+++ /dev/null
-/*
- * distancecommand.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 5/7/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "distancecommand.h"
-
-//**********************************************************************************************************************
-vector<string> DistanceCommand::setParameters(){
- try {
- CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "OldFastaColumn",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",false,true); parameters.push_back(pfasta);
- CommandParameter poutput("output", "Multiple", "column-lt-square", "column", "", "", "",false,false); 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); parameters.push_back(pprocessors);
- CommandParameter pcutoff("cutoff", "Number", "", "1.0", "", "", "",false,false); 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);
- }
-}
-//**********************************************************************************************************************
-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; }
- }
-
- //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 (((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"; }
-
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "DistanceCommand", "DistanceCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int DistanceCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- int startTime = time(NULL);
-
- //save number of new sequence
- numNewFasta = alignDB.getNumSeqs();
-
- //sanity check the oldfasta and column file as well as add oldfasta sequences to alignDB
- if ((oldfastafile != "") && (column != "")) { if (!(sanityCheck())) { return 0; } }
-
- 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;
-
- if (output == "lt") { //does the user want lower triangle phylip formatted file
- outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip.dist";
- m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
-
- //output numSeqs to phylip formatted dist file
- }else if (output == "column") { //user wants column format
- outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "dist";
- 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());
- }
-
- m->mothurRemove(outputFile);
- }else { //assume square
- outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square.dist";
- m->mothurRemove(outputFile);
- outputTypes["phylip"].push_back(outputFile);
- }
-
-
-#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);
- }
- }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);
- }
-
- 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
- }
-
- 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);
- }
- }
- 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; }
- }
- }
- }
-
- 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);
- }
-
- }
-
- createProcesses(outputFile);
- }
- //#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;
- }
-
- if (outputDir != "") {
- string newOutputName = outputDir + m->getSimpleName(outputFile);
- rename(outputFile.c_str(), newOutputName.c_str());
- m->mothurRemove(outputFile);
- outputFile = newOutputName;
- }
- }
-
-
- #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 Name: "); 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);
- }
- }
-
- //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++){
- CloseHandle(hThreadArray[i]);
- delete pDataArray[i];
- }
-#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 {
- 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(); }
- }
- }
- }
-
- 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 += " "; }
- }
- 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; }
- }
- if (output == "lt") { outFile << dist << '\t'; }
- }
-
- if (output == "lt") { outFile << endl; }
-
- if(i % 100 == 0){
- m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
- }
-
- }
- m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-
- 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 {
- 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(); }
- }
- }
- }
-
- int startTime = time(NULL);
-
- //column file
- ofstream outFile(dFileName.c_str(), ios::trunc);
- outFile.setf(ios::fixed, ios::showpoint);
- outFile << setprecision(4);
-
- 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->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
- }
-
- }
- m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
-
- outFile.close();
- delete distCalculator;
-
- return 1;
- }
- catch(exception& e) {
- m->errorOut(e, "DistanceCommand", "driver");
- 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->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
- cout << i << '\t' << (time(NULL) - startTime) << endl;
- }
-
-
- //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->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
- cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
- 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){
- 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<i;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){
- //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
- cout << i << '\t' << (time(NULL) - startTime) << endl;
- }
-
-
- //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->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
- cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
- 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){
- //m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
- cout << i << '\t' << (time(NULL) - startTime) << endl;
- }
-
-
- //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->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
- cout << (endLine-1) << '\t' << (time(NULL) - startTime) << endl;
- MPI_File_close(&outMPI);
- delete distCalculator;
- return 1;
- }
- catch(exception& e) {
- m->errorOut(e, "DistanceCommand", "driverMPI");
- exit(1);
- }
-}
-#endif
-/**************************************************************************************************
-int DistanceCommand::convertMatrix(string outputFile) {
- try{
-
- //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{
-
- //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;
- 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;
-
- 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++) {
- 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;
-
- }
- catch(exception& e) {
- m->errorOut(e, "DistanceCommand", "convertToLowerTriangle");
- exit(1);
- }
-}
-**************************************************************************************************/
-//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);
- }
-}
-/**************************************************************************************************/
-
-
-
-
projects / mothur.git / blobdiff