polish: sortdiamond modularity
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parent
4c0b989047
commit
680c5392e6
1 changed files with 68 additions and 60 deletions
128
sortdiamond.cpp
128
sortdiamond.cpp
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@ -64,6 +64,70 @@ string revcomp(const string &seq) {
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return revseq;
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}
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void readInputFile(const string &filename,
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map<string, pair<double, string>> &max_map) {
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ifstream infile(filename);
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if (!infile) {
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cerr << "Error opening input file: " << filename << endl;
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return;
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}
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string line;
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while (getline(infile, line)) {
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istringstream iss(line);
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string fields[20];
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int i = 0;
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while (iss >> fields[i] && i < 20) {
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i++;
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}
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string key = fields[1];
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double value = stod(fields[11]);
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// Check if the key already exists in the map
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if (max_map.find(key) != max_map.end()) {
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// If the new value is greater, update the map
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if (value > max_map[key].first) {
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max_map[key] = make_pair(value, line);
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}
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} else {
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// If the key does not exist, insert the new key-value
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// pair
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max_map[key] = make_pair(value, line);
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}
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}
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infile.close();
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}
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void processMap(const map<string, pair<double, string>> &max_map,
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vector<pair<string, string>> &result) {
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for (const auto &entry : max_map) {
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istringstream iss(entry.second.second);
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string fields[20];
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int i = 0;
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while (iss >> fields[i] && i < 20) {
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i++;
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}
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if (stoi(fields[6]) > stoi(fields[7])) {
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fields[17] = revcomp(fields[17]);
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}
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result.push_back(make_pair(">" + fields[1], fields[17]));
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}
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sort(result.begin(), result.end());
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}
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void writeOutputFile(const string &filename,
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const vector<pair<string, string>> &result) {
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ofstream outfile(filename);
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if (!outfile) {
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cerr << "Error opening output file: " << filename << endl;
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return;
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}
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for (const auto &entry : result) {
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outfile << entry.first << "\n" << entry.second << "\n";
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}
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outfile.close();
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}
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int main(int argc, char *argv[]) {
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if (argc != 3) {
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cerr << "Usage: " << argv[0] << " <input_file> <output_file>"
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@ -74,69 +138,13 @@ int main(int argc, char *argv[]) {
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string in_name = argv[1];
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string ot_name = argv[2];
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ifstream infile(in_name);
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if (!infile) {
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cerr << "Error opening input file: " << in_name << endl;
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return 1;
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}
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ofstream outfile(ot_name);
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if (!outfile) {
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cerr << "Error opening output file: " << ot_name << endl;
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return 1;
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}
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map<string, pair<double, string>>
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max_map; // Key: sseqid, Value: pair<score, line>
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string line;
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while (getline(infile, line)) {
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istringstream iss(line);
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string fields[20]; // Adjust size if needed
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int i = 0;
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while (iss >> fields[i] && i < 20) {
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i++;
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}
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string key = fields[1];
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double value = stod(fields[11]);
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if (max_map.find(key) != max_map.end()) {
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if (value > max_map[key].first) {
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max_map[key] = make_pair(value, line);
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}
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} else {
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max_map[key] = make_pair(value, line);
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}
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}
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map<string, pair<double, string>> max_map;
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readInputFile(in_name, max_map);
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vector<pair<string, string>> result;
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processMap(max_map, result);
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for (const auto &entry : max_map) {
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istringstream iss(entry.second.second);
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string fields[20]; // Adjust size if needed
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int i = 0;
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while (iss >> fields[i] && i < 20) {
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i++;
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}
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if (stoi(fields[6]) > stoi(fields[7])) {
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fields[17] = revcomp(fields[17]);
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}
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result.push_back(make_pair(">" + fields[1], fields[17]));
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}
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sort(result.begin(), result.end());
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for (const auto &entry : result) {
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outfile << entry.first << "\n" << entry.second << endl;
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}
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infile.close();
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outfile.close();
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writeOutputFile(ot_name, result);
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return 0;
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}
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