int64,120:int64," "121:int64,122:int64,123:int64,124:int64,125:int64,126:int64,127:int64"; conf["schemaUrl"] = schema; conf["chunkStart"] = (uint64_t)0; conf["chunkEnd"] = (uint64_t)status.length; conf["hdfsConfigurationFile"] = std::string("../ddc/test/data/server.conf") ; boost::shared_ptr<Rcpp::DataFrame> dfptr = boost::any_cast<boost::shared_ptr<Rcpp::DataFrame>>(ddc_read(url, objType, conf)); Rcpp::DataFrame df = Rcpp::DataFrame(*(dfptr.get())); LOG(INFO) << "Got dataframe of size " << df.size(); }
// [[Rcpp::export]] void write_vcf_body_gz( Rcpp::DataFrame fix, Rcpp::DataFrame gt, std::string filename , int mask=0 ) { // http://stackoverflow.com/a/5649224 // fix DataFrame Rcpp::StringVector chrom = fix["CHROM"]; Rcpp::StringVector pos = fix["POS"]; Rcpp::StringVector id = fix["ID"]; Rcpp::StringVector ref = fix["REF"]; Rcpp::StringVector alt = fix["ALT"]; Rcpp::StringVector qual = fix["QUAL"]; Rcpp::StringVector filter = fix["FILTER"]; Rcpp::StringVector info = fix["INFO"]; // gt DataFrame Rcpp::StringMatrix gt_cm = DataFrame_to_StringMatrix(gt); Rcpp::StringVector column_names(gt.size()); column_names = gt.attr("names"); int i = 0; int j = 0; gzFile *fi = (gzFile *)gzopen(filename.c_str(),"ab"); // gzFile *fi = (gzFile *)gzopen(filename.c_str(),"abw"); for(i=0; i<chrom.size(); i++){ Rcpp::checkUserInterrupt(); if(mask == 1 && filter(i) != "PASS" ){ // Don't print variant. } else { std::string tmpstring; tmpstring = chrom(i); tmpstring = tmpstring + "\t" + pos(i) + "\t"; if(id(i) == NA_STRING){ tmpstring = tmpstring + "."; } else { tmpstring = tmpstring + id(i); } tmpstring = tmpstring + "\t" + ref(i) + "\t" + alt(i) + "\t"; if(qual(i) == NA_STRING){ tmpstring = tmpstring + "." + "\t"; } else { tmpstring = tmpstring + qual(i) + "\t"; } if(filter(i) == NA_STRING){ tmpstring = tmpstring + "." + "\t"; } else { tmpstring = tmpstring + filter(i) + "\t"; } tmpstring = tmpstring + info(i); // gt portion for(j=0; j<column_names.size(); j++){ if(gt_cm(i, j) == NA_STRING){ tmpstring = tmpstring + "\t" + "./."; } else { tmpstring = tmpstring + "\t" + gt_cm(i, j); } } // gzwrite(fi,"my decompressed data",strlen("my decompressed data")); // gzwrite(fi,"\n",strlen("\n")); // std::string tmpstring = "test string\n"; gzwrite(fi, (char *)tmpstring.c_str(), tmpstring.size()); gzwrite(fi,"\n",strlen("\n")); } } gzclose(fi); return; }
// [[Rcpp::export]] void write_vcf_body( Rcpp::DataFrame fix, Rcpp::DataFrame gt, std::string filename , int mask=0 ) { //int write_vcf_body( Rcpp::DataFrame fix, Rcpp::DataFrame gt, std::string filename , int mask=0 ) { // fix DataFrame Rcpp::StringVector chrom = fix["CHROM"]; Rcpp::StringVector pos = fix["POS"]; Rcpp::StringVector id = fix["ID"]; Rcpp::StringVector ref = fix["REF"]; Rcpp::StringVector alt = fix["ALT"]; Rcpp::StringVector qual = fix["QUAL"]; Rcpp::StringVector filter = fix["FILTER"]; Rcpp::StringVector info = fix["INFO"]; // gt DataFrame Rcpp::StringMatrix gt_cm = DataFrame_to_StringMatrix(gt); Rcpp::StringVector column_names(gt.size()); column_names = gt.attr("names"); // column_names = gt_cm.attr("col.names"); // delete gt; int i = 0; int j = 0; // Uncompressed. std::ofstream myfile; myfile.open (filename.c_str(), std::ios::out | std::ios::app | std::ios::binary); // gzFile *fi = (gzFile *)gzopen("file.gz","wb"); for(i=0; i<chrom.size(); i++){ Rcpp::checkUserInterrupt(); if(mask == 1 && filter(i) == "PASS" ){ // Don't print variant. } else { myfile << chrom(i); myfile << "\t"; myfile << pos(i); myfile << "\t"; if(id(i) == NA_STRING){ myfile << "."; myfile << "\t"; } else { myfile << id(i); myfile << "\t"; } myfile << ref(i); myfile << "\t"; myfile << alt(i); myfile << "\t"; if(qual(i) == NA_STRING){ myfile << "."; myfile << "\t"; } else { myfile << qual(i); myfile << "\t"; } if(filter(i) == NA_STRING){ myfile << "."; myfile << "\t"; } else { myfile << filter(i); myfile << "\t"; } if(info(i) == NA_STRING){ myfile << "."; myfile << "\t"; } else { myfile << info(i); } // gt region. myfile << "\t"; myfile << gt_cm(i, 0); for(j=1; j<column_names.size(); j++){ myfile << "\t"; myfile << gt_cm(i, j); } myfile << "\n"; } } myfile.close(); return; }