//**********************************************************************************************************************
vector<string> FilterSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(phard);
- CommandParameter ptrump("trump", "String", "", "*", "", "", "",false,false); parameters.push_back(ptrump);
- CommandParameter psoft("soft", "Number", "", "0", "", "", "",false,false); parameters.push_back(psoft);
- CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pvertical);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-filter",false,true, true); parameters.push_back(pfasta);
+ CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(phard);
+ CommandParameter ptrump("trump", "String", "", "*", "", "", "","",false,false, true); parameters.push_back(ptrump);
+ CommandParameter psoft("soft", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psoft);
+ CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "","",false,false, true); parameters.push_back(pvertical);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false, true); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
+string FilterSeqsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "fasta") { pattern = "[filename],filter.fasta"; }
+ else if (type == "filter") { pattern = "[filename],filter"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
FilterSeqsCommand::FilterSeqsCommand(){
try {
abort = true; calledHelp = true;
fasta = validParameter.validFile(parameters, "fasta", false);
if (fasta == "not found") {
fasta = m->getFastaFile();
- if (fasta != "") { fastafileNames.push_back(fasta); m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ if (fasta != "") {
+ fastafileNames.push_back(fasta);
+ m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine();
+ string simpleName = m->getSimpleName(fasta);
+ filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
+ }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else {
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
vertical = validParameter.validFile(parameters, "vertical", false);
if (vertical == "not found") {
ofstream outFilter;
//prevent giantic file name
- string filterFile;
- if (fastafileNames.size() > 3) { filterFile = outputDir + "merge.filter"; }
- else { filterFile = outputDir + filterFileName + ".filter"; }
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + filterFileName + ".";
+ if (fastafileNames.size() > 3) { variables["[filename]"] = outputDir + "merge."; }
+ string filterFile = getOutputFileName("filter", variables);
m->openOutputFile(filterFile, outFilter);
outFilter << filter << endl;
for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
- string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s]));
+ string filteredFasta = getOutputFileName("fasta", variables);
#ifdef USE_MPI
int pid, numSeqsPerProcessor, num;
int tag = 2001;
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
- vector<unsigned long long> positions = m->divideFile(fastafileNames[s], processors);
-
+
+ vector<unsigned long long> positions;
+ if (savedPositions.size() != 0) { positions = savedPositions[s]; }
+ else {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ positions = m->divideFile(fastafileNames[s], processors);
+#else
+ if(processors != 1){
+ int numFastaSeqs = 0;
+ positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
+ }
+#endif
+ }
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ //vector<unsigned long long> positions = m->divideFile(fastafileNames[s], processors);
+
for (int i = 0; i < (positions.size()-1); i++) {
lines.push_back(new linePair(positions[i], positions[(i+1)]));
}
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+
if(processors == 1){
int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
numSeqs += numFastaSeqs;
}else{
- int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s]);
+ int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s], filteredFasta);
numSeqs += numFastaSeqs;
-
- rename((fastafileNames[s] + toString(processIDS[0]) + ".temp").c_str(), filteredFasta.c_str());
-
- //append fasta files
- for(int i=1;i<processors;i++){
- m->appendFiles((fastafileNames[s] + toString(processIDS[i]) + ".temp"), filteredFasta);
- m->mothurRemove((fastafileNames[s] + toString(processIDS[i]) + ".temp"));
- }
}
if (m->control_pressed) { return 1; }
#else
+ if(processors == 1){
+ lines.push_back(new linePair(0, 1000));
int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
numSeqs += numFastaSeqs;
+ }else {
+ int numFastaSeqs = positions.size()-1;
+ //positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs);
+
+ //figure out how many sequences you have to process
+ int numSeqsPerProcessor = numFastaSeqs / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numSeqsPerProcessor;
+ if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; }
+ lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
+ }
+
+ numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s], filteredFasta);
+ numSeqs += numFastaSeqs;
+ }
if (m->control_pressed) { return 1; }
#endif
}
- if((i+1) % 100 == 0){ cout << (i+1) << endl; m->mothurOutJustToLog(toString(i+1) + "\n"); }
+ if((i+1) % 100 == 0){ cout << (i+1) << endl; }
}
if(outputString != ""){ //output to file
delete buf;
}
- if((num) % 100 != 0){ cout << (num) << endl; m->mothurOutJustToLog(toString(num) + "\n"); }
+ if((num) % 100 != 0){ cout << (num) << endl; }
return 0;
}
count++;
}
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = in.tellg();
if ((pos == -1) || (pos >= filePos->end)) { break; }
#else
#endif
//report progress
- if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count)+"\n"); }
}
//report progress
- if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count)+"\n"); }
out.close();
}
/**************************************************************************************************/
-int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
+int FilterSeqsCommand::createProcessesRunFilter(string F, string filename, string filteredFastaName) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- int process = 0;
+
+ int process = 1;
int num = 0;
processIDS.clear();
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
//loop through and create all the processes you want
while (process != processors) {
}
}
+ num = driverRunFilter(F, filteredFastaName, filename, lines[0]);
+
//force parent to wait until all the processes are done
- for (int i=0;i<processors;i++) {
+ for (int i=0;i<processIDS.size();i++) {
int temp = processIDS[i];
wait(&temp);
}
m->openInputFile(tempFile, in);
if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
in.close(); m->mothurRemove(tempFile);
+
+ m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filteredFastaName);
+ m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
}
-
+
+#else
+
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the filterData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //Taking advantage of shared memory to allow both threads to add info to F.
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<filterRunData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=0; i<processors-1; i++){
+
+ string extension = "";
+ if (i != 0) { extension = toString(i) + ".temp"; }
+
+ filterRunData* tempFilter = new filterRunData(filter, filename, (filteredFastaName + extension), m, lines[i]->start, lines[i]->end, alignmentLength, i);
+ pDataArray.push_back(tempFilter);
+ processIDS.push_back(i);
+
+ hThreadArray[i] = CreateThread(NULL, 0, MyRunFilterThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ }
+
+ num = driverRunFilter(F, (filteredFastaName + toString(processors-1) + ".temp"), filename, lines[processors-1]);
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
- return num;
-#endif
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ num += pDataArray[i]->count;
+ if (pDataArray[i]->count != pDataArray[i]->end) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
+ }
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+
+ for (int i = 1; i < processors; i++) {
+ m->appendFiles((filteredFastaName + toString(i) + ".temp"), filteredFastaName);
+ m->mothurRemove((filteredFastaName + toString(i) + ".temp"));
+ }
+#endif
+
+ return num;
+
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
#else
- vector<unsigned long long> positions = m->divideFile(fastafileNames[s], processors);
- for (int i = 0; i < (positions.size()-1); i++) {
- lines.push_back(new linePair(positions[i], positions[(i+1)]));
- }
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ vector<unsigned long long> positions;
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ positions = m->divideFile(fastafileNames[s], processors);
+ for (int i = 0; i < (positions.size()-1); i++) {
+ lines.push_back(new linePair(positions[i], positions[(i+1)]));
+ }
+
if(processors == 1){
int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
numSeqs += numFastaSeqs;
int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
numSeqs += numFastaSeqs;
}
-
- if (m->control_pressed) { return filterString; }
#else
- int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
- numSeqs += numFastaSeqs;
- if (m->control_pressed) { return filterString; }
+ if(processors == 1){
+ lines.push_back(new linePair(0, 1000));
+ int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
+ numSeqs += numFastaSeqs;
+ }else {
+ int numFastaSeqs = 0;
+ positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
+
+ //figure out how many sequences you have to process
+ int numSeqsPerProcessor = numFastaSeqs / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numSeqsPerProcessor;
+ if(i == (processors - 1)){ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor; }
+ lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
+ }
+
+ numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
+ numSeqs += numFastaSeqs;
+ }
#endif
+ //save the file positions so we can reuse them in the runFilter function
+ savedPositions[s] = positions;
+
+ if (m->control_pressed) { return filterString; }
#endif
}
MPI_Barrier(MPI_COMM_WORLD);
#endif
-
+
return filterString;
}
catch(exception& e) {
count++;
}
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = in.tellg();
if ((pos == -1) || (pos >= filePos->end)) { break; }
#else
#endif
//report progress
- if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count)+"\n"); }
}
//report progress
- if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+ if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count)+"\n"); }
in.close();
return count;
cout.flush();
//report progress
- if((i+1) % 100 == 0){ cout << (i+1) << endl; m->mothurOutJustToLog(toString(i+1) + "\n"); }
+ if((i+1) % 100 == 0){ cout << (i+1) << endl; }
}
//report progress
- if((num) % 100 != 0){ cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n"); }
+ if((num) % 100 != 0){ cout << num << endl; }
return 0;
}
int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- int process = 1;
+ int process = 1;
int num = 0;
processIDS.clear();
-
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
//loop through and create all the processes you want
while (process != processors) {
int pid = fork();
m->mothurRemove(tempFilename);
}
- return num;
-#endif
+
+#else
+
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the filterData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //Taking advantage of shared memory to allow both threads to add info to F.
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<filterData*> pDataArray;
+ DWORD dwThreadIdArray[processors];
+ HANDLE hThreadArray[processors];
+
+ //Create processor worker threads.
+ for( int i=0; i<processors; i++ ){
+
+ filterData* tempFilter = new filterData(filename, m, lines[i]->start, lines[i]->end, alignmentLength, trump, vertical, soft, hard, i);
+ pDataArray.push_back(tempFilter);
+ processIDS.push_back(i);
+
+ hThreadArray[i] = CreateThread(NULL, 0, MyCreateFilterThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ }
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ num += pDataArray[i]->count;
+ if (pDataArray[i]->count != pDataArray[i]->end) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
+ }
+ F.mergeFilter(pDataArray[i]->F.getFilter());
+
+ for (int k = 0; k < alignmentLength; k++) { F.a[k] += pDataArray[i]->F.a[k]; }
+ for (int k = 0; k < alignmentLength; k++) { F.t[k] += pDataArray[i]->F.t[k]; }
+ for (int k = 0; k < alignmentLength; k++) { F.g[k] += pDataArray[i]->F.g[k]; }
+ for (int k = 0; k < alignmentLength; k++) { F.c[k] += pDataArray[i]->F.c[k]; }
+ for (int k = 0; k < alignmentLength; k++) { F.gap[k] += pDataArray[i]->F.gap[k]; }
+
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+
+#endif
+ return num;
+
}
catch(exception& e) {
m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
projects / mothur.git / blobdiff