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; }
path = path.substr(0, (tempPath.find_last_of('m')));
string uchimeCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
uchimeCommand = path + "uchime"; // format the database, -o option gives us the ability
#else
uchimeCommand = path + "uchime.exe";
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; }
if (chimealns) { m->openOutputFile(alnsFileName, out2); out2.close(); }
int totalSeqs = 0;
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1) { totalSeqs = driverGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, 0, groups.size(), groups); }
else { totalSeqs = createProcessesGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, groups); }
- #else
- totalSeqs = driverGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, 0, groups.size(), groups);
- #endif
+
if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
int totalChimeras = deconvoluteResults(parser, outputFileName, accnosFileName, alnsFileName);
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;
string inputString = "fasta=" + inputFile;
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
-
+ m->mothurCalling = true;
+
Command* uniqueCommand = new DeconvoluteCommand(inputString);
uniqueCommand->execute();
map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
delete uniqueCommand;
-
+ m->mothurCalling = false;
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
nameFile = filenames["name"][0];
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;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- tempUchime= new char[10];
- *tempUchime = '\0';
- strncat(tempUchime, "./uchime ", 9);
+
+ 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) || (__linux__) || (__unix__) || (__unix)
+ 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) || (__linux__) || (__unix__) || (__unix)
+#else
+ commandString = "\"" + commandString + "\"";
+#endif
system(commandString.c_str());
//free memory
processIDS.clear();
int process = 1;
int num = 0;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- //break up file into multiple files
vector<string> files;
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ //break up file into multiple files
m->divideFile(filename, processors, files);
if (m->control_pressed) { return 0; }
}
in.close(); m->mothurRemove(tempFile);
}
+#else
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the preClusterData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ //divide file
+ int count = 0;
+ int spot = 0;
+ map<int, ofstream*> filehandles;
+ map<int, ofstream*>::iterator it3;
+
+ ofstream* temp;
+ for (int i = 0; i < processors; i++) {
+ temp = new ofstream;
+ filehandles[i] = temp;
+ m->openOutputFile(filename+toString(i)+".temp", *(temp));
+ files.push_back(filename+toString(i)+".temp");
+ }
+
+ ifstream in;
+ m->openInputFile(filename, in);
+
+ while(!in.eof()) {
+
+ if (m->control_pressed) { in.close(); for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { (*(it3->second)).close(); delete it3->second; } return 0; }
+
+ Sequence tempSeq(in); m->gobble(in);
+
+ if (tempSeq.getName() != "") {
+ tempSeq.printSequence(*(filehandles[spot]));
+ spot++; count++;
+ if (spot == processors) { spot = 0; }
+ }
+ }
+ in.close();
+
+ //delete memory
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ (*(it3->second)).close();
+ delete it3->second;
+ }
+
+ //sanity check for number of processors
+ if (count < processors) { processors = count; }
+
+ vector<uchimeData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+ vector<string> dummy; //used so that we can use the same struct for MyUchimeSeqsThreadFunction and MyUchimeThreadFunction
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+ // Allocate memory for thread data.
+ string extension = toString(i) + ".temp";
+
+ uchimeData* tempUchime = new uchimeData(outputFileName+extension, templatefile, files[i], "", "", "", accnos+extension, alns+extension, dummy, m, 0, 0, i);
+ tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract);
+ tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);
+
+ pDataArray.push_back(tempUchime);
+ processIDS.push_back(i);
+
+ //MySeqSumThreadFunction 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, MyUchimeSeqsThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ }
+ //using the main process as a worker saves time and memory
+ num = driver(outputFileName, files[0], accnos, alns, numChimeras);
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ num += pDataArray[i]->count;
+ numChimeras += pDataArray[i]->numChimeras;
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+#endif
+
//append output files
- for(int i=0;i<processIDS[i];i++){
+ for(int i=0;i<processIDS.size();i++){
m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp"));
//get rid of the file pieces.
for (int i = 0; i < files.size(); i++) { m->mothurRemove(files[i]); }
-#endif
return num;
}
catch(exception& e) {
lines.push_back(linePair(startIndex, endIndex));
}
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
int temp = processIDS[i];
wait(&temp);
}
-#endif
for (int i = 0; i < processIDS.size(); i++) {
ifstream in;
if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
in.close(); m->mothurRemove(tempFile);
}
+
+#else
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //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,
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<uchimeData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+ // Allocate memory for thread data.
+ string extension = toString(i) + ".temp";
+
+ uchimeData* tempUchime = new uchimeData(outputFName+extension, templatefile, filename+extension, fastafile, namefile, groupfile, accnos+extension, alns+extension, groups, m, lines[i].start, lines[i].end, i);
+ tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract);
+ tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);
+
+ pDataArray.push_back(tempUchime);
+ processIDS.push_back(i);
+
+ //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]);
+ }
+
+
+ //using the main process as a worker saves time and memory
+ num = driverGroups(parser, outputFName, filename, accnos, alns, lines[0].start, lines[0].end, groups);
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ num += pDataArray[i]->count;
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+#endif
+
+
//append output files
- for(int i=0;i<processIDS[i];i++){
+ for(int i=0;i<processIDS.size();i++){
m->appendFiles((outputFName + toString(processIDS[i]) + ".temp"), outputFName);
m->mothurRemove((outputFName + toString(processIDS[i]) + ".temp"));
projects / mothur.git / blobdiff