string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
abskew = validParameter.validFile(parameters, "abskew", false); if (abskew == "not found"){ useAbskew = false; abskew = "1.9"; }else{ useAbskew = true; }
if (useAbskew && templatefile != "self") { m->mothurOut("The abskew parameter is only valid with template=self, ignoring."); m->mothurOutEndLine(); useAbskew = false; }
if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
nameFile = nameFileNames[s];
}else { nameFile = getNamesFile(fastaFileNames[s]); }
-
+
map<string, string> seqs;
readFasta(fastaFileNames[s], seqs); if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
int numSeqs = 0;
int numChimeras = 0;
- //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+
if(processors == 1){ numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); }
else{ numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); }
- //#else
- // numSeqs = driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras);
- //#endif
+
+ //add headings
+ ofstream out;
+ m->openOutputFile(outputFileName+".temp", out);
+ out << "Score\tQuery\tParentA\tParentB\tIdQM\tIdQA\tIdQB\tIdAB\tIdQT\tLY\tLN\tLA\tRY\tRN\tRA\tDiv\tYN\n";
+ out.close();
+
+ m->appendFiles(outputFileName, outputFileName+".temp");
+ m->mothurRemove(outputFileName); rename((outputFileName+".temp").c_str(), outputFileName.c_str());
+
if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
//remove file made for uchime
ofstream out;
m->openOutputFile(outputFileName+".temp", out); out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+ out << "Score\tQuery\tParentA\tParentB\tIdQM\tIdQA\tIdQB\tIdAB\tIdQT\tLY\tLN\tLA\tRY\tRN\tRA\tDiv\tYN\n";
float temp1;
string parent1, parent2, temp2, temp3, temp4, temp5, temp6, temp7, temp8, temp9, temp10, temp11, temp12, temp13, flag;
int ChimeraUchimeCommand::driver(string outputFName, string filename, string accnos, string alns, int& numChimeras){
try {
+
+ outputFName = m->getFullPathName(outputFName);
+ filename = m->getFullPathName(filename);
+ alns = m->getFullPathName(alns);
+
//to allow for spaces in the path
outputFName = "\"" + outputFName + "\"";
filename = "\"" + filename + "\"";
alns = "\"" + alns + "\"";
vector<char*> cPara;
-
- char* tempUchime;
+
+ string path = m->argv;
+ string tempPath = path;
+ for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+ path = path.substr(0, (tempPath.find_last_of('m')));
+
+ string uchimeCommand = path;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- tempUchime= new char[10];
- *tempUchime = '\0';
- strncat(tempUchime, "./uchime ", 9);
+ uchimeCommand += "uchime ";
#else
- tempUchime= new char[8];
- *tempUchime = '\0';
- strncat(tempUchime, "uchime ", 7);
+ uchimeCommand += "uchime";
+ uchimeCommand = "\"" + uchimeCommand + "\"";
#endif
+
+ char* tempUchime;
+ tempUchime= new char[uchimeCommand.length()+1];
+ *tempUchime = '\0';
+ strncat(tempUchime, uchimeCommand.c_str(), uchimeCommand.length());
cPara.push_back(tempUchime);
char* tempIn = new char[8];
//uchime_main(numArgs, uchimeParameters);
//cout << "commandString = " << commandString << endl;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+ commandString = "\"" + commandString + "\"";
+#endif
system(commandString.c_str());
//free memory
#else
//////////////////////////////////////////////////////////////////////////////////////////////////////
- //Windows version shared memory, so be careful when passing variables through the preClusterData struct.
+ //Windows version shared memory, so be careful when passing variables through the uchimeData struct.
//Above fork() will clone, so memory is separate, but that's not the case with windows,
//////////////////////////////////////////////////////////////////////////////////////////////////////
pDataArray.push_back(tempUchime);
processIDS.push_back(i);
- //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
+ //MyUchimeThreadFunction is in header. It must be global or static to work with the threads.
//default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
hThreadArray[i-1] = CreateThread(NULL, 0, MyUchimeThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
}