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add: variable arguments for sortdiamond

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This commit is contained in:
kuoi 2024-07-05 12:56:21 +10:00
parent df84006179
commit a68b31a3ce
1 changed files with 61 additions and 20 deletions
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81
sortdiamond.cpp
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@ -7,6 +7,11 @@
using namespace std; using namespace std;
const int n_intarr = 5;
string revcomp(const string &seq);
int maxInts(int intnums[n_intarr]);
// Function to generate reverse complement of a DNA sequence // Function to generate reverse complement of a DNA sequence
string revcomp(const string &seq) { string revcomp(const string &seq) {
string revseq; string revseq;
@ -65,7 +70,8 @@ string revcomp(const string &seq) {
} }
void readInputFile(const string &filename, void readInputFile(const string &filename,
map<string, pair<double, string>> &max_map) { map<string, pair<double, string>> &max_map,
const int *intnums, const int intmax) {
ifstream infile(filename); ifstream infile(filename);
if (!infile) { if (!infile) {
cerr << "Error opening input file: " << filename << endl; cerr << "Error opening input file: " << filename << endl;
@ -75,15 +81,15 @@ void readInputFile(const string &filename,
string line; string line;
while (getline(infile, line)) { while (getline(infile, line)) {
istringstream iss(line); istringstream iss(line);
string fields[20]; string fields[intmax + 1];
int i = 0; int i = 0;
while (iss >> fields[i] && i < 20) { while (iss >> fields[i] && i < (intmax + 1)) {
i++; i++;
} }
// subject seq id // subject seq id
string key = fields[1]; string key = fields[intnums[0]];
// bit score // bit score
double value = stod(fields[11]); double value = stod(fields[intnums[3]]);
// Check if the key already exists in the map // Check if the key already exists in the map
if (max_map.find(key) != max_map.end()) { if (max_map.find(key) != max_map.end()) {
// If the new value is greater, update the map // If the new value is greater, update the map
@ -100,19 +106,21 @@ void readInputFile(const string &filename,
} }
void processMap(const map<string, pair<double, string>> &max_map, void processMap(const map<string, pair<double, string>> &max_map,
vector<pair<string, string>> &result) { vector<pair<string, string>> &result, const int *intnums,
const int intmax) {
for (const auto &entry : max_map) { for (const auto &entry : max_map) {
istringstream iss(entry.second.second); istringstream iss(entry.second.second);
string fields[20]; string fields[intmax + 1];
int i = 0; int i = 0;
while (iss >> fields[i] && i < 20) { while (iss >> fields[i] && i < (intmax + 1)) {
i++; i++;
} }
// check if qstart is larger than qend // check if qstart is larger than qend
if (stoi(fields[6]) > stoi(fields[7])) { if (stoi(fields[intnums[1]]) > stoi(fields[intnums[2]])) {
fields[17] = revcomp(fields[17]); fields[intnums[4]] = revcomp(fields[intnums[4]]);
} }
result.push_back(make_pair(">" + fields[1], fields[17])); result.push_back(
make_pair(">" + fields[intnums[0]], fields[intnums[4]]));
} }
sort(result.begin(), result.end()); sort(result.begin(), result.end());
} }
@ -131,23 +139,56 @@ void writeOutputFile(const string &filename,
outfile.close(); outfile.close();
} }
void splitInts(const std::string &str, int intnums[n_intarr]) {
istringstream iss(str);
int numi = 0;
string tmpstr;
while (std::getline(iss, tmpstr, ',') && numi < n_intarr) {
intnums[numi] = std::stoi(tmpstr);
cout << intnums[numi] << endl;
numi++;
}
}
int maxInts(int intnums[n_intarr]) {
int intmax = intnums[0];
for (int i = 1; i < n_intarr; i++) {
if (intnums[i] > intmax) {
intmax = intnums[i];
}
}
cout << intmax << endl;
return intmax;
}
int main(int argc, char *argv[]) { int main(int argc, char *argv[]) {
if (argc != 3) { int intnums[n_intarr] = {1, 6, 7, 11, 17};
cerr << "Usage: " << argv[0] << " <input_file> <output_file>" int intmax = 17;
if (argc == 4) {
splitInts(argv[3], intnums);
intmax = maxInts(intnums);
} else if (argc != 3) {
cerr << "Usage: " << argv[0]
<< " <input_file> <output_file> "
"<sseq,qstart,qend,bitscore,qseq>"
<< endl; << endl;
return 1; return 1;
} }
string in_name = argv[1]; if (argc == 3 || argc == 4) {
string ot_name = argv[2]; string in_name = argv[1];
string ot_name = argv[2];
map<string, pair<double, string>> max_map; map<string, pair<double, string>> max_map;
readInputFile(in_name, max_map); readInputFile(in_name, max_map, intnums, intmax);
vector<pair<string, string>> result; vector<pair<string, string>> result;
processMap(max_map, result); processMap(max_map, result, intnums, intmax);
writeOutputFile(ot_name, result); writeOutputFile(ot_name, result);
}
return 0; return 0;
} }