143 lines
2.5 KiB
C++
143 lines
2.5 KiB
C++
#include <algorithm>
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#include <fstream>
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#include <iostream>
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#include <map>
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#include <sstream>
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#include <vector>
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using namespace std;
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// Function to generate reverse complement of a DNA sequence
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string revcomp(const string &seq) {
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string revseq;
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for (auto it = seq.rbegin(); it != seq.rend(); ++it) {
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switch (*it) {
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case 'A':
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revseq += 'T';
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break;
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case 'T':
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revseq += 'A';
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break;
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case 'C':
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revseq += 'G';
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break;
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case 'G':
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revseq += 'C';
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break;
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case 'R':
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revseq += 'Y';
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break;
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case 'Y':
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revseq += 'R';
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break;
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case 'S':
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revseq += 'S';
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break;
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case 'W':
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revseq += 'W';
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break;
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case 'K':
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revseq += 'M';
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break;
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case 'M':
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revseq += 'K';
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break;
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case 'B':
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revseq += 'V';
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break;
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case 'D':
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revseq += 'H';
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break;
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case 'H':
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revseq += 'D';
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break;
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case 'V':
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revseq += 'B';
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break;
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case 'N':
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revseq += 'N';
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break;
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default:
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break;
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}
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}
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return revseq;
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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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<< endl;
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return 1;
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}
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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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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]; // 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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return 0;
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}
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