+++ /dev/null
-/*
- * seqcoordcommand.cpp
- * Mothur
- *
- * Created by Pat Schloss on 5/30/09.
- * Copyright 2009 Patrick D. Schloss. All rights reserved.
- *
- */
-
-#include "seqsummarycommand.h"
-
-
-//**********************************************************************************************************************
-vector<string> SeqSummaryCommand::setParameters(){
- try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- 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, "SeqSummaryCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string SeqSummaryCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The summary.seqs command reads a fastafile and summarizes the sequences.\n";
- helpString += "The summary.seqs command parameters are fasta, name and processors, fasta is required, unless you have a valid current fasta file.\n";
- helpString += "The name parameter allows you to enter a name file associated with your fasta file. \n";
- helpString += "The summary.seqs command should be in the following format: \n";
- helpString += "summary.seqs(fasta=yourFastaFile, processors=2) \n";
- helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "SeqSummaryCommand", "getHelpString");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-SeqSummaryCommand::SeqSummaryCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["summary"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
- exit(1);
- }
-}
-//***************************************************************************************************************
-
-SeqSummaryCommand::SeqSummaryCommand(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("summary.seqs");
- 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("fasta");
- //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["fasta"] = 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
- fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not open") { abort = true; }
- else if (fastafile == "not found") {
- fastafile = m->getFastaFile();
- if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
- }else { m->setFastaFile(fastafile); }
-
- 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(fastafile); //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(fastafile);
- parser.getNameFile(files);
- }
-
- }
- }
- catch(exception& e) {
- m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
- exit(1);
- }
-}
-//***************************************************************************************************************
-
-int SeqSummaryCommand::execute(){
- try{
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- //set current fasta to fastafile
- m->setFastaFile(fastafile);
-
- string summaryFile = outputDir + m->getSimpleName(fastafile) + ".summary";
-
- int numSeqs = 0;
-
- vector<int> startPosition;
- vector<int> endPosition;
- vector<int> seqLength;
- vector<int> ambigBases;
- vector<int> longHomoPolymer;
-
- if (namefile != "") { nameMap = m->readNames(namefile); }
-
- if (m->control_pressed) { return 0; }
-
-#ifdef USE_MPI
- int pid, numSeqsPerProcessor;
- int tag = 2001;
- int startTag = 1; int endTag = 2; int lengthTag = 3; int baseTag = 4; int lhomoTag = 5;
- int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
- vector<unsigned long long> MPIPos;
-
- MPI_Status status;
- MPI_Status statusOut;
- MPI_File inMPI;
- MPI_File outMPI;
- MPI_Comm_size(MPI_COMM_WORLD, &processors);
- MPI_Comm_rank(MPI_COMM_WORLD, &pid);
-
- char tempFileName[1024];
- strcpy(tempFileName, fastafile.c_str());
-
- char sumFileName[1024];
- strcpy(sumFileName, summaryFile.c_str());
-
- MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
- MPI_File_open(MPI_COMM_WORLD, sumFileName, outMode, MPI_INFO_NULL, &outMPI);
-
- if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
-
- if (pid == 0) { //you are the root process
- //print header
- string outputString = "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs\n";
- int length = outputString.length();
- char* buf2 = new char[length];
- memcpy(buf2, outputString.c_str(), length);
-
- MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &statusOut);
- delete buf2;
-
- MPIPos = m->setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
-
- for(int i = 1; i < processors; i++) {
- MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
- MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
- }
-
- //figure out how many sequences you have to do
- numSeqsPerProcessor = numSeqs / processors;
- int startIndex = pid * numSeqsPerProcessor;
- if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
-
- //do your part
- MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
-
- }else { //i am the child process
-
- MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
- MPIPos.resize(numSeqs+1);
- MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
-
- //figure out how many sequences you have to align
- numSeqsPerProcessor = numSeqs / processors;
- int startIndex = pid * numSeqsPerProcessor;
- if(pid == (processors - 1)){ numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; }
-
- //do your part
- MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
- }
-
- MPI_File_close(&inMPI);
- MPI_File_close(&outMPI);
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
-
- if (pid == 0) {
- //get the info from the child processes
- for(int i = 1; i < processors; i++) {
- int size;
- MPI_Recv(&size, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
-
- vector<int> temp; temp.resize(size+1);
-
- for(int j = 0; j < 5; j++) {
-
- MPI_Recv(&temp[0], (size+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
- int receiveTag = temp[temp.size()-1]; //child process added a int to the end to indicate what count this is for
-
- if (receiveTag == startTag) {
- for (int k = 0; k < size; k++) { startPosition.push_back(temp[k]); }
- }else if (receiveTag == endTag) {
- for (int k = 0; k < size; k++) { endPosition.push_back(temp[k]); }
- }else if (receiveTag == lengthTag) {
- for (int k = 0; k < size; k++) { seqLength.push_back(temp[k]); }
- }else if (receiveTag == baseTag) {
- for (int k = 0; k < size; k++) { ambigBases.push_back(temp[k]); }
- }else if (receiveTag == lhomoTag) {
- for (int k = 0; k < size; k++) { longHomoPolymer.push_back(temp[k]); }
- }
- }
- }
-
- }else{
-
- //send my counts
- int size = startPosition.size();
- MPI_Send(&size, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
-
- startPosition.push_back(startTag);
- int ierr = MPI_Send(&(startPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
- endPosition.push_back(endTag);
- ierr = MPI_Send (&(endPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
- seqLength.push_back(lengthTag);
- ierr = MPI_Send(&(seqLength[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
- ambigBases.push_back(baseTag);
- ierr = MPI_Send(&(ambigBases[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
- longHomoPolymer.push_back(lhomoTag);
- ierr = MPI_Send(&(longHomoPolymer[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
- }
-
- MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
-#else
- vector<unsigned long long> positions;
- #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(new linePair(positions[i], positions[(i+1)])); }
- #else
- positions = m->setFilePosFasta(fastafile, 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(new linePair(positions[startIndex], numSeqsPerProcessor));
- }
- #endif
-
-
- if(processors == 1){
- numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
- }else{
- numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile);
- }
-
- if (m->control_pressed) { return 0; }
-#endif
-
- #ifdef USE_MPI
- if (pid == 0) {
- #endif
-
- sort(startPosition.begin(), startPosition.end());
- sort(endPosition.begin(), endPosition.end());
- sort(seqLength.begin(), seqLength.end());
- sort(ambigBases.begin(), ambigBases.end());
- sort(longHomoPolymer.begin(), longHomoPolymer.end());
- int size = startPosition.size();
-
- //find means
- float meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer;
- meanStartPosition = 0; meanEndPosition = 0; meanSeqLength = 0; meanAmbigBases = 0; meanLongHomoPolymer = 0;
- for (int i = 0; i < size; i++) {
- meanStartPosition += startPosition[i];
- meanEndPosition += endPosition[i];
- meanSeqLength += seqLength[i];
- meanAmbigBases += ambigBases[i];
- meanLongHomoPolymer += longHomoPolymer[i];
- }
- //this is an int divide so the remainder is lost
- meanStartPosition /= (float) size; meanEndPosition /= (float) size; meanLongHomoPolymer /= (float) size; meanSeqLength /= (float) size; meanAmbigBases /= (float) size;
-
- int ptile0_25 = int(size * 0.025);
- int ptile25 = int(size * 0.250);
- int ptile50 = int(size * 0.500);
- int ptile75 = int(size * 0.750);
- int ptile97_5 = int(size * 0.975);
- int ptile100 = size - 1;
-
- //to compensate for blank sequences that would result in startPosition and endPostion equalling -1
- if (startPosition[0] == -1) { startPosition[0] = 0; }
- if (endPosition[0] == -1) { endPosition[0] = 0; }
-
- if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; }
-
- m->mothurOutEndLine();
- m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer\tNumSeqs"); m->mothurOutEndLine();
- m->mothurOut("Minimum:\t" + toString(startPosition[0]) + "\t" + toString(endPosition[0]) + "\t" + toString(seqLength[0]) + "\t" + toString(ambigBases[0]) + "\t" + toString(longHomoPolymer[0]) + "\t" + toString(1)); m->mothurOutEndLine();
- m->mothurOut("2.5%-tile:\t" + toString(startPosition[ptile0_25]) + "\t" + toString(endPosition[ptile0_25]) + "\t" + toString(seqLength[ptile0_25]) + "\t" + toString(ambigBases[ptile0_25]) + "\t"+ toString(longHomoPolymer[ptile0_25]) + "\t" + toString(ptile0_25+1)); m->mothurOutEndLine();
- m->mothurOut("25%-tile:\t" + toString(startPosition[ptile25]) + "\t" + toString(endPosition[ptile25]) + "\t" + toString(seqLength[ptile25]) + "\t" + toString(ambigBases[ptile25]) + "\t" + toString(longHomoPolymer[ptile25]) + "\t" + toString(ptile25+1)); m->mothurOutEndLine();
- m->mothurOut("Median: \t" + toString(startPosition[ptile50]) + "\t" + toString(endPosition[ptile50]) + "\t" + toString(seqLength[ptile50]) + "\t" + toString(ambigBases[ptile50]) + "\t" + toString(longHomoPolymer[ptile50]) + "\t" + toString(ptile50+1)); m->mothurOutEndLine();
- m->mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75]) + "\t" + toString(ptile75+1)); m->mothurOutEndLine();
- m->mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5]) + "\t" + toString(ptile97_5+1)); m->mothurOutEndLine();
- m->mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100]) + "\t" + toString(ptile100+1)); m->mothurOutEndLine();
- m->mothurOut("Mean:\t" + toString(meanStartPosition) + "\t" + toString(meanEndPosition) + "\t" + toString(meanSeqLength) + "\t" + toString(meanAmbigBases) + "\t" + toString(meanLongHomoPolymer)); m->mothurOutEndLine();
-
- if (namefile == "") { m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); }
- else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(startPosition.size())); m->mothurOutEndLine(); }
-
- if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; }
-
- 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();
-
- #ifdef USE_MPI
- }
- #endif
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "SeqSummaryCommand", "execute");
- exit(1);
- }
-}
-/**************************************************************************************/
-int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile, linePair* filePos) {
- try {
-
- ofstream outSummary;
- m->openOutputFile(sumFile, outSummary);
-
- //print header if you are process 0
- if (filePos->start == 0) {
- outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs" << endl;
- }
-
- ifstream in;
- m->openInputFile(filename, in);
-
- in.seekg(filePos->start);
-
- bool done = false;
- int count = 0;
-
- while (!done) {
-
- if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
-
- Sequence 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; }
- }
-
- //for each sequence this sequence represents
- for (int i = 0; i < num; i++) {
- startPosition.push_back(current.getStartPos());
- endPosition.push_back(current.getEndPos());
- seqLength.push_back(current.getNumBases());
- ambigBases.push_back(current.getAmbigBases());
- longHomoPolymer.push_back(current.getLongHomoPolymer());
- }
-
- count++;
- outSummary << current.getName() << '\t';
- outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
- outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
- outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
- }
-
- #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) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
- }
- //report progress
- //if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); }
-
- in.close();
-
- return count;
- }
- catch(exception& e) {
- m->errorOut(e, "SeqSummaryCommand", "driverCreateSummary");
- exit(1);
- }
-}
-#ifdef USE_MPI
-/**************************************************************************************/
-int SeqSummaryCommand::MPICreateSummary(int start, int num, vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long long>& MPIPos) {
- try {
-
- int pid;
- MPI_Status status;
- MPI_Comm_rank(MPI_COMM_WORLD, &pid);
-
- for(int i=0;i<num;i++){
-
- if (m->control_pressed) { return 0; }
-
- //read next sequence
- int length = MPIPos[start+i+1] - MPIPos[start+i];
-
- char* buf4 = new char[length];
- MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
-
- string tempBuf = buf4;
- if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
- istringstream iss (tempBuf,istringstream::in);
- delete buf4;
-
- Sequence current(iss);
-
- 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()) { cout << "[ERROR]: " << current.getName() << " is not in your namefile, please correct." << endl; m->control_pressed = true; }
- else { num = it->second; }
- }
-
- //for each sequence this sequence represents
- for (int i = 0; i < num; i++) {
- startPosition.push_back(current.getStartPos());
- endPosition.push_back(current.getEndPos());
- seqLength.push_back(current.getNumBases());
- ambigBases.push_back(current.getAmbigBases());
- longHomoPolymer.push_back(current.getLongHomoPolymer());
- }
-
- string outputString = current.getName() + "\t" + toString(current.getStartPos()) + "\t" + toString(current.getEndPos()) + "\t";
- outputString += toString(current.getNumBases()) + "\t" + toString(current.getAmbigBases()) + "\t" + toString(current.getLongHomoPolymer()) + "\t" + toString(num) + "\n";
-
- //output to file
- length = outputString.length();
- char* buf3 = new char[length];
- memcpy(buf3, outputString.c_str(), length);
-
- MPI_File_write_shared(outMPI, buf3, length, MPI_CHAR, &status);
- delete buf3;
- }
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "SeqSummaryCommand", "MPICreateSummary");
- exit(1);
- }
-}
-#endif
-/**************************************************************************************************/
-int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile) {
- try {
- 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();
-
- 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 = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile + toString(getpid()) + ".temp", lines[process]);
-
- //pass numSeqs to parent
- ofstream out;
- string tempFile = fastafile + toString(getpid()) + ".num.temp";
- m->openOutputFile(tempFile, out);
-
- out << num << endl;
- out << startPosition.size() << endl;
- for (int k = 0; k < startPosition.size(); k++) { out << startPosition[k] << '\t'; } out << endl;
- for (int k = 0; k < endPosition.size(); k++) { out << endPosition[k] << '\t'; } out << endl;
- for (int k = 0; k < seqLength.size(); k++) { out << seqLength[k] << '\t'; } out << endl;
- for (int k = 0; k < ambigBases.size(); k++) { out << ambigBases[k] << '\t'; } out << endl;
- for (int k = 0; k < longHomoPolymer.size(); k++) { out << longHomoPolymer[k] << '\t'; } 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
- num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile, 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 = fastafile + toString(processIDS[i]) + ".num.temp";
- ifstream in;
- m->openInputFile(tempFilename, in);
-
- int temp, tempNum;
- in >> tempNum; m->gobble(in); num += tempNum;
- in >> tempNum; m->gobble(in);
- for (int k = 0; k < tempNum; k++) { in >> temp; startPosition.push_back(temp); } m->gobble(in);
- for (int k = 0; k < tempNum; k++) { in >> temp; endPosition.push_back(temp); } m->gobble(in);
- for (int k = 0; k < tempNum; k++) { in >> temp; seqLength.push_back(temp); } m->gobble(in);
- for (int k = 0; k < tempNum; k++) { in >> temp; ambigBases.push_back(temp); } m->gobble(in);
- for (int k = 0; k < tempNum; k++) { in >> temp; longHomoPolymer.push_back(temp); } m->gobble(in);
-
- in.close();
- m->mothurRemove(tempFilename);
-
- m->appendFiles((sumFile + toString(processIDS[i]) + ".temp"), sumFile);
- m->mothurRemove((sumFile + toString(processIDS[i]) + ".temp"));
- }
-
-#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<seqSumData*> 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.
- seqSumData* tempSum = new seqSumData(filename, (sumFile+extension), m, lines[i]->start, lines[i]->end, namefile, nameMap);
- pDataArray.push_back(tempSum);
-
- //MySeqSumThreadFunction 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, MySeqSumThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
- }
-
- //do your part
- num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, (sumFile+toString(processors-1)+".temp"), lines[processors-1]);
- processIDS.push_back(processors-1);
-
- //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++){
- num += pDataArray[i]->count;
- for (int k = 0; k < pDataArray[i]->startPosition.size(); k++) { startPosition.push_back(pDataArray[i]->startPosition[k]); }
- for (int k = 0; k < pDataArray[i]->endPosition.size(); k++) { endPosition.push_back(pDataArray[i]->endPosition[k]); }
- for (int k = 0; k < pDataArray[i]->seqLength.size(); k++) { seqLength.push_back(pDataArray[i]->seqLength[k]); }
- for (int k = 0; k < pDataArray[i]->ambigBases.size(); k++) { ambigBases.push_back(pDataArray[i]->ambigBases[k]); }
- for (int k = 0; k < pDataArray[i]->longHomoPolymer.size(); k++) { longHomoPolymer.push_back(pDataArray[i]->longHomoPolymer[k]); }
- CloseHandle(hThreadArray[i]);
- delete pDataArray[i];
- }
-
- //append files
- for(int i=0;i<processIDS.size();i++){
- m->appendFiles((sumFile + toString(processIDS[i]) + ".temp"), sumFile);
- m->mothurRemove((sumFile + toString(processIDS[i]) + ".temp"));
- }
-#endif
- return num;
- }
- catch(exception& e) {
- m->errorOut(e, "SeqSummaryCommand", "createProcessesCreateSummary");
- exit(1);
- }
-}
-/**********************************************************************************************************************/
-
-
-
projects / mothur.git / blobdiff