使用 C++ 并行计算物种矩阵的相对丰度

#include #include #include #include #include #include <omp.h>

using namespace std;

// 读取包含行名和列名的物种矩阵 vector<vector> readMatrix(const string& filename) { ifstream file(filename); if (!file) { cerr << "Failed to open file: " << filename << endl; exit(1); }

vector<vector<double>> matrix;

// 读取列名
string line;
getline(file, line);
stringstream colNames(line);
string colName;
while (colNames >> colName) {
    matrix.push_back(vector<double>());
}

// 读取行名和矩阵数据
string rowName;
double value;
while (file >> rowName) {
    for (int i = 0; i < matrix.size(); i++) {
        file >> value;
        matrix[i].push_back(value);
    }
}

file.close();

return matrix;

}

// 计算相对丰度 vector<vector> calculateRelativeAbundance(const vector<vector>& matrix) { vector<vector> relAbundance(matrix.size(), vector(matrix[0].size()));

double rowSum;
#pragma omp parallel for private(rowSum)
for (int i = 0; i < matrix.size(); i++) {
    rowSum = 0.0;
    for (int j = 0; j < matrix[i].size(); j++) {
        rowSum += matrix[i][j];
    }

    for (int j = 0; j < matrix[i].size(); j++) {
        relAbundance[i][j] = matrix[i][j] / rowSum;
    }
}

return relAbundance;

}

// 输出带有行名和列名的矩阵表格 void printMatrix(const vector<vector>& matrix, const vector& rowNames, const vector& colNames) { // 输出列名 cout << "\t"; for (const auto& name : colNames) { cout << name << "\t"; } cout << endl;

// 输出行名和矩阵数据
for (int i = 0; i < matrix.size(); i++) {
    cout << rowNames[i] << "\t";
    for (int j = 0; j < matrix[i].size(); j++) {
        cout << matrix[i][j] << "\t";
    }
    cout << endl;
}

}

int main() { // 读取物种矩阵 vector<vector> matrix = readMatrix("matrix.txt");

// 读取行名和列名
ifstream file("matrix.txt");
string rowNamesLine;
getline(file, rowNamesLine);
stringstream rowNamesStream(rowNamesLine);
string rowName;
vector<string> rowNames;
while (rowNamesStream >> rowName) {
    rowNames.push_back(rowName);
}
file.close();

// 计算相对丰度
vector<vector<double>> relAbundance = calculateRelativeAbundance(matrix);

// 输出带有行名和列名的矩阵表格
printMatrix(relAbundance, rowNames, rowNames);

return 0;

}