*/
#include "distancecommand.h"
-#include "ignoregaps.h"
-#include "eachgapdist.h"
-#include "eachgapignore.h"
-#include "onegapdist.h"
-#include "onegapignore.h"
//**********************************************************************************************************************
-
-DistanceCommand::DistanceCommand(){
+vector<string> DistanceCommand::setParameters(){
try {
- globaldata = GlobalData::getInstance();
- validCalculator = new ValidCalculators();
- countends = globaldata->getCountEnds();
- convert(globaldata->getProcessors(), processors);
- convert(globaldata->getCutOff(), cutoff);
-
- //open file
- string filename = globaldata->getFastaFile();
- openInputFile(filename, in);
-
-
- int i;
- if (isTrue(countends) == true) {
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("distance", globaldata->Estimators[i]) == true) {
- if (globaldata->Estimators[i] == "nogaps") {
- distCalculator = new ignoreGaps();
- }else if (globaldata->Estimators[i] == "eachgap") {
- distCalculator = new eachGapDist();
- }else if (globaldata->Estimators[i] == "onegap") {
- distCalculator = new oneGapDist(); }
- }
+ CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "OldFastaColumn","column",false,false); parameters.push_back(pcolumn);
+ CommandParameter poldfasta("oldfasta", "InputTypes", "", "", "none", "none", "OldFastaColumn","",false,false); parameters.push_back(poldfasta);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","phylip-column",false,true, true); parameters.push_back(pfasta);
+ CommandParameter poutput("output", "Multiple", "column-lt-square-phylip", "column", "", "", "","phylip-column",false,false, true); parameters.push_back(poutput);
+ CommandParameter pcalc("calc", "Multiple", "nogaps-eachgap-onegap", "onegap", "", "", "","",false,false); parameters.push_back(pcalc);
+ CommandParameter pcountends("countends", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pcountends);
+ CommandParameter pcompress("compress", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pcompress);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false, true); parameters.push_back(pprocessors);
+ CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "","",false,false, true); parameters.push_back(pcutoff);
+ 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, "DistanceCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string DistanceCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The dist.seqs command reads a file containing sequences and creates a distance file.\n";
+ helpString += "The dist.seqs command parameters are fasta, oldfasta, column, calc, countends, output, compress, cutoff and processors. \n";
+ helpString += "The fasta parameter is required, unless you have a valid current fasta file.\n";
+ helpString += "The oldfasta and column parameters allow you to append the distances calculated to the column file.\n";
+ helpString += "The calc parameter allows you to specify the method of calculating the distances. Your options are: nogaps, onegap or eachgap. The default is onegap.\n";
+ helpString += "The countends parameter allows you to specify whether to include terminal gaps in distance. Your options are: T or F. The default is T.\n";
+ helpString += "The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n";
+ helpString += "The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n";
+ helpString += "The processors parameter allows you to specify number of processors to use. The default is 1.\n";
+ helpString += "The compress parameter allows you to indicate that you want the resulting distance file compressed. The default is false.\n";
+ helpString += "The dist.seqs command should be in the following format: \n";
+ helpString += "dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n";
+ helpString += "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string DistanceCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "phylip") { pattern = "[filename],[outputtag],dist"; }
+ else if (type == "column") { pattern = "[filename],dist"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+DistanceCommand::DistanceCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ outputTypes["column"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "DistanceCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+DistanceCommand::DistanceCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+ Estimators.clear();
+
+ //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("dist.seqs");
+ map<string, string>::iterator it2;
+
+ //check to make sure all parameters are valid for command
+ for (it2 = parameters.begin(); it2 != parameters.end(); it2++) {
+ if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) { abort = true; }
}
- }else {
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("distance", globaldata->Estimators[i]) == true) {
- if (globaldata->Estimators[i] == "nogaps") {
- distCalculator = new ignoreGaps();
- }else if (globaldata->Estimators[i] == "eachgap") {
- distCalculator = new eachGapIgnoreTermGapDist();
- }else if (globaldata->Estimators[i] == "onegap") {
- distCalculator = new oneGapIgnoreTermGapDist();
- }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["phylip"] = tempOutNames;
+ outputTypes["column"] = tempOutNames;
+
+ //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;
+ it2 = parameters.find("fasta");
+ //user has given a template file
+ if(it2 != parameters.end()){
+ path = m->hasPath(it2->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["fasta"] = inputDir + it2->second; }
+ }
+
+ it2 = parameters.find("oldfasta");
+ //user has given a template file
+ if(it2 != parameters.end()){
+ path = m->hasPath(it2->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["oldfasta"] = inputDir + it2->second; }
+ }
+
+ it2 = parameters.find("column");
+ //user has given a template file
+ if(it2 != parameters.end()){
+ path = m->hasPath(it2->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["column"] = inputDir + it2->second; }
}
}
+
+ //check for required parameters
+ fastafile = validParameter.validFile(parameters, "fasta", true);
+ if (fastafile == "not found") {
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine();
+ ifstream inFASTA;
+ m->openInputFile(fastafile, inFASTA);
+ alignDB = SequenceDB(inFASTA);
+ inFASTA.close();
+ }else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else if (fastafile == "not open") { abort = true; }
+ else{
+ ifstream inFASTA;
+ m->openInputFile(fastafile, inFASTA);
+ alignDB = SequenceDB(inFASTA);
+ inFASTA.close();
+ m->setFastaFile(fastafile);
+ }
+
+ oldfastafile = validParameter.validFile(parameters, "oldfasta", true);
+ if (oldfastafile == "not found") { oldfastafile = ""; }
+ else if (oldfastafile == "not open") { abort = true; }
+
+ column = validParameter.validFile(parameters, "column", true);
+ if (column == "not found") { column = ""; }
+ else if (column == "not open") { abort = true; }
+ else { m->setColumnFile(column); }
+
+ //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
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ calc = validParameter.validFile(parameters, "calc", false);
+ if (calc == "not found") { calc = "onegap"; }
+ else {
+ if (calc == "default") { calc = "onegap"; }
+ }
+ m->splitAtDash(calc, Estimators);
+
+ string temp;
+ temp = validParameter.validFile(parameters, "countends", false); if(temp == "not found"){ temp = "T"; }
+ convert(temp, countends);
+
+ temp = validParameter.validFile(parameters, "cutoff", false); if(temp == "not found"){ temp = "1.0"; }
+ m->mothurConvert(temp, cutoff);
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
+ temp = validParameter.validFile(parameters, "compress", false); if(temp == "not found"){ temp = "F"; }
+ convert(temp, compress);
+
+ output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "column"; }
+ if (output == "phylip") { output = "lt"; }
+
+ if (((column != "") && (oldfastafile == "")) || ((column == "") && (oldfastafile != ""))) { m->mothurOut("If you provide column or oldfasta, you must provide both."); m->mothurOutEndLine(); abort=true; }
+
+ if ((column != "") && (oldfastafile != "") && (output != "column")) { m->mothurOut("You have provided column and oldfasta, indicating you want to append distances to your column file. Your output must be in column format to do so."); m->mothurOutEndLine(); abort=true; }
+
+ if ((output != "column") && (output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are column, lt and square. I will use column."); m->mothurOutEndLine(); output = "column"; }
+
}
-
- //reset calc for next command
- globaldata->setCalc("");
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function DistanceCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "DistanceCommand", "DistanceCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the DistanceCommand class function DistanceCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
int DistanceCommand::execute(){
try {
- //reads fasta file and fills sequenceDB
- if(globaldata->getFastaFile() != "") { seqDB = new SequenceDB(in); }
- else { cout << "Error no fasta file." << endl; return 0; }
-
- int numSeqs = seqDB->getNumSeqs();
- cutoff += 0.005;
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
- string distFile = getRootName(globaldata->getFastaFile()) + "dist";
+ int startTime = time(NULL);
- remove(distFile.c_str());
+ //save number of new sequence
+ numNewFasta = alignDB.getNumSeqs();
- //# if defined (_WIN32)
- //figure out how to implement the fork and wait commands in windows
- // driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
- //# endif
+ //sanity check the oldfasta and column file as well as add oldfasta sequences to alignDB
+ if ((oldfastafile != "") && (column != "")) { if (!(sanityCheck())) { return 0; } }
-#if defined (__APPLE__) || (__MACH__)
- if(processors == 1){
- driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
- }
- else if(processors == 2){
+ if (m->control_pressed) { return 0; }
+
+ int numSeqs = alignDB.getNumSeqs();
+ cutoff += 0.005;
+
+ if (!alignDB.sameLength()) { m->mothurOut("[ERROR]: your sequences are not the same length, aborting."); m->mothurOutEndLine(); return 0; }
+
+ string outputFile;
+
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+ if (output == "lt") { //does the user want lower triangle phylip formatted file
+ variables["[outputtag]"] = "phylip";
+ outputFile = getOutputFileName("phylip", variables);
+ m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
- int pid = fork();
- if(pid > 0){
- driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", cutoff);
- appendFiles((distFile+"tempa"), distFile);
- remove((distFile + "tempa").c_str());
- }
- else{
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", cutoff);
- appendFiles((distFile+"tempb"), distFile);
- remove((distFile + "tempb").c_str());
+ //output numSeqs to phylip formatted dist file
+ }else if (output == "column") { //user wants column format
+ outputFile = getOutputFileName("column", variables);
+ outputTypes["column"].push_back(outputFile);
+
+ //so we don't accidentally overwrite
+ if (outputFile == column) {
+ string tempcolumn = column + ".old";
+ rename(column.c_str(), tempcolumn.c_str());
}
- wait(NULL);
+ m->mothurRemove(outputFile);
+ }else { //assume square
+ variables["[outputtag]"] = "square";
+ outputFile = getOutputFileName("phylip", variables);
+ m->mothurRemove(outputFile);
+ outputTypes["phylip"].push_back(outputFile);
}
- else if(processors == 3){
- int pid1 = fork();
- if(pid1 > 0){
- int pid2 = fork();
- if(pid2 > 0){
- driver(distCalculator, seqDB, 0, sqrt(3) * numSeqs / 3, distFile + "tempa", cutoff);
- appendFiles(distFile+"tempa", distFile);
- remove((distFile + "tempa").c_str());
- }
- else{
- driver(distCalculator, seqDB, sqrt(3) * numSeqs / 3, sqrt(6) * numSeqs / 3, distFile + "tempb", cutoff);
- appendFiles(distFile+"tempb", distFile);
- remove((distFile + "tempb").c_str());
+
+
+#ifdef USE_MPI
+
+ int pid, start, end;
+ int tag = 2001;
+
+ MPI_Status status;
+ MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ //each process gets where it should start and stop in the file
+ if (output != "square") {
+ start = int (sqrt(float(pid)/float(processors)) * numSeqs);
+ end = int (sqrt(float(pid+1)/float(processors)) * numSeqs);
+ }else{
+ start = int ((float(pid)/float(processors)) * numSeqs);
+ end = int ((float(pid+1)/float(processors)) * numSeqs);
+ }
+
+ if (output == "column") {
+ MPI_File outMPI;
+ int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+
+ //char* filename = new char[outputFile.length()];
+ //memcpy(filename, outputFile.c_str(), outputFile.length());
+
+ char filename[1024];
+ strcpy(filename, outputFile.c_str());
+
+ MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
+ //delete filename;
+
+ if (pid == 0) { //you are the root process
+
+ //do your part
+ string outputMyPart;
+
+ driverMPI(start, end, outMPI, cutoff);
+
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); return 0; }
+
+ //wait on chidren
+ for(int i = 1; i < processors; i++) {
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); return 0; }
+
+ char buf[5];
+ MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
}
- wait(NULL);
+ }else { //you are a child process
+ //do your part
+ driverMPI(start, end, outMPI, cutoff);
+
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); return 0; }
+
+ char buf[5];
+ strcpy(buf, "done");
+ //tell parent you are done.
+ MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
}
- else{
- driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", cutoff);
- appendFiles(distFile+"tempc", distFile);
- remove((distFile + "tempc").c_str());
- }
- wait(NULL);
- }
- else if(processors == 4){
- int pid1 = fork();
- if(pid1 > 0){
- int pid2 = fork();
- if(pid2 > 0){
- driver(distCalculator, seqDB, 0, numSeqs / 2, distFile + "tempa", cutoff);
- appendFiles(distFile+"tempa", distFile);
- remove((distFile + "tempa").c_str());
- }
- else{
- driver(distCalculator, seqDB, numSeqs / 2, (numSeqs/sqrt(2)), distFile + "tempb", cutoff);
- appendFiles(distFile+"tempb", distFile);
- remove((distFile + "tempb").c_str());
+
+ MPI_File_close(&outMPI);
+
+ }else { //lower triangle format
+ if (pid == 0) { //you are the root process
+
+ //do your part
+ string outputMyPart;
+ unsigned long long mySize;
+
+ if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
+ else { driverMPI(start, end, outputFile, mySize, output); }
+
+ if (m->control_pressed) { outputTypes.clear(); return 0; }
+
+ int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
+ MPI_File outMPI;
+ MPI_File inMPI;
+
+ //char* filename = new char[outputFile.length()];
+ //memcpy(filename, outputFile.c_str(), outputFile.length());
+
+ char filename[1024];
+ strcpy(filename, outputFile.c_str());
+
+ MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
+ //delete filename;
+
+ //wait on chidren
+ for(int b = 1; b < processors; b++) {
+ unsigned long long fileSize;
+
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); return 0; }
+
+ MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
+
+ string outTemp = outputFile + toString(b) + ".temp";
+
+ char* buf = new char[outTemp.length()];
+ memcpy(buf, outTemp.c_str(), outTemp.length());
+
+ MPI_File_open(MPI_COMM_SELF, buf, MPI_MODE_DELETE_ON_CLOSE|MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
+ delete buf;
+
+ int count = 0;
+ while (count < fileSize) {
+ char buf2[1];
+ MPI_File_read(inMPI, buf2, 1, MPI_CHAR, &status);
+ MPI_File_write(outMPI, buf2, 1, MPI_CHAR, &status);
+ count += 1;
+ }
+
+ MPI_File_close(&inMPI); //deleted on close
}
- wait(NULL);
+
+ MPI_File_close(&outMPI);
+ }else { //you are a child process
+ //do your part
+ unsigned long long size;
+ if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
+ else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
+
+ if (m->control_pressed) { return 0; }
+
+ //tell parent you are done.
+ MPI_Send(&size, 1, MPI_LONG, 0, tag, MPI_COMM_WORLD);
}
- else{
- int pid3 = fork();
- if(pid3 > 0){
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), (sqrt(3) * numSeqs / 2), distFile + "tempc", cutoff);
- appendFiles(distFile+"tempc", distFile);
- remove((distFile + "tempc").c_str());
+ }
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+#else
+
+ //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ //if you don't need to fork anything
+ if(processors == 1){
+ if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
+ else { driver(0, numSeqs, outputFile, "square"); }
+ }else{ //you have multiple processors
+
+ unsigned long long numDists = 0;
+
+ if (output == "square") {
+ numDists = numSeqs * numSeqs;
+ }else {
+ for(int i=0;i<numSeqs;i++){
+ for(int j=0;j<i;j++){
+ numDists++;
+ if (numDists > processors) { break; }
+ }
}
- else{
- driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", cutoff);
- appendFiles(distFile+"tempd", distFile);
- remove((distFile + "tempd").c_str());
+ }
+
+ if (numDists < processors) { processors = numDists; }
+
+ for (int i = 0; i < processors; i++) {
+ distlinePair tempLine;
+ lines.push_back(tempLine);
+ if (output != "square") {
+ lines[i].start = int (sqrt(float(i)/float(processors)) * numSeqs);
+ lines[i].end = int (sqrt(float(i+1)/float(processors)) * numSeqs);
+ }else{
+ lines[i].start = int ((float(i)/float(processors)) * numSeqs);
+ lines[i].end = int ((float(i+1)/float(processors)) * numSeqs);
}
- wait(NULL);
+
}
- wait(NULL);
+
+ createProcesses(outputFile);
}
- wait(NULL);
-#elif (linux) || (__linux)
- if(processors == 1){
- driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
- }
- else if(processors == 2){
+ //#else
+ //ifstream inFASTA;
+ //if (output != "square") { driver(0, numSeqs, outputFile, cutoff); }
+ //else { driver(0, numSeqs, outputFile, "square"); }
+ //#endif
+
+#endif
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFile); return 0; }
+
+ #ifdef USE_MPI
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if (pid == 0) { //only one process should output to screen
+ #endif
+
+ //if (output == "square") { convertMatrix(outputFile); }
+
+ ifstream fileHandle;
+ fileHandle.open(outputFile.c_str());
+ if(fileHandle) {
+ m->gobble(fileHandle);
+ if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff."); m->mothurOutEndLine(); }
+ }
+
+ //append the old column file to the new one
+ if ((oldfastafile != "") && (column != "")) {
+ //we had to rename the column file so we didnt overwrite above, but we want to keep old name
+ if (outputFile == column) {
+ string tempcolumn = column + ".old";
+ m->appendFiles(tempcolumn, outputFile);
+ m->mothurRemove(tempcolumn);
+ }else{
+ m->appendFiles(outputFile, column);
+ m->mothurRemove(outputFile);
+ outputFile = column;
+ }
- int pid = fork();
- if(pid > 0){
- driver(distCalculator, seqDB, 0, (numSeqs/sqrt(2)), distFile + "tempa", cutoff);
- appendFiles((distFile+"tempa"), distFile);
- remove((distFile + "tempa").c_str());
+ if (outputDir != "") {
+ string newOutputName = outputDir + m->getSimpleName(outputFile);
+ rename(outputFile.c_str(), newOutputName.c_str());
+ m->mothurRemove(outputFile);
+ outputFile = newOutputName;
}
- else{
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), numSeqs, distFile + "tempb", cutoff);
- appendFiles((distFile+"tempb"), distFile);
- remove((distFile + "tempb").c_str());
+ }
+
+
+ #ifdef USE_MPI
+ }
+ #endif
+
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFile); return 0; }
+
+ //set phylip file as new current phylipfile
+ string current = "";
+ itTypes = outputTypes.find("phylip");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
+ }
+
+ //set column file as new current columnfile
+ itTypes = outputTypes.find("column");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
+ }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ m->mothurOut(outputFile); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+ m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
+
+
+ if (m->isTrue(compress)) {
+ m->mothurOut("Compressing..."); m->mothurOutEndLine();
+ m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
+ system(("gzip -v " + outputFile).c_str());
+ outputNames.push_back(outputFile + ".gz");
+ }else { outputNames.push_back(outputFile); }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "execute");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void DistanceCommand::createProcesses(string filename) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ int process = 1;
+ processIDS.clear();
+
+ //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){
+ if (output != "square") { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", cutoff); }
+ else { driver(lines[process].start, lines[process].end, filename + toString(getpid()) + ".temp", "square"); }
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine();
+ perror(" : ");
+ for (int i=0;i<processIDS.size();i++) { int temp = processIDS[i]; kill (temp, SIGINT); }
+ exit(0);
}
- wait();
+ }
+
+ //parent does its part
+ if (output != "square") { driver(lines[0].start, lines[0].end, filename, cutoff); }
+ else { driver(lines[0].start, lines[0].end, filename, "square"); }
+
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+#else
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the distanceData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //that's why the distance calculator was moved inside of the driver to make separate copies.
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<distanceData*> pDataArray; //[processors-1];
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+
+ //Create processor-1 worker threads.
+ for( int i=0; i<processors-1; i++ ){
+ // Allocate memory for thread data.
+ distanceData* tempDist = new distanceData(lines[i+1].start, lines[i+1].end, (filename + toString(i) + ".temp"), cutoff, alignDB, Estimators, m, output, numNewFasta, countends);
+ pDataArray.push_back(tempDist);
+ processIDS.push_back(i);
+
+ //MyDistThreadFunction 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, MyDistThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ }
+
+ //do your part
+ if (output != "square") { driver(lines[0].start, lines[0].end, filename, cutoff); }
+ else { driver(lines[0].start, lines[0].end, filename, "square"); }
+
+ //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++){
+ if (pDataArray[i]->count != (pDataArray[i]->endLine-pDataArray[i]->startLine)) {
+ m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->endLine-pDataArray[i]->startLine) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
+ }
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
}
- else if(processors == 3){
- int pid1 = fork();
- if(pid1 > 0){
- int pid2 = fork();
- if(pid2 > 0){
- driver(distCalculator, seqDB, 0, sqrt(3) * numSeqs / 3, distFile + "tempa", cutoff);
- appendFiles(distFile+"tempa", distFile);
- remove((distFile + "tempa").c_str());
+#endif
+
+ //append and remove temp files
+ for (int i=0;i<processIDS.size();i++) {
+ m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
+ m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "createProcesses");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+/////// need to fix to work with calcs and sequencedb
+int DistanceCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
+ try {
+ ValidCalculators validCalculator;
+ Dist* distCalculator;
+ if (m->isTrue(countends) == true) {
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
+ if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (Estimators[i] == "eachgap") { distCalculator = new eachGapDist(); }
+ else if (Estimators[i] == "onegap") { distCalculator = new oneGapDist(); }
}
- else{
- driver(distCalculator, seqDB, sqrt(3) * numSeqs / 3, sqrt(6) * numSeqs / 3, distFile + "tempb", cutoff);
- appendFiles(distFile+"tempb", distFile);
- remove((distFile + "tempb").c_str());
+ }
+ }else {
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
+ if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (Estimators[i] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
+ else if (Estimators[i] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
}
- wait();
}
- else{
- driver(distCalculator, seqDB, sqrt(6) * numSeqs / 3, numSeqs, distFile + "tempc", cutoff);
- appendFiles(distFile+"tempc", distFile);
- remove((distFile + "tempc").c_str());
- }
- wait();
- }
- else if(processors == 4){
- int pid1 = fork();
- if(pid1 > 0){
- int pid2 = fork();
- if(pid2 > 0){
- driver(distCalculator, seqDB, 0, numSeqs / 2, distFile + "tempa", cutoff);
- appendFiles(distFile+"tempa", distFile);
- remove((distFile + "tempa").c_str());
+ }
+
+ int startTime = time(NULL);
+
+ //column file
+ ofstream outFile(dFileName.c_str(), ios::trunc);
+ outFile.setf(ios::fixed, ios::showpoint);
+ outFile << setprecision(4);
+
+ if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl; }
+
+ for(int i=startLine;i<endLine;i++){
+ if(output == "lt") {
+ string name = alignDB.get(i).getName();
+ if (name.length() < 10) { //pad with spaces to make compatible
+ while (name.length() < 10) { name += " "; }
}
- else{
- driver(distCalculator, seqDB, numSeqs / 2, (numSeqs/sqrt(2)), distFile + "tempb", cutoff);
- appendFiles(distFile+"tempb", distFile);
- remove((distFile + "tempb").c_str());
+ outFile << name << '\t';
+ }
+ for(int j=0;j<i;j++){
+
+ if (m->control_pressed) { delete distCalculator; outFile.close(); return 0; }
+
+ //if there was a column file given and we are appending, we don't want to calculate the distances that are already in the column file
+ //the alignDB contains the new sequences and then the old, so if i an oldsequence and j is an old sequence then break out of this loop
+ if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
+
+ distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
+ double dist = distCalculator->getDist();
+
+ if(dist <= cutoff){
+ if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
}
- wait();
+ if (output == "lt") { outFile << dist << '\t'; }
}
- else{
- int pid3 = fork();
- if(pid3 > 0){
- driver(distCalculator, seqDB, (numSeqs/sqrt(2)), (sqrt(3) * numSeqs / 2), distFile + "tempc", cutoff);
- appendFiles(distFile+"tempc", distFile);
- remove((distFile + "tempc").c_str());
+
+ if (output == "lt") { outFile << endl; }
+
+ if(i % 100 == 0){
+ m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
+ }
+
+ }
+ m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
+
+ outFile.close();
+ delete distCalculator;
+
+ return 1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "driver");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+/////// need to fix to work with calcs and sequencedb
+int DistanceCommand::driver(int startLine, int endLine, string dFileName, string square){
+ try {
+ ValidCalculators validCalculator;
+ Dist* distCalculator;
+ if (m->isTrue(countends) == true) {
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
+ if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (Estimators[i] == "eachgap") { distCalculator = new eachGapDist(); }
+ else if (Estimators[i] == "onegap") { distCalculator = new oneGapDist(); }
}
- else{
- driver(distCalculator, seqDB, (sqrt(3) * numSeqs / 2), numSeqs, distFile + "tempd", cutoff);
- appendFiles(distFile+"tempd", distFile);
- remove((distFile + "tempd").c_str());
+ }
+ }else {
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
+ if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (Estimators[i] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
+ else if (Estimators[i] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
}
- wait();
}
- wait();
}
- wait();
-#else
- driver(distCalculator, seqDB, 0, numSeqs, distFile, cutoff);
-#endif
+ int startTime = time(NULL);
- delete distCalculator;
+ //column file
+ ofstream outFile(dFileName.c_str(), ios::trunc);
+ outFile.setf(ios::fixed, ios::showpoint);
+ outFile << setprecision(4);
- return 0;
+ if(startLine == 0){ outFile << alignDB.getNumSeqs() << endl; }
+ for(int i=startLine;i<endLine;i++){
+
+ string name = alignDB.get(i).getName();
+ //pad with spaces to make compatible
+ if (name.length() < 10) { while (name.length() < 10) { name += " "; } }
+
+ outFile << name << '\t';
+
+ for(int j=0;j<alignDB.getNumSeqs();j++){
+
+ if (m->control_pressed) { delete distCalculator; outFile.close(); return 0; }
+
+ distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
+ double dist = distCalculator->getDist();
+
+ outFile << dist << '\t';
+ }
+
+ outFile << endl;
+
+ if(i % 100 == 0){
+ m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
+ }
+
+ }
+ m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
+
+ outFile.close();
+ delete distCalculator;
+
+ return 1;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "DistanceCommand", "driver");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the DistanceCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
+#ifdef USE_MPI
+/**************************************************************************************************/
+/////// need to fix to work with calcs and sequencedb
+int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
+ try {
+
+ ValidCalculators validCalculator;
+ Dist* distCalculator;
+ if (m->isTrue(countends) == true) {
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
+ if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (Estimators[i] == "eachgap") { distCalculator = new eachGapDist(); }
+ else if (Estimators[i] == "onegap") { distCalculator = new oneGapDist(); }
+ }
+ }
+ }else {
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
+ if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (Estimators[i] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
+ else if (Estimators[i] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
+ }
+ }
+ }
+
+
+ MPI_Status status;
+ int startTime = time(NULL);
+
+ string outputString = "";
+
+ for(int i=startLine;i<endLine;i++){
+
+ for(int j=0;j<i;j++){
+
+ if (m->control_pressed) { delete distCalculator; return 0; }
+
+ //if there was a column file given and we are appending, we don't want to calculate the distances that are already in the column file
+ //the alignDB contains the new sequences and then the old, so if i an oldsequence and j is an old sequence then break out of this loop
+ if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
+
+ distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
+ double dist = distCalculator->getDist();
+
+ if(dist <= cutoff){
+ outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
+ }
+ }
+
+ if(i % 100 == 0){
+ m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
+ }
+
+
+ //send results to parent
+ int length = outputString.length();
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
+
+ MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
+ outputString = "";
+ delete buf;
+
+ }
+
+ m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
+ delete distCalculator;
+ return 1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "driverMPI");
+ exit(1);
+ }
+}
/**************************************************************************************************/
/////// need to fix to work with calcs and sequencedb
-int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLine, int endLine, string dFileName, float cutoff){
+int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size){
try {
+ ValidCalculators validCalculator;
+ Dist* distCalculator;
+ if (m->isTrue(countends) == true) {
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
+ if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (Estimators[i] == "eachgap") { distCalculator = new eachGapDist(); }
+ else if (Estimators[i] == "onegap") { distCalculator = new oneGapDist(); }
+ }
+ }
+ }else {
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
+ if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (Estimators[i] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
+ else if (Estimators[i] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
+ }
+ }
+ }
+
+
+ MPI_Status status;
+
+ MPI_File outMPI;
+ int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+
+ //char* filename = new char[file.length()];
+ //memcpy(filename, file.c_str(), file.length());
+
+ char filename[1024];
+ strcpy(filename, file.c_str());
+
+ MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
+ //delete filename;
+
int startTime = time(NULL);
- ofstream distFile(dFileName.c_str(), ios::trunc);
- distFile.setf(ios::fixed, ios::showpoint);
- distFile << setprecision(4);
+ string outputString = "";
+ size = 0;
+
+ if(startLine == 0){ outputString += toString(alignDB.getNumSeqs()) + "\n"; }
for(int i=startLine;i<endLine;i++){
+
+ string name = alignDB.get(i).getName();
+ if (name.length() < 10) { //pad with spaces to make compatible
+ while (name.length() < 10) { name += " "; }
+ }
+ outputString += name + "\t";
for(int j=0;j<i;j++){
- distCalculator->calcDist(*(align->get(i)), *(align->get(j)));
+
+ if (m->control_pressed) { delete distCalculator; return 0; }
+
+ distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
double dist = distCalculator->getDist();
- if(dist <= cutoff){
- distFile << align->get(i)->getName() << ' ' << align->get(j)->getName() << ' ' << dist << endl;
+ outputString += toString(dist) + "\t";
+ }
+
+ outputString += "\n";
+
+
+ if(i % 100 == 0){
+ m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); }
+
+
+ //send results to parent
+ int length = outputString.length();
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
+
+ MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
+ size += outputString.length();
+ outputString = "";
+ delete buf;
+ }
+
+ m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
+
+ MPI_File_close(&outMPI);
+ delete distCalculator;
+
+ return 1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "driverMPI");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+/////// need to fix to work with calcs and sequencedb
+int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size, string square){
+ try {
+ ValidCalculators validCalculator;
+ Dist* distCalculator;
+ if (m->isTrue(countends) == true) {
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
+ if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (Estimators[i] == "eachgap") { distCalculator = new eachGapDist(); }
+ else if (Estimators[i] == "onegap") { distCalculator = new oneGapDist(); }
}
+ }
+ }else {
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
+ if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
+ else if (Estimators[i] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
+ else if (Estimators[i] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
+ }
+ }
+ }
+
+ MPI_Status status;
+
+ MPI_File outMPI;
+ int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+
+ //char* filename = new char[file.length()];
+ //memcpy(filename, file.c_str(), file.length());
+
+ char filename[1024];
+ strcpy(filename, file.c_str());
+
+ MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
+ //delete filename;
+
+ int startTime = time(NULL);
+
+ string outputString = "";
+ size = 0;
+
+ if(startLine == 0){ outputString += toString(alignDB.getNumSeqs()) + "\n"; }
+
+ for(int i=startLine;i<endLine;i++){
+
+ string name = alignDB.get(i).getName();
+ if (name.length() < 10) { //pad with spaces to make compatible
+ while (name.length() < 10) { name += " "; }
+ }
+ outputString += name + "\t";
+
+ for(int j=0;j<alignDB.getNumSeqs();j++){
+
+ if (m->control_pressed) { delete distCalculator; return 0; }
+
+ distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
+ double dist = distCalculator->getDist();
+ outputString += toString(dist) + "\t";
}
+
+ outputString += "\n";
+
+
if(i % 100 == 0){
- cout << i << '\t' << time(NULL) - startTime << endl;
+ m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
}
+
+ //send results to parent
+ int length = outputString.length();
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
+
+ MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
+ size += outputString.length();
+ outputString = "";
+ delete buf;
}
- cout << endLine-1 << '\t' << time(NULL) - startTime << endl;
+ m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
+
+ MPI_File_close(&outMPI);
+ delete distCalculator;
return 1;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function driver. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "DistanceCommand", "driverMPI");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the DistanceCommand class function driver. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
+#endif
+/**************************************************************************************************
+int DistanceCommand::convertMatrix(string outputFile) {
+ try{
-/**************************************************************************************************/
-void DistanceCommand::appendFiles(string temp, string filename) {
+ //sort file by first column so the distances for each row are together
+ string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
+
+ //use the unix sort
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ string command = "sort -n " + outputFile + " -o " + outfile;
+ system(command.c_str());
+ #else //sort using windows sort
+ string command = "sort " + outputFile + " /O " + outfile;
+ system(command.c_str());
+ #endif
+
+
+ //output to new file distance for each row and save positions in file where new row begins
+ ifstream in;
+ m->openInputFile(outfile, in);
+
+ ofstream out;
+ m->openOutputFile(outputFile, out);
+
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ out << alignDB.getNumSeqs() << endl;
+
+ //get first currentRow
+ string first, currentRow, second;
+ float dist;
+ map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
+ map<string, float>::iterator it;
+
+ in >> first;
+ currentRow = first;
+
+ rowDists[first] = 0.00; //distance to yourself is 0.0
+
+ in.seekg(0);
+ //m->openInputFile(outfile, in);
+
+ while(!in.eof()) {
+ if (m->control_pressed) { in.close(); m->mothurRemove(outfile); out.close(); return 0; }
+
+ in >> first >> second >> dist; m->gobble(in);
+
+ if (first != currentRow) {
+ //print out last row
+ out << currentRow << '\t'; //print name
+
+ //print dists
+ for (it = rowDists.begin(); it != rowDists.end(); it++) {
+ out << it->second << '\t';
+ }
+ out << endl;
+
+ //start new row
+ currentRow = first;
+ rowDists.clear();
+ rowDists[first] = 0.00;
+ rowDists[second] = dist;
+ }else{
+ rowDists[second] = dist;
+ }
+ }
+ //print out last row
+ out << currentRow << '\t'; //print name
+
+ //print dists
+ for (it = rowDists.begin(); it != rowDists.end(); it++) {
+ out << it->second << '\t';
+ }
+ out << endl;
+
+ in.close();
+ out.close();
+
+ m->mothurRemove(outfile);
+
+ return 1;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "convertMatrix");
+ exit(1);
+ }
+}
+**************************************************************************************************
+int DistanceCommand::convertToLowerTriangle(string outputFile) {
try{
- ofstream output;
- ifstream input;
+
+ //sort file by first column so the distances for each row are together
+ string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
+
+ //use the unix sort
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ string command = "sort -n " + outputFile + " -o " + outfile;
+ system(command.c_str());
+ #else //sort using windows sort
+ string command = "sort " + outputFile + " /O " + outfile;
+ system(command.c_str());
+ #endif
+
+
+ //output to new file distance for each row and save positions in file where new row begins
+ ifstream in;
+ m->openInputFile(outfile, in);
+
+ ofstream out;
+ m->openOutputFile(outputFile, out);
+
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ out << alignDB.getNumSeqs() << endl;
- //open output file in append mode
- openOutputFileAppend(filename, output);
+ //get first currentRow
+ string first, currentRow, second;
+ float dist;
+ int i, j;
+ i = 0; j = 0;
+ map<string, float> rowDists; //take advantage of the fact that maps are already sorted by key
+ map<string, float>::iterator it;
- //open temp file for reading
- openInputFile(temp, input);
+ in >> first;
+ currentRow = first;
- string line;
- //read input file and write to output file
- while(input.eof() != true) {
- getline(input, line); //getline removes the newline char
- if (line != "") {
- output << line << endl; // Appending back newline char
+ rowDists[first] = 0.00; //distance to yourself is 0.0
+
+ in.seekg(0);
+ //m->openInputFile(outfile, in);
+
+ while(!in.eof()) {
+ if (m->control_pressed) { in.close(); m->mothurRemove(outfile); out.close(); return 0; }
+
+ in >> first >> second >> dist; m->gobble(in);
+
+ if (first != currentRow) {
+ //print out last row
+ out << currentRow << '\t'; //print name
+
+ //print dists
+ for (it = rowDists.begin(); it != rowDists.end(); it++) {
+ if (j >= i) { break; }
+ out << it->second << '\t';
+ j++;
+ }
+ out << endl;
+
+ //start new row
+ currentRow = first;
+ rowDists.clear();
+ rowDists[first] = 0.00;
+ rowDists[second] = dist;
+ j = 0;
+ i++;
+ }else{
+ rowDists[second] = dist;
}
- }
+ }
+ //print out last row
+ out << currentRow << '\t'; //print name
+
+ //print dists
+ for (it = rowDists.begin(); it != rowDists.end(); it++) {
+ out << it->second << '\t';
+ }
+ out << endl;
+
+ in.close();
+ out.close();
+
+ m->mothurRemove(outfile);
+
+ return 1;
- input.close();
- output.close();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the DistanceCommand class Function appendFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "DistanceCommand", "convertToLowerTriangle");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the DistanceCommand class function appendFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+**************************************************************************************************/
+//its okay if the column file does not contain all the names in the fasta file, since some distance may have been above a cutoff,
+//but no sequences can be in the column file that are not in oldfasta. also, if a distance is above the cutoff given then remove it.
+//also check to make sure the 2 files have the same alignment length.
+bool DistanceCommand::sanityCheck() {
+ try{
+ bool good = true;
+
+ //make sure the 2 fasta files have the same alignment length
+ ifstream in;
+ m->openInputFile(fastafile, in);
+ int fastaAlignLength = 0;
+ if (in) {
+ Sequence tempIn(in);
+ fastaAlignLength = tempIn.getAligned().length();
+ }
+ in.close();
+
+ ifstream in2;
+ m->openInputFile(oldfastafile, in2);
+ int oldfastaAlignLength = 0;
+ if (in2) {
+ Sequence tempIn2(in2);
+ oldfastaAlignLength = tempIn2.getAligned().length();
+ }
+ in2.close();
+
+ if (fastaAlignLength != oldfastaAlignLength) { m->mothurOut("fasta files do not have the same alignment length."); m->mothurOutEndLine(); return false; }
+
+ //read fasta file and save names as well as adding them to the alignDB
+ set<string> namesOldFasta;
+
+ ifstream inFasta;
+ m->openInputFile(oldfastafile, inFasta);
+
+ while (!inFasta.eof()) {
+ if (m->control_pressed) { inFasta.close(); return good; }
+
+ Sequence temp(inFasta);
+
+ if (temp.getName() != "") {
+ namesOldFasta.insert(temp.getName()); //save name
+ alignDB.push_back(temp); //add to DB
+ }
+
+ m->gobble(inFasta);
+ }
+
+ inFasta.close();
+
+ //read through the column file checking names and removing distances above the cutoff
+ ifstream inDist;
+ m->openInputFile(column, inDist);
+
+ ofstream outDist;
+ string outputFile = column + ".temp";
+ m->openOutputFile(outputFile, outDist);
+
+ string name1, name2;
+ float dist;
+ while (!inDist.eof()) {
+ if (m->control_pressed) { inDist.close(); outDist.close(); m->mothurRemove(outputFile); return good; }
+
+ inDist >> name1 >> name2 >> dist; m->gobble(inDist);
+
+ //both names are in fasta file and distance is below cutoff
+ if ((namesOldFasta.count(name1) == 0) || (namesOldFasta.count(name2) == 0)) { good = false; break; }
+ else{
+ if (dist <= cutoff) {
+ outDist << name1 << '\t' << name2 << '\t' << dist << endl;
+ }
+ }
+ }
+
+ inDist.close();
+ outDist.close();
+
+ if (good) {
+ m->mothurRemove(column);
+ rename(outputFile.c_str(), column.c_str());
+ }else{
+ m->mothurRemove(outputFile); //temp file is bad because file mismatch above
+ }
+
+ return good;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DistanceCommand", "sanityCheck");
exit(1);
- }
+ }
}
-/**************************************************************************************************/
\ No newline at end of file
+/**************************************************************************************************/
+
+
+
+
projects / mothur.git / blobdiff