--- /dev/null
+/*
+ * summaryqualcommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 11/28/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "summaryqualcommand.h"
+
+
+//**********************************************************************************************************************
+vector<string> SummaryQualCommand::setParameters(){
+ try {
+ CommandParameter pqual("qfile", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pqual);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ 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);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryQualCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string SummaryQualCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The summary.qual command reads a quality file and an optional name file, and summarizes the quality information.\n";
+ helpString += "The summary.tax command parameters are qfile, name and processors. qfile is required, unless you have a valid current quality file.\n";
+ helpString += "The name parameter allows you to enter a name file associated with your quality file. \n";
+ helpString += "The summary.qual command should be in the following format: \n";
+ helpString += "summary.qual(qfile=yourQualityFile) \n";
+ helpString += "Note: No spaces between parameter labels (i.e. qfile), '=' and parameters (i.e.yourQualityFile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryQualCommand", "getHelpString");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+SummaryQualCommand::SummaryQualCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryQualCommand", "SummaryQualCommand");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+
+SummaryQualCommand::SummaryQualCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string,string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("qfile");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["qfile"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+
+ //check for required parameters
+ qualfile = validParameter.validFile(parameters, "qfile", true);
+ if (qualfile == "not open") { qualfile = ""; abort = true; }
+ else if (qualfile == "not found") {
+ qualfile = m->getQualFile();
+ if (qualfile != "") { m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current quality file and the qfile parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setQualFile(qualfile); }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { namefile = ""; abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ outputDir += m->hasPath(qualfile); //if user entered a file with a path then preserve it
+ }
+
+ string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
+ if (namefile == "") {
+ vector<string> files; files.push_back(qualfile);
+ parser.getNameFile(files);
+ }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryQualCommand", "SummaryQualCommand");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+int SummaryQualCommand::execute(){
+ try{
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ int start = time(NULL);
+ int numSeqs = 0;
+
+ vector<int> position;
+ vector<int> averageQ;
+ vector< vector<int> > scores;
+
+ if (m->control_pressed) { return 0; }
+
+ if (namefile != "") { nameMap = m->readNames(namefile); }
+
+ vector<unsigned long long> positions;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ positions = m->divideFile(qualfile, processors);
+ for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
+#else
+ if (processors == 1) {
+ lines.push_back(linePair(0, 1000));
+ }else {
+ positions = m->setFilePosFasta(qualfile, numSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
+
+ //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
+
+
+ if(processors == 1){ numSeqs = driverCreateSummary(position, averageQ, scores, qualfile, lines[0]); }
+ else{ numSeqs = createProcessesCreateSummary(position, averageQ, scores, qualfile); }
+
+ if (m->control_pressed) { return 0; }
+
+ //print summary file
+ string summaryFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + "qual.summary";
+ printQual(summaryFile, position, averageQ, scores);
+
+ if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; }
+
+ //output results to screen
+ cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
+ m->mothurOutEndLine();
+ m->mothurOut("Position\tNumSeqs\tAverageQ"); m->mothurOutEndLine();
+ for (int i = 0; i < position.size(); i+=100) {
+ float average = averageQ[i] / (float) position[i];
+ cout << i << '\t' << position[i] << '\t' << average;
+ m->mothurOutJustToLog(toString(i) + "\t" + toString(position[i]) + "\t" + toString(average)); m->mothurOutEndLine();
+ }
+
+ m->mothurOutEndLine();
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(summaryFile); m->mothurOutEndLine(); outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryQualCommand", "execute");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+int SummaryQualCommand::driverCreateSummary(vector<int>& position, vector<int>& averageQ, vector< vector<int> >& scores, string filename, linePair filePos) {
+ try {
+ ifstream in;
+ m->openInputFile(filename, in);
+
+ in.seekg(filePos.start);
+
+ bool done = false;
+ int count = 0;
+
+ while (!done) {
+
+ if (m->control_pressed) { in.close(); return 1; }
+
+ QualityScores current(in); m->gobble(in);
+
+ if (current.getName() != "") {
+
+ int num = 1;
+ if (namefile != "") {
+ //make sure this sequence is in the namefile, else error
+ map<string, int>::iterator it = nameMap.find(current.getName());
+
+ if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else { num = it->second; }
+ }
+
+ vector<int> thisScores = current.getQualityScores();
+
+ //resize to num of positions setting number of seqs with that size to 1
+ if (position.size() < thisScores.size()) { position.resize(thisScores.size(), 0); }
+ if (averageQ.size() < thisScores.size()) { averageQ.resize(thisScores.size(), 0); }
+ if (scores.size() < thisScores.size()) {
+ scores.resize(thisScores.size());
+ for (int i = 0; i < scores.size(); i++) { scores[i].resize(41, 0); }
+ }
+
+ //increase counts of number of seqs with this position
+ //average is really the total, we will average in execute
+ for (int i = 0; i < thisScores.size(); i++) {
+ position[i] += num;
+ averageQ[i] += (thisScores[i] * num); //weighting for namesfile
+ if (thisScores[i] > 40) { m->mothurOut("[ERROR]: " + current.getName() + " has a quality scores of " + toString(thisScores[i]) + ", expecting values to be less than 40."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else { scores[i][thisScores[i]] += num; }
+ }
+
+ count += num;
+ }
+
+#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
+ }
+
+ in.close();
+
+ return count;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryQualCommand", "driverCreateSummary");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int SummaryQualCommand::createProcessesCreateSummary(vector<int>& position, vector<int>& averageQ, vector< vector<int> >& scores, string filename) {
+ try {
+ int process = 1;
+ int numSeqs = 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();
+
+ 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){
+ numSeqs = driverCreateSummary(position, averageQ, scores, qualfile, lines[process]);
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = qualfile + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+
+ out << numSeqs << endl;
+ out << position.size() << endl;
+ for (int k = 0; k < position.size(); k++) { out << position[k] << '\t'; } out << endl;
+ for (int k = 0; k < averageQ.size(); k++) { out << averageQ[k] << '\t'; } out << endl;
+ for (int k = 0; k < scores.size(); k++) {
+ for (int j = 0; j < 41; j++) {
+ out << scores[k][j] << '\t';
+ }
+ out << endl;
+ }
+ out << 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
+ numSeqs = driverCreateSummary(position, averageQ, scores, qualfile, lines[0]);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ //parent reads in and combine Filter info
+ for (int i = 0; i < processIDS.size(); i++) {
+ string tempFilename = qualfile + toString(processIDS[i]) + ".num.temp";
+ ifstream in;
+ m->openInputFile(tempFilename, in);
+
+ int temp, tempNum;
+ in >> tempNum; m->gobble(in); numSeqs += tempNum;
+ in >> tempNum; m->gobble(in);
+
+ if (position.size() < tempNum) { position.resize(tempNum, 0); }
+ if (averageQ.size() < tempNum) { averageQ.resize(tempNum, 0); }
+ if (scores.size() < tempNum) {
+ scores.resize(tempNum);
+ for (int i = 0; i < scores.size(); i++) { scores[i].resize(41, 0); }
+ }
+
+ for (int k = 0; k < tempNum; k++) { in >> temp; position[k] += temp; } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; averageQ[k] += temp; } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) {
+ for (int j = 0; j < 41; j++) {
+ in >> temp; scores[k][j] += temp;
+ m->gobble(in);
+ }
+ }
+
+ in.close();
+ m->mothurRemove(tempFilename);
+ }
+
+#else
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the seqSumQualData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //Taking advantage of shared memory to pass results vectors.
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<seqSumQualData*> pDataArray;
+ DWORD dwThreadIdArray[processors];
+ HANDLE hThreadArray[processors];
+
+ //Create processor worker threads.
+ for( int i=0; i<processors; i++ ){
+
+ // Allocate memory for thread data.
+ seqSumQualData* tempSum = new seqSumQualData(filename, m, lines[i].start, lines[i].end, namefile, nameMap);
+ pDataArray.push_back(tempSum);
+ processIDS.push_back(i);
+
+ hThreadArray[i] = CreateThread(NULL, 0, MySeqSumQualThreadFunction, 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++){
+ numSeqs += pDataArray[i]->count;
+ int tempNum = pDataArray[i]->position.size();
+ if (position.size() < tempNum) { position.resize(tempNum, 0); }
+ if (averageQ.size() < tempNum) { averageQ.resize(tempNum, 0); }
+ if (scores.size() < tempNum) {
+ scores.resize(tempNum);
+ for (int i = 0; i < scores.size(); i++) { scores[i].resize(41, 0); }
+ }
+
+ for (int k = 0; k < tempNum; k++) { position[k] += pDataArray[i]->position[k]; }
+ for (int k = 0; k < tempNum; k++) { averageQ[k] += pDataArray[i]->averageQ[k]; }
+ for (int k = 0; k < tempNum; k++) { for (int j = 0; j < 41; j++) { scores[k][j] += pDataArray[i]->scores[k][j]; } }
+
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+#endif
+ return numSeqs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryQualCommand", "createProcessesCreateSummary");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int SummaryQualCommand::printQual(string sumFile, vector<int>& position, vector<int>& averageQ, vector< vector<int> >& scores) {
+ try {
+ ofstream out;
+ m->openOutputFile(sumFile, out);
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+ outputNames.push_back(sumFile); outputTypes["summary"].push_back(sumFile);
+
+ //print headings
+ out << "Position\tnumSeqs\tAverageQ\t";
+ for (int i = 0; i < 41; i++) { out << "q" << i << '\t'; }
+ out << endl;
+
+ for (int i = 0; i < position.size(); i++) {
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+ float average = averageQ[i] / (float) position[i];
+ out << i << '\t' << position[i] << '\t' << average << '\t';
+
+ for (int j = 0; j < 41; j++) {
+ out << scores[i][j] << '\t';
+ }
+ out << endl;
+ }
+
+ out.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryQualCommand", "printQual");
+ exit(1);
+ }
+}
+
+/**************************************************************************************/
+
+
projects / mothur.git / blobdiff