*/
#include "seqsummarycommand.h"
+#include "sequence.hpp"
//***************************************************************************************************************
-SeqSummaryCommand::SeqSummaryCommand(){
+SeqSummaryCommand::SeqSummaryCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
+ abort = false;
- if(globaldata->getFastaFile() != "") { readSeqs = new ReadFasta(globaldata->inputFileName); }
- else if(globaldata->getNexusFile() != "") { readSeqs = new ReadNexus(globaldata->inputFileName); }
- else if(globaldata->getClustalFile() != "") { readSeqs = new ReadClustal(globaldata->inputFileName); }
- else if(globaldata->getPhylipFile() != "") { readSeqs = new ReadPhylip(globaldata->inputFileName); }
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
- readSeqs->read();
- db = readSeqs->getDB();
- numSeqs = db->size();
+ else {
+ //valid paramters for this command
+ string Array[] = {"fasta","processors","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ 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("fasta");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = 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; }
+ }
+ }
+
+ //check for required parameters
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not open") { abort = true; }
+ else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the summary.seqs command."); m->mothurOutEndLine(); abort = true; }
+
+ //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 += 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 = "1"; }
+ convert(temp, processors);
+
+
+ }
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SeqCoordCommand class Function SeqCoordCommand. 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 SeqCoordCommand class function SeqCoordCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+
+void SeqSummaryCommand::help(){
+ try {
+ m->mothurOut("The summary.seqs command reads a fastafile and summarizes the sequences.\n");
+ m->mothurOut("The summary.seqs command parameters are fasta and processors, fasta is required.\n");
+ m->mothurOut("The summary.seqs command should be in the following format: \n");
+ m->mothurOut("summary.seqs(fasta=yourFastaFile, processors=2) \n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SeqSummaryCommand", "help");
exit(1);
- }
+ }
}
//***************************************************************************************************************
-SeqSummaryCommand::~SeqSummaryCommand(){
-}
+SeqSummaryCommand::~SeqSummaryCommand(){ /* do nothing */ }
//***************************************************************************************************************
int SeqSummaryCommand::execute(){
try{
- ofstream outfile;
- string summaryFile = getRootName(globaldata->inputFileName) + "summary";
- openOutputFile(summaryFile, outfile);
-
- vector<int> startPosition(numSeqs, 0);
- vector<int> endPosition(numSeqs, 0);
- vector<int> seqLength(numSeqs, 0);
- vector<int> ambigBases(numSeqs, 0);
- vector<int> longHomoPolymer(numSeqs, 0);
-
- if(db->get(0).getIsAligned() == 1){
- outfile << "seqname\tstart\tend\tlength\tambiguities\tlonghomopolymer" << endl;
- for(int i = 0; i < numSeqs; i++) {
- Sequence current = db->get(i);
- startPosition[i] = current.getStartPos();
- endPosition[i] = current.getEndPos();
- seqLength[i] = current.getNumBases();
- ambigBases[i] = current.getAmbigBases();
- longHomoPolymer[i] = current.getLongHomoPolymer();
- outfile << current.getName() << '\t' << startPosition[i] << '\t' << endPosition[i] << '\t' << seqLength[i] << '\t' << ambigBases[i] << '\t' << longHomoPolymer[i] << endl;
- }
- }
- else{
- outfile << "seqname\tlength\tambiguities\tlonghomopolymer" << endl;
- for(int i=0;i<numSeqs;i++){
- Sequence current = db->get(i);
- seqLength[i] = current.getNumBases();
- ambigBases[i] = current.getAmbigBases();
- longHomoPolymer[i] = current.getLongHomoPolymer();
- outfile << current.getName() << '\t' << seqLength[i] << '\t' << ambigBases[i] << '\t' << longHomoPolymer[i] << endl;
- }
- }
+ if (abort == true) { return 0; }
+
+ string summaryFile = outputDir + getSimpleName(fastafile) + ".summary";
+
+ int numSeqs = 0;
+ vector<int> startPosition;
+ vector<int> endPosition;
+ vector<int> seqLength;
+ vector<int> ambigBases;
+ vector<int> longHomoPolymer;
+
+#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<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\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 = 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
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ ifstream inFASTA;
+ openInputFile(fastafile, inFASTA);
+ getNumSeqs(inFASTA, numSeqs);
+ inFASTA.close();
+
+ lines.push_back(new linePair(0, numSeqs));
+
+ driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
+ }else{
+ numSeqs = setLines(fastafile);
+ createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile);
+
+ rename((summaryFile + toString(processIDS[0]) + ".temp").c_str(), summaryFile.c_str());
+ //append files
+ for(int i=1;i<processors;i++){
+ appendFiles((summaryFile + toString(processIDS[i]) + ".temp"), summaryFile);
+ remove((summaryFile + toString(processIDS[i]) + ".temp").c_str());
+ }
+ }
+
+ if (m->control_pressed) { return 0; }
+ #else
+ ifstream inFASTA;
+ openInputFile(fastafile, inFASTA);
+ getNumSeqs(inFASTA, numSeqs);
+ inFASTA.close();
+
+ lines.push_back(new linePair(0, numSeqs));
+
+ driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
+ if (m->control_pressed) { return 0; }
+ #endif
+#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 median = int(numSeqs * 0.500);
- int lowestPtile = int(numSeqs * 0.025);
- int lowPtile = int(numSeqs * 0.250);
- int highPtile = int(numSeqs * 0.750);
- int highestPtile = int(numSeqs * 0.975);
- int max = numSeqs - 1;
-
- cout << endl;
- if(db->get(0).getIsAligned() == 1){
- sort(startPosition.begin(), startPosition.end());
- sort(endPosition.begin(), endPosition.end());
+ 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;
+
+ //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) { remove(summaryFile.c_str()); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer"); 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])); 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])); 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])); 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])); 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])); 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])); 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])); m->mothurOutEndLine();
+ m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine();
+
+ if (m->control_pressed) { remove(summaryFile.c_str()); return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(summaryFile); m->mothurOutEndLine();
+ 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* line) {
+ try {
+
+ ofstream outSummary;
+ openOutputFile(sumFile, outSummary);
+
+ //print header if you are process 0
+ if (line->start == 0) {
+ outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer" << endl;
+ }
+
+ ifstream in;
+ openInputFile(filename, in);
+
+ in.seekg(line->start);
+
+ for(int i=0;i<line->num;i++){
+
+ if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
- cout << "\t\tStart\tEnd\tLength\tN's\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[lowestPtile] << '\t' << endPosition[lowestPtile] << '\t' << seqLength[lowestPtile] << '\t' << ambigBases[lowestPtile] << '\t' << longHomoPolymer[lowestPtile] << endl;
- cout << "25%-tile:\t" << startPosition[lowPtile] << '\t' << endPosition[lowPtile] << '\t' << seqLength[lowPtile] << '\t' << ambigBases[lowPtile] << '\t' << longHomoPolymer[lowPtile] << endl;
- cout << "Median: \t" << startPosition[median] << '\t' << endPosition[median] << '\t' << seqLength[median] << '\t' << ambigBases[median] << '\t' << longHomoPolymer[median] << endl;
- cout << "75%-tile:\t" << startPosition[highPtile] << '\t' << endPosition[highPtile] << '\t' << seqLength[highPtile] << '\t' << ambigBases[highPtile] << '\t' << longHomoPolymer[highPtile] << endl;
- cout << "97.5%-tile:\t" << startPosition[highestPtile] << '\t' << endPosition[highestPtile] << '\t' << seqLength[highestPtile] << '\t' << ambigBases[highestPtile] << '\t' << longHomoPolymer[highestPtile] << endl;
- cout << "Maximum:\t" << startPosition[max] << '\t' << endPosition[max] << '\t' << seqLength[max] << '\t' << ambigBases[max] << '\t' << longHomoPolymer[max] << endl;
+ Sequence current(in);
+
+ if (current.getName() != "") {
+ 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());
+
+ outSummary << current.getName() << '\t';
+ outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
+ outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
+ outSummary << current.getLongHomoPolymer() << endl;
+ }
+ gobble(in);
}
- else{
- cout << "\t\tLength\tN's\tPolymer" << endl;
- cout << "Minimum:\t" << seqLength[0] << '\t' << ambigBases[0] << '\t' << longHomoPolymer[0] << endl;
- cout << "2.5%-tile:\t" << seqLength[lowestPtile] << '\t' << ambigBases[lowestPtile] << '\t' << longHomoPolymer[lowestPtile] << endl;
- cout << "25%-tile:\t" << seqLength[lowPtile] << '\t' << ambigBases[lowPtile] << '\t' << longHomoPolymer[lowPtile] << endl;
- cout << "Median: \t" << seqLength[median] << '\t' << ambigBases[median] << '\t' << longHomoPolymer[median] << endl;
- cout << "75%-tile:\t"<< seqLength[highPtile] << '\t' << ambigBases[highPtile] << '\t' << longHomoPolymer[highPtile] << endl;
- cout << "97.5%-tile:\t"<< seqLength[highestPtile] << '\t' << ambigBases[highestPtile] << '\t' << longHomoPolymer[highestPtile] << endl;
- cout << "Maximum:\t" << seqLength[max] << '\t' << ambigBases[max] << '\t' << longHomoPolymer[max] << endl;
+ in.close();
+
+ return 0;
+ }
+ 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<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() != "") {
+ 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()) + "\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;
+ }
}
- cout << "# of Seqs:\t" << numSeqs << endl;
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the FilterSeqsCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "SeqSummaryCommand", "MPICreateSummary");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the FilterSeqsCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+#endif
+/**************************************************************************************************/
+int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 0;
+ int exitCommand = 1;
+ processIDS.clear();
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = vfork();
+
+ 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){
+ driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile + toString(getpid()) + ".temp", lines[process]);
+ exit(0);
+ }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+ }
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processors;i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ return exitCommand;
+#endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SeqSummaryCommand", "createProcessesCreateSummary");
exit(1);
}
-
}
+/**************************************************************************************************/
+
+int SeqSummaryCommand::setLines(string filename) {
+ try {
+
+ vector<unsigned long int> positions;
+
+ ifstream inFASTA;
+ openInputFile(filename, inFASTA);
+
+ string input;
+ while(!inFASTA.eof()){
+ input = getline(inFASTA);
+
+ if (input.length() != 0) {
+ if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
+ }
+ }
+ inFASTA.close();
+
+ int numFastaSeqs = positions.size();
+
+ FILE * pFile;
+ unsigned long int size;
+
+ //get num bytes in file
+ pFile = fopen (filename.c_str(),"rb");
+ if (pFile==NULL) perror ("Error opening file");
+ else{
+ fseek (pFile, 0, SEEK_END);
+ size=ftell (pFile);
+ fclose (pFile);
+ }
+
+ int numSeqsPerProcessor = numFastaSeqs / processors;
+
+ for (int i = 0; i < processors; i++) {
+ unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
+ if(i == processors - 1){
+ numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
+ }else{
+ unsigned long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
+ }
+ lines.push_back(new linePair(startPos, numSeqsPerProcessor));
+ }
+
+ return numFastaSeqs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SeqSummaryCommand", "setLines");
+ exit(1);
+ }
+}
//***************************************************************************************************************
projects / mothur.git / blobdiff