+++ /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);
- }
-}
-
-/**************************************************************************************/
-
-
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