//
#include "sffmultiplecommand.h"
+#include "sffinfocommand.h"
+#include "seqsummarycommand.h"
+#include "trimflowscommand.h"
+#include "shhhercommand.h"
+#include "trimseqscommand.h"
//**********************************************************************************************************************
CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
CommandParameter psignal("signal", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(psignal);
CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pnoise);
- CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "",false,false); parameters.push_back(pallfiles);
CommandParameter porder("order", "String", "", "", "", "", "",false,false); parameters.push_back(porder);
+ //shhh.flows
+ CommandParameter plookup("lookup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plookup);
+ CommandParameter pcutoff("cutoff", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(pcutoff);
+ CommandParameter pmaxiter("maxiter", "Number", "", "1000", "", "", "",false,false); parameters.push_back(pmaxiter);
+ CommandParameter plarge("large", "Number", "", "-1", "", "", "",false,false); parameters.push_back(plarge);
+ CommandParameter psigma("sigma", "Number", "", "60", "", "", "",false,false); parameters.push_back(psigma);
+ CommandParameter pmindelta("mindelta", "Number", "", "0.000001", "", "", "",false,false); parameters.push_back(pmindelta);
+
+ //trim.seqs parameters
+ CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "",false,false); parameters.push_back(pallfiles);
+ CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
+ CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxambig);
+ CommandParameter pminlength("minlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pminlength);
+ CommandParameter pmaxlength("maxlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pmaxlength);
+ CommandParameter pkeepforward("keepforward", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkeepforward);
+ CommandParameter pqtrim("qtrim", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pqtrim);
+ CommandParameter pqthreshold("qthreshold", "Number", "", "0", "", "", "",false,false); parameters.push_back(pqthreshold);
+ CommandParameter pqaverage("qaverage", "Number", "", "0", "", "", "",false,false); parameters.push_back(pqaverage);
+ CommandParameter prollaverage("rollaverage", "Number", "", "0", "", "", "",false,false); parameters.push_back(prollaverage);
+ CommandParameter pqwindowaverage("qwindowaverage", "Number", "", "0", "", "", "",false,false); parameters.push_back(pqwindowaverage);
+ CommandParameter pqstepsize("qstepsize", "Number", "", "1", "", "", "",false,false); parameters.push_back(pqstepsize);
+ CommandParameter pqwindowsize("qwindowsize", "Number", "", "50", "", "", "",false,false); parameters.push_back(pqwindowsize);
+ CommandParameter pkeepfirst("keepfirst", "Number", "", "0", "", "", "",false,false); parameters.push_back(pkeepfirst);
+ CommandParameter premovelast("removelast", "Number", "", "0", "", "", "",false,false); parameters.push_back(premovelast);
+
+
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);
try {
string helpString = "";
helpString += "The sff.multiple command reads a file containing sff filenames and optional oligos filenames. It runs the files through sffinfo, trim.flows, shhh.flows and trim.seqs combining the results.\n";
- helpString += "The sff.multiple command parameters are file, trim, maxhomop, maxflows, minflows, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, signal, noise, allfiles, order. file is required. \n";
+ helpString += "The sff.multiple command parameters are: ";
+ vector<string> parameters = setParameters();
+ for (int i = 0; i < parameters.size()-1; i++) {
+ helpString += parameters[i] + ", ";
+ }
+ helpString += parameters[parameters.size()-1] + ".\n";
helpString += "The file parameter allows you to enter the a file containing the list of sff files and optional oligos files.\n";
helpString += "The trim parameter allows you to indicate if you would like a sequences and quality scores generated by sffinfo trimmed to the clipQualLeft and clipQualRight values. Default=True. \n";
+ helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
+ helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
+ helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
+ helpString += "The maxlength parameter allows you to set and maximum sequence length. \n";
+ helpString += "The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs + sdiffs + ldiffs.\n";
+ helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n";
+ helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
+ helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
+ helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
+ helpString += "The qfile parameter allows you to provide a quality file.\n";
+ helpString += "The qthreshold parameter allows you to set a minimum quality score allowed. \n";
+ helpString += "The qaverage parameter allows you to set a minimum average quality score allowed. \n";
+ helpString += "The qwindowsize parameter allows you to set a number of bases in a window. Default=50.\n";
+ helpString += "The qwindowaverage parameter allows you to set a minimum average quality score allowed over a window. \n";
+ helpString += "The rollaverage parameter allows you to set a minimum rolling average quality score allowed over a window. \n";
+ helpString += "The qstepsize parameter allows you to set a number of bases to move the window over. Default=1.\n";
+ helpString += "The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n";
+ helpString += "The keepforward parameter allows you to indicate whether you want the forward primer removed or not. The default is F, meaning remove the forward primer.\n";
+ helpString += "The qtrim parameter will trim sequence from the point that they fall below the qthreshold and put it in the .trim file if set to true. The default is T.\n";
+ helpString += "The keepfirst parameter trims the sequence to the first keepfirst number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements. \n";
+ helpString += "The removelast removes the last removelast number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements.\n";
+
helpString += "Example sff.multiple(file=mySffOligosFile.txt, trim=F).\n";
helpString += "Note: No spaces between parameter labels (i.e. file), '=' and parameters (i.e.mySffOligosFile.txt).\n";
return helpString;
it = outputTypes.find(type);
if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
else {
- //if (type == "fasta") { outputFileName = "fasta"; }
- //else if (type == "flow") { outputFileName = "flow"; }
- // else if (type == "sfftxt") { outputFileName = "sff.txt"; }
- //else if (type == "qfile") { outputFileName = "qual"; }
- //else {
- m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;
- //}
+ m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;
}
return outputFileName;
}
string temp;
temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found"){ temp = "T"; }
trim = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "450"; }
+ m->mothurConvert(temp, minFlows);
+
+ temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "450"; }
+ m->mothurConvert(temp, maxFlows);
+
+ temp = validParameter.validFile(parameters, "maxhomop", false); if (temp == "not found"){ temp = "9"; }
+ m->mothurConvert(temp, maxHomoP);
+
+ temp = validParameter.validFile(parameters, "signal", false); if (temp == "not found"){ temp = "0.50"; }
+ m->mothurConvert(temp, signal);
+
+ temp = validParameter.validFile(parameters, "noise", false); if (temp == "not found"){ temp = "0.70"; }
+ m->mothurConvert(temp, noise);
+
+ temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found"){ temp = "0"; }
+ m->mothurConvert(temp, bdiffs);
+
+ temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found"){ temp = "0"; }
+ m->mothurConvert(temp, pdiffs);
+
+ temp = validParameter.validFile(parameters, "ldiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, ldiffs);
+
+ temp = validParameter.validFile(parameters, "sdiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, sdiffs);
+
+ temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs; temp = toString(tempTotal); }
+ m->mothurConvert(temp, tdiffs);
+
+ if(tdiffs == 0){ tdiffs = bdiffs + pdiffs + ldiffs + sdiffs; }
+
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
+ flowOrder = validParameter.validFile(parameters, "order", false);
+ if (flowOrder == "not found"){ flowOrder = "TACG"; }
+ else if(flowOrder.length() != 4){
+ m->mothurOut("The value of the order option must be four bases long\n");
+ }
+
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found"){ temp = "0.01"; }
+ m->mothurConvert(temp, cutoff);
+
+ temp = validParameter.validFile(parameters, "mindelta", false); if (temp == "not found"){ temp = "0.000001"; }
+ m->mothurConvert(temp, minDelta);
+
+ temp = validParameter.validFile(parameters, "maxiter", false); if (temp == "not found"){ temp = "1000"; }
+ m->mothurConvert(temp, maxIters);
+
+ temp = validParameter.validFile(parameters, "large", false); if (temp == "not found"){ temp = "0"; }
+ m->mothurConvert(temp, largeSize);
+ if (largeSize != 0) { large = true; }
+ else { large = false; }
+ if (largeSize < 0) { m->mothurOut("The value of the large cannot be negative.\n"); }
+
+ temp = validParameter.validFile(parameters, "sigma", false);if (temp == "not found") { temp = "60"; }
+ m->mothurConvert(temp, sigma);
+
+ temp = validParameter.validFile(parameters, "flip", false);
+ if (temp == "not found") { flip = 0; }
+ else { flip = m->isTrue(temp); }
+
+ temp = validParameter.validFile(parameters, "maxambig", false); if (temp == "not found") { temp = "-1"; }
+ m->mothurConvert(temp, maxAmbig);
+
+ temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, minLength);
+
+ temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, maxLength);
+
+ temp = validParameter.validFile(parameters, "qthreshold", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, qThreshold);
+
+ temp = validParameter.validFile(parameters, "qtrim", false); if (temp == "not found") { temp = "t"; }
+ qtrim = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "rollaverage", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, qRollAverage);
+
+ temp = validParameter.validFile(parameters, "qwindowaverage", false);if (temp == "not found") { temp = "0"; }
+ convert(temp, qWindowAverage);
+
+ temp = validParameter.validFile(parameters, "qwindowsize", false); if (temp == "not found") { temp = "50"; }
+ convert(temp, qWindowSize);
+
+ temp = validParameter.validFile(parameters, "qstepsize", false); if (temp == "not found") { temp = "1"; }
+ convert(temp, qWindowStep);
+
+ temp = validParameter.validFile(parameters, "qaverage", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, qAverage);
+
+ temp = validParameter.validFile(parameters, "keepfirst", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, keepFirst);
+
+ temp = validParameter.validFile(parameters, "removelast", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, removeLast);
+
+ temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; }
+ allFiles = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "keepforward", false); if (temp == "not found") { temp = "F"; }
+ keepforward = m->isTrue(temp);
+
+ numFPrimers = 0;
+ numRPrimers = 0;
+ numLinkers = 0;
+ numSpacers = 0;
}
}
catch(exception& e) {
if (m->control_pressed) { return 0; }
+ if (sffFiles.size() < processors) { processors = sffFiles.size(); }
+
+ if (processors == 1) { driver(sffFiles, oligosFiles, 0, sffFiles.size()); }
+ else { createProcesses(sffFiles, oligosFiles); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
- //set fasta file as new current fastafile
- string current = "";
- itTypes = outputTypes.find("fasta");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
- }
-
- itTypes = outputTypes.find("qfile");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
- }
-
- itTypes = outputTypes.find("flow");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFlowFile(current); }
- }
-
//report output filenames
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
}
}
//**********************************************************************************************************************
+int SffMultipleCommand::driver(vector<string> sffFiles, vector<string> oligosFiles, int start, int end){
+ try {
+ int count = 0;
+ for (int i = start; i < end; i++) {
+ string sff = sffFiles[i];
+ string oligos = oligosFiles[i];
+
+ //run sff.info
+ string inputString = "sff=" + sff + ", flow=T";
+ if (trim) { inputString += ", trim=T"; }
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: sffinfo(" + inputString + ")"); m->mothurOutEndLine();
+ m->mothurCalling = true;
+
+ Command* sffCommand = new SffInfoCommand(inputString);
+ sffCommand->execute();
+
+ map<string, vector<string> > filenames = sffCommand->getOutputFiles();
+
+ delete sffCommand;
+ m->mothurCalling = false;
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
+ //run summary.seqs on the fasta file
+ string fastaFile = "";
+ map<string, vector<string> >::iterator it = filenames.find("fasta");
+ if (it != filenames.end()) { if ((it->second).size() != 0) { fastaFile = (it->second)[0]; } }
+ else { m->mothurOut("[ERROR]: sffinfo did not create a fasta file, quitting.\n"); m->control_pressed = true; break; }
+
+ inputString = "fasta=" + fastaFile;
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: summary.seqs(" + inputString + ")"); m->mothurOutEndLine();
+ m->mothurCalling = true;
+
+ Command* summarySeqsCommand = new SeqSummaryCommand(inputString);
+ summarySeqsCommand->execute();
+
+ delete summarySeqsCommand;
+ m->mothurCalling = false;
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
+ count++;
+ }
+
+ return count;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SffMultipleCommand", "driver");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SffMultipleCommand::createProcesses(vector<string> sffFiles, vector<string> oligosFiles){
+ try {
+ vector<int> processIDS;
+ int process = 1;
+ int num = 0;
+
+ //divide the groups between the processors
+ vector<linePair> lines;
+ vector<int> numFilesToComplete;
+ int numFilesPerProcessor = sffFiles.size() / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numFilesPerProcessor;
+ int endIndex = (i+1) * numFilesPerProcessor;
+ if(i == (processors - 1)){ endIndex = sffFiles.size(); }
+ lines.push_back(linePair(startIndex, endIndex));
+ numFilesToComplete.push_back((endIndex-startIndex));
+ }
+
+#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){
+ num = driver(sffFiles, oligosFiles, lines[process].start, lines[process].end);
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+ out << num << 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 my part
+ num = driver(sffFiles, oligosFiles, lines[0].start, lines[0].end);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+#else
+
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the sffMultiplesData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ /*
+ vector<shhhFlowsData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor worker threads.
+ for( int i=0; i<processors-1; i++ ){
+ // Allocate memory for thread data.
+ string extension = "";
+ if (i != 0) { extension = toString(i) + ".temp"; }
+
+ shhhFlowsData* tempFlow = new shhhFlowsData(filenames, (compositeFASTAFileName + extension), (compositeNamesFileName + extension), outputDir, flowOrder, jointLookUp, singleLookUp, m, lines[i].start, lines[i].end, cutoff, sigma, minDelta, maxIters, i);
+ pDataArray.push_back(tempFlow);
+ processIDS.push_back(i);
+
+ hThreadArray[i] = CreateThread(NULL, 0, ShhhFlowsThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ }
+
+ //using the main process as a worker saves time and memory
+ //do my part
+ driver(filenames, compositeFASTAFileName, compositeNamesFileName, lines[processors-1].start, lines[processors-1].end);
+
+ //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++){
+ for(int j=0; j < pDataArray[i]->outputNames.size(); j++){ outputNames.push_back(pDataArray[i]->outputNames[j]); }
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+ */
+#endif
+
+ for (int i=0;i<processIDS.size();i++) {
+ ifstream in;
+ string tempFile = toString(processIDS[i]) + ".num.temp";
+ m->openInputFile(tempFile, in);
+ if (!in.eof()) {
+ int tempNum = 0;
+ in >> tempNum;
+ if (tempNum != numFilesToComplete[i+1]) {
+ m->mothurOut("[ERROR]: main process expected " + toString(processIDS[i]) + " to complete " + toString(numFilesToComplete[i+1]) + " files, and it only reported completing " + toString(tempNum) + ". This will cause file mismatches. The flow files may be too large to process with multiple processors. \n");
+ }
+ }
+ in.close(); m->mothurRemove(tempFile);
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhherCommand", "createProcesses");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
projects / mothur.git / blobdiff