*/
#include "seqsummarycommand.h"
-#include "sequence.hpp"
+
+//**********************************************************************************************************************
+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);
+ }
+}
+//**********************************************************************************************************************
+string SeqSummaryCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "summary") { outputFileName = "summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SeqSummaryCommand", "getOutputFileNameTag");
+ 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){
+SeqSummaryCommand::SeqSummaryCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"fasta"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
- parser = new OptionParser();
- parser->parse(option, parameters); delete parser;
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter("summary.seqs");
+ map<string,string>::iterator it;
- ValidParameters* validParameter = new ValidParameters();
-
//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 (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);
+ fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { abort = true; }
- else if (fastafile == "not found") { fastafile = ""; cout << "fasta is a required parameter for the summary.seqs command." << endl; abort = true; }
- else { globaldata->setFastaFile(fastafile); globaldata->setFormat("fasta"); }
+ 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);
+ }
- delete validParameter;
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SeqSummaryCommand class Function SeqSummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the SeqSummaryCommand class function SeqSummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-void SeqSummaryCommand::help(){
- try {
- cout << "The summary.seqs command reads a fastafile and ...." << "\n";
- cout << "The summary.seqs command parameter is fasta and it is required." << "\n";
- cout << "The summary.seqs command should be in the following format: " << "\n";
- cout << "summary.seqs(fasta=yourFastaFile) " << "\n";
- cout << "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile)." << "\n" << "\n";
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SeqSummaryCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SeqSummaryCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
-
-//***************************************************************************************************************
-
-SeqSummaryCommand::~SeqSummaryCommand(){ /* do nothing */ }
-
//***************************************************************************************************************
int SeqSummaryCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
- ifstream inFASTA;
- openInputFile(fastafile, inFASTA);
+ //set current fasta to fastafile
+ m->setFastaFile(fastafile);
+
+ string summaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("summary");
+
int numSeqs = 0;
-
- ofstream outSummary;
- string summaryFile = fastafile + ".summary";
- openOutputFile(summaryFile, outSummary);
vector<int> startPosition;
vector<int> endPosition;
vector<int> ambigBases;
vector<int> longHomoPolymer;
- outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer" << endl;
+ 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);
- while(!inFASTA.eof()){
- Sequence current(inFASTA);
- 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());
+ 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]); }
+ }
+ }
+ }
- outSummary << current.getName() << '\t';
- outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
- outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
- outSummary << current.getLongHomoPolymer() << endl;
+ }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
- numSeqs++;
- gobble(inFASTA);
- }
- inFASTA.close();
+
+ 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(); }
- int ptile0_25 = int(numSeqs * 0.025);
- int ptile25 = int(numSeqs * 0.250);
- int ptile50 = int(numSeqs * 0.500);
- int ptile75 = int(numSeqs * 0.750);
- int ptile97_5 = int(numSeqs * 0.975);
- int ptile100 = numSeqs - 1;
-
- cout << endl;
- cout << "\t\tStart\tEnd\tNBases\tAmbigs\tPolymer" << endl;
- cout << "Minimum:\t" << startPosition[0] << '\t' << endPosition[0] << '\t' << seqLength[0] << '\t' << ambigBases[0] << '\t' << longHomoPolymer[0] << endl;
- cout << "2.5%-tile:\t" << startPosition[ptile0_25] << '\t' << endPosition[ptile0_25] << '\t' << seqLength[ptile0_25] << '\t' << ambigBases[ptile0_25] << '\t' << longHomoPolymer[ptile0_25] << endl;
- cout << "25%-tile:\t" << startPosition[ptile25] << '\t' << endPosition[ptile25] << '\t' << seqLength[ptile25] << '\t' << ambigBases[ptile25] << '\t' << longHomoPolymer[ptile25] << endl;
- cout << "Median: \t" << startPosition[ptile50] << '\t' << endPosition[ptile50] << '\t' << seqLength[ptile50] << '\t' << ambigBases[ptile50] << '\t' << longHomoPolymer[ptile50] << endl;
- cout << "75%-tile:\t" << startPosition[ptile75] << '\t' << endPosition[ptile75] << '\t' << seqLength[ptile75] << '\t' << ambigBases[ptile75] << '\t' << longHomoPolymer[ptile75] << endl;
- cout << "97.5%-tile:\t" << startPosition[ptile97_5] << '\t' << endPosition[ptile97_5] << '\t' << seqLength[ptile97_5] << '\t' << ambigBases[ptile97_5] << '\t' << longHomoPolymer[ptile97_5] << endl;
- cout << "Maximum:\t" << startPosition[ptile100] << '\t' << endPosition[ptile100] << '\t' << seqLength[ptile100] << '\t' << ambigBases[ptile100] << '\t' << longHomoPolymer[ptile100] << endl;
- cout << "# of Seqs:\t" << numSeqs << endl;
+ 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) {
- cout << "Standard Error: " << e.what() << " has occurred in the SeqSummaryCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SeqSummaryCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SeqSummaryCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/**************************************************************************************/
+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);
+ }
+}
+/**********************************************************************************************************************/
-//***************************************************************************************************************