map<string, string>::iterator itUnique;
int total = 0;
+ //edit accnos file
+ ifstream in2;
+ m->openInputFile(accnosFileName, in2);
+
+ ofstream out2;
+ m->openOutputFile(accnosFileName+".temp", out2);
+
+ string name;
+ set<string> namesInFile; //this is so if a sequence is found to be chimera in several samples we dont write it to the results file more than once
+ set<string>::iterator itNames;
+ set<string> chimerasInFile;
+ set<string>::iterator itChimeras;
+
+
+ while (!in2.eof()) {
+ if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; }
+
+ in2 >> name; m->gobble(in2);
+
+ //find unique name
+ itUnique = uniqueNames.find(name);
+
+ if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else {
+ itChimeras = chimerasInFile.find((itUnique->second));
+
+ if (itChimeras == chimerasInFile.end()) {
+ out2 << itUnique->second << endl;
+ chimerasInFile.insert((itUnique->second));
+ total++;
+ }
+ }
+ }
+ in2.close();
+ out2.close();
+
+ m->mothurRemove(accnosFileName);
+ rename((accnosFileName+".temp").c_str(), accnosFileName.c_str());
+
+
+
//edit chimera file
ifstream in;
m->openInputFile(outputFileName, in);
m->openOutputFile(outputFileName+".temp", out); out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
float temp1;
- string name, rest, parent1, parent2;
- set<string> namesInFile; //this is so if a sequence is found to be chimera in several samples we dont write it to the results file more than once
- set<string>::iterator itNames;
-
+ string parent1, parent2, temp2, temp3, temp4, temp5, temp6, temp7, temp8, temp9, temp10, temp11, temp12, temp13, flag;
+ name = "";
+ namesInFile.clear();
//assumptions - in file each read will always look like - if uchime source is updated, revisit this code.
- /*
+ /* 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
0.000000 F11Fcsw_33372/ab=18/ * * * * * * * * * * * * * * N
0.018300 F11Fcsw_14980/ab=16/ F11Fcsw_1915/ab=35/ F11Fcsw_6032/ab=42/ 79.9 78.7 78.2 78.7 79.2 3 0 5 11 10 20 1.46 N
*/
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove((outputFileName+".temp")); return 0; }
+ bool print = false;
in >> temp1; m->gobble(in);
in >> name; m->gobble(in);
in >> parent1; m->gobble(in);
in >> parent2; m->gobble(in);
- rest = m->getline(in); m->gobble(in);
+ in >> temp2 >> temp3 >> temp4 >> temp5 >> temp6 >> temp7 >> temp8 >> temp9 >> temp10 >> temp11 >> temp12 >> temp13 >> flag;
+ m->gobble(in);
//parse name - name will look like U68590/ab=1/
string restOfName = "";
if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
else {
- itNames = namesInFile.find((itUnique->second));
+ name = itUnique->second;
+ //is this name already in the file
+ itNames = namesInFile.find((name));
- if (itNames == namesInFile.end()) {
- out << temp1 << '\t' << itUnique->second << restOfName << '\t';
- namesInFile.insert((itUnique->second));
-
- //parse parent1 names
- if (parent1 != "*") {
- restOfName = "";
- pos = parent1.find_first_of('/');
- if (pos != string::npos) {
- restOfName = parent1.substr(pos);
- parent1 = parent1.substr(0, pos);
- }
+ if (itNames == namesInFile.end()) { //no not in file
+ if (flag == "N") { //are you really a no??
+ //is this sequence really not chimeric??
+ itChimeras = chimerasInFile.find(name);
- itUnique = uniqueNames.find(parent1);
- if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parentA "+ parent1 + "."); m->mothurOutEndLine(); m->control_pressed = true; }
- else {
- out << itUnique->second << restOfName << '\t';
- }
- }else { out << parent1 << '\t'; }
+ //then you really are a no so print, otherwise skip
+ if (itChimeras == chimerasInFile.end()) { print = true; }
+ }else{ print = true; }
+ }
+ }
+
+ if (print) {
+ out << temp1 << '\t' << name << restOfName << '\t';
+ namesInFile.insert(name);
+
+ //parse parent1 names
+ if (parent1 != "*") {
+ restOfName = "";
+ pos = parent1.find_first_of('/');
+ if (pos != string::npos) {
+ restOfName = parent1.substr(pos);
+ parent1 = parent1.substr(0, pos);
+ }
- //parse parent2 names
- if (parent2 != "*") {
- restOfName = "";
- pos = parent2.find_first_of('/');
- if (pos != string::npos) {
- restOfName = parent2.substr(pos);
- parent2 = parent2.substr(0, pos);
- }
-
- itUnique = uniqueNames.find(parent2);
- if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parentB "+ parent2 + "."); m->mothurOutEndLine(); m->control_pressed = true; }
- else {
- out << itUnique->second << restOfName << '\t';
- }
- }else { out << parent2 << '\t'; }
+ itUnique = uniqueNames.find(parent1);
+ if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parentA "+ parent1 + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else { out << itUnique->second << restOfName << '\t'; }
+ }else { out << parent1 << '\t'; }
+
+ //parse parent2 names
+ if (parent2 != "*") {
+ restOfName = "";
+ pos = parent2.find_first_of('/');
+ if (pos != string::npos) {
+ restOfName = parent2.substr(pos);
+ parent2 = parent2.substr(0, pos);
+ }
- out << rest << endl;
- }
+ itUnique = uniqueNames.find(parent2);
+ if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parentB "+ parent2 + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else { out << itUnique->second << restOfName << '\t'; }
+ }else { out << parent2 << '\t'; }
+
+ out << temp2 << '\t' << temp3 << '\t' << temp4 << '\t' << temp5 << '\t' << temp6 << '\t' << temp7 << '\t' << temp8 << '\t' << temp9 << '\t' << temp10 << '\t' << temp11 << '\t' << temp12 << temp13 << '\t' << flag << endl;
}
}
in.close();
m->mothurRemove(outputFileName);
rename((outputFileName+".temp").c_str(), outputFileName.c_str());
- //edit accnos file
- ifstream in2;
- m->openInputFile(accnosFileName, in2);
-
- ofstream out2;
- m->openOutputFile(accnosFileName+".temp", out2);
-
- name = "";
- namesInFile.clear();
-
- while (!in2.eof()) {
- if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; }
-
- in2 >> name; m->gobble(in2);
-
- //find unique name
- itUnique = uniqueNames.find(name);
-
- if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
- else {
- itNames = namesInFile.find((itUnique->second));
-
- if (itNames == namesInFile.end()) {
- out2 << itUnique->second << endl;
- namesInFile.insert((itUnique->second));
- total++;
- }
- }
- }
- in2.close();
- out2.close();
-
- m->mothurRemove(accnosFileName);
- rename((accnosFileName+".temp").c_str(), accnosFileName.c_str());
-
+
//edit anls file
//assumptions - in file each read will always look like - if uchime source is updated, revisit this code.
/*
projects / mothur.git / blobdiff