vector<string> ChopSeqsCommand::setParameters(){
try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter pnumbases("numbases", "Number", "", "0", "", "", "",false,true); parameters.push_back(pnumbases);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter pnumbases("numbases", "Number", "", "0", "", "", "",false,true); parameters.push_back(pnumbases);
CommandParameter pcountgaps("countgaps", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcountgaps);
CommandParameter pshort("short", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pshort);
CommandParameter pkeep("keep", "Multiple", "front-back", "front", "", "", "",false,false); parameters.push_back(pkeep);
helpString += "The keep parameter allows you to specify whether you want to keep the front or the back of your sequence, default=front.\n";
helpString += "The countgaps parameter allows you to specify whether you want to count gaps as bases, default=false.\n";
helpString += "The short parameter allows you to specify you want to keep sequences that are too short to chop, default=false.\n";
- helpString += "For example, if you ran chop.seqs with numbases=200 and short=t, if a sequence had 100 bases mothur would keep the sequence rather than eliminate it.\n";
+ helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
+ helpString += "For example, if you ran chop.seqs with numbases=200 and short=t, if a sequence had 100 bases mothur would keep the sequence rather than eliminate it.\n";
helpString += "Example chop.seqs(fasta=amazon.fasta, numbases=200, keep=front).\n";
helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
return helpString;
string temp = validParameter.validFile(parameters, "numbases", false); if (temp == "not found") { temp = "0"; }
m->mothurConvert(temp, numbases);
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
temp = validParameter.validFile(parameters, "countgaps", false); if (temp == "not found") { temp = "f"; }
countGaps = m->isTrue(temp);
string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta");
string outputFileNameAccnos = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("accnos");
+
+
+ vector<unsigned long long> positions;
+ vector<linePair> lines;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ positions = m->divideFile(fastafile, processors);
+ for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
+#else
+ int numSeqs = 0;
+ positions = m->setFilePosFasta(fastafile, numSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
- ofstream outAcc;
- m->openOutputFile(outputFileNameAccnos, outAcc);
-
- ifstream in;
- m->openInputFile(fastafile, in);
-
- bool wroteAccnos = false;
-
- while (!in.eof()) {
-
- Sequence seq(in);
-
- if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); outAcc.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputFileNameAccnos); return 0; }
-
- if (seq.getName() != "") {
- string newSeqString = getChopped(seq);
-
- //output trimmed sequence
- if (newSeqString != "") {
- out << ">" << seq.getName() << endl << newSeqString << endl;
- }else{
- outAcc << seq.getName() << endl;
- wroteAccnos = true;
- }
- }
- }
- in.close();
- out.close();
- outAcc.close();
+ //figure out how many sequences you have to process
+ int numSeqsPerProcessor = numSeqs / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numSeqsPerProcessor;
+ if(i == (processors - 1)){ numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; }
+ lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
+ }
+#endif
+
+ bool wroteAccnos = false;
+ if(processors == 1) { wroteAccnos = driver(lines[0], fastafile, outputFileName, outputFileNameAccnos); }
+ else { wroteAccnos = createProcesses(lines, fastafile, outputFileName, outputFileNameAccnos); }
+
+ if (m->control_pressed) { return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();
exit(1);
}
}
+/**************************************************************************************************/
+bool ChopSeqsCommand::createProcesses(vector<linePair> lines, string filename, string outFasta, string outAccnos) {
+ try {
+ int process = 1;
+ bool wroteAccnos = false;
+ vector<int> processIDS;
+ vector<string> nonBlankAccnosFiles;
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ wroteAccnos = driver(lines[process], filename, outFasta + toString(getpid()) + ".temp", outAccnos + toString(getpid()) + ".temp");
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = fastafile + toString(getpid()) + ".bool.temp";
+ m->openOutputFile(tempFile, out);
+ out << wroteAccnos << endl;
+ out.close();
+
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ //do your part
+ wroteAccnos = driver(lines[0], filename, outFasta, outAccnos);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+
+ if (wroteAccnos) { nonBlankAccnosFiles.push_back(outAccnos); }
+ else { m->mothurRemove(outAccnos); } //remove so other files can be renamed to it
+
+ //parent reads in and combine Filter info
+ for (int i = 0; i < processIDS.size(); i++) {
+ string tempFilename = fastafile + toString(processIDS[i]) + ".bool.temp";
+ ifstream in;
+ m->openInputFile(tempFilename, in);
+
+ bool temp;
+ in >> temp; m->gobble(in);
+ if (temp) { wroteAccnos = temp; nonBlankAccnosFiles.push_back(outAccnos + toString(processIDS[i]) + ".temp"); }
+ else { m->mothurRemove((outAccnos + toString(processIDS[i]) + ".temp")); }
+
+ in.close();
+ m->mothurRemove(tempFilename);
+ }
+#else
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the seqSumData 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 vectors.
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<chopData*> 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"; processIDS.push_back(i); }
+ // Allocate memory for thread data.
+ chopData* tempChop = new chopData(filename, (outFasta+extension), (outAccnos+extension), m, lines[i].start, lines[i].end, keep, countGaps, numbases, Short);
+ pDataArray.push_back(tempChop);
+
+ //MyChopThreadFunction 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] = CreateThread(NULL, 0, MyChopThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ }
+
+ //do your part
+ wroteAccnos = driver(lines[processors-1], filename, (outFasta + toString(processors-1) + ".temp"), (outAccnos + toString(processors-1) + ".temp"));
+ processIDS.push_back(processors-1);
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ if (wroteAccnos) { nonBlankAccnosFiles.push_back(outAccnos); }
+ else { m->mothurRemove(outAccnos); } //remove so other files can be renamed to it
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ if (pDataArray[i]->wroteAccnos) { wroteAccnos = pDataArray[i]->wroteAccnos; nonBlankAccnosFiles.push_back(outAccnos + toString(processIDS[i]) + ".temp"); }
+ else { m->mothurRemove((outAccnos + toString(processIDS[i]) + ".temp")); }
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+#endif
+
+ for (int i = 0; i < processIDS.size(); i++) {
+ m->appendFiles((outFasta + toString(processIDS[i]) + ".temp"), outFasta);
+ m->mothurRemove((outFasta + toString(processIDS[i]) + ".temp"));
+ }
+
+ if (nonBlankAccnosFiles.size() != 0) {
+ m->renameFile(nonBlankAccnosFiles[0], outAccnos);
+
+ for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
+ m->appendFiles(nonBlankAccnosFiles[h], outAccnos);
+ m->mothurRemove(nonBlankAccnosFiles[h]);
+ }
+ }else { //recreate the accnosfile if needed
+ ofstream out;
+ m->openOutputFile(outAccnos, out);
+ out.close();
+ }
+
+ return wroteAccnos;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChopSeqsCommand", "createProcesses");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+bool ChopSeqsCommand::driver(linePair filePos, string filename, string outFasta, string outAccnos) {
+ try {
+
+ ofstream out;
+ m->openOutputFile(outFasta, out);
+
+ ofstream outAcc;
+ m->openOutputFile(outAccnos, outAcc);
+
+ ifstream in;
+ m->openInputFile(filename, in);
+
+ in.seekg(filePos.start);
+
+ bool done = false;
+ bool wroteAccnos = false;
+ int count = 0;
+
+ while (!done) {
+
+ if (m->control_pressed) { in.close(); out.close(); return 1; }
+
+ Sequence seq(in); m->gobble(in);
+
+ if (m->control_pressed) { in.close(); out.close(); outAcc.close(); m->mothurRemove(outFasta); m->mothurRemove(outAccnos); return 0; }
+
+ if (seq.getName() != "") {
+ string newSeqString = getChopped(seq);
+
+ //output trimmed sequence
+ if (newSeqString != "") {
+ out << ">" << seq.getName() << endl << newSeqString << endl;
+ }else{
+ outAcc << seq.getName() << endl;
+ wroteAccnos = true;
+ }
+ count++;
+ }
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ unsigned long long pos = in.tellg();
+ if ((pos == -1) || (pos >= filePos.end)) { break; }
+#else
+ if (in.eof()) { break; }
+#endif
+ //report progress
+ if((count) % 1000 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+
+ }
+ //report progress
+ if((count) % 1000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
+
+
+ in.close();
+ out.close();
+ outAcc.close();
+
+ return wroteAccnos;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChopSeqsCommand", "driver");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
string ChopSeqsCommand::getChopped(Sequence seq) {
try {
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