add: variable arguments for sortdiamond
This commit is contained in:
parent
df84006179
commit
a68b31a3ce
1 changed files with 61 additions and 20 deletions
|
@ -7,6 +7,11 @@
|
|||
|
||||
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
|
||||
string revcomp(const string &seq) {
|
||||
string revseq;
|
||||
|
@ -65,7 +70,8 @@ string revcomp(const string &seq) {
|
|||
}
|
||||
|
||||
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);
|
||||
if (!infile) {
|
||||
cerr << "Error opening input file: " << filename << endl;
|
||||
|
@ -75,15 +81,15 @@ void readInputFile(const string &filename,
|
|||
string line;
|
||||
while (getline(infile, line)) {
|
||||
istringstream iss(line);
|
||||
string fields[20];
|
||||
string fields[intmax + 1];
|
||||
int i = 0;
|
||||
while (iss >> fields[i] && i < 20) {
|
||||
while (iss >> fields[i] && i < (intmax + 1)) {
|
||||
i++;
|
||||
}
|
||||
// subject seq id
|
||||
string key = fields[1];
|
||||
string key = fields[intnums[0]];
|
||||
// bit score
|
||||
double value = stod(fields[11]);
|
||||
double value = stod(fields[intnums[3]]);
|
||||
// Check if the key already exists in the map
|
||||
if (max_map.find(key) != max_map.end()) {
|
||||
// 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,
|
||||
vector<pair<string, string>> &result) {
|
||||
vector<pair<string, string>> &result, const int *intnums,
|
||||
const int intmax) {
|
||||
for (const auto &entry : max_map) {
|
||||
istringstream iss(entry.second.second);
|
||||
string fields[20];
|
||||
string fields[intmax + 1];
|
||||
int i = 0;
|
||||
while (iss >> fields[i] && i < 20) {
|
||||
while (iss >> fields[i] && i < (intmax + 1)) {
|
||||
i++;
|
||||
}
|
||||
// check if qstart is larger than qend
|
||||
if (stoi(fields[6]) > stoi(fields[7])) {
|
||||
fields[17] = revcomp(fields[17]);
|
||||
if (stoi(fields[intnums[1]]) > stoi(fields[intnums[2]])) {
|
||||
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());
|
||||
}
|
||||
|
@ -131,23 +139,56 @@ void writeOutputFile(const string &filename,
|
|||
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[]) {
|
||||
if (argc != 3) {
|
||||
cerr << "Usage: " << argv[0] << " <input_file> <output_file>"
|
||||
int intnums[n_intarr] = {1, 6, 7, 11, 17};
|
||||
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;
|
||||
return 1;
|
||||
}
|
||||
|
||||
string in_name = argv[1];
|
||||
string ot_name = argv[2];
|
||||
if (argc == 3 || argc == 4) {
|
||||
string in_name = argv[1];
|
||||
string ot_name = argv[2];
|
||||
|
||||
map<string, pair<double, string>> max_map;
|
||||
readInputFile(in_name, max_map);
|
||||
map<string, pair<double, string>> max_map;
|
||||
readInputFile(in_name, max_map, intnums, intmax);
|
||||
|
||||
vector<pair<string, string>> result;
|
||||
processMap(max_map, result);
|
||||
vector<pair<string, string>> result;
|
||||
processMap(max_map, result, intnums, intmax);
|
||||
|
||||
writeOutputFile(ot_name, result);
|
||||
writeOutputFile(ot_name, result);
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
|
Loading…
Reference in a new issue