+++ /dev/null
-/*
- * pairwiseseqscommand.cpp
- * Mothur
- *
- * Created by westcott on 10/20/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "pairwiseseqscommand.h"
-
-//**********************************************************************************************************************
-vector<string> PairwiseSeqsCommand::setParameters(){
- try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
- CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
- CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
- CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
- CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- 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 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, "PairwiseSeqsCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string PairwiseSeqsCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The pairwise.seqs command reads a fasta file and creates distance matrix.\n";
- helpString += "The pairwise.seqs command parameters are fasta, align, match, mismatch, gapopen, gapextend, calc, output, cutoff and processors.\n";
- helpString += "The fasta parameter is required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
- helpString += "The align parameter allows you to specify the alignment method to use. Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n";
- helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
- helpString += "The mistmatch parameter allows you to specify the penalty for having different bases. The default is -1.0.\n";
- helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
- helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\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 compress parameter allows you to indicate that you want the resulting distance file compressed. The default is false.\n";
- helpString += "The pairwise.seqs command should be in the following format: \n";
- helpString += "pairwise.seqs(fasta=yourfastaFile, align=yourAlignmentMethod) \n";
- helpString += "Example pairwise.seqs(fasta=candidate.fasta, align=blast)\n";
- helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "PairwiseSeqsCommand", "getHelpString");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-PairwiseSeqsCommand::PairwiseSeqsCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["phylip"] = tempOutNames;
- outputTypes["column"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "PairwiseSeqsCommand", "PairwiseSeqsCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-PairwiseSeqsCommand::PairwiseSeqsCommand(string option) {
- try {
- abort = false; calledHelp = false;
-
- //allow user to run help
- if(option == "help") { help(); abort = true; calledHelp = true; }
- else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
- vector<string> myArray = setParameters();
-
- OptionParser parser(option);
- map<string, string> parameters = parser.getParameters();
-
- ValidParameters validParameter("pairwise.seqs");
- map<string, string>::iterator it;
-
- //check to make sure all parameters are valid for command
- for (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
- }
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["phylip"] = tempOutNames;
- outputTypes["column"] = tempOutNames;
-
- //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 = ""; }
-
-
- //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 = ""; }
-
- fastaFileName = validParameter.validFile(parameters, "fasta", false);
- if (fastaFileName == "not found") {
- //if there is a current fasta file, use it
- string filename = m->getFastaFile();
- if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
- else {
- m->splitAtDash(fastaFileName, fastaFileNames);
-
- //go through files and make sure they are good, if not, then disregard them
- for (int i = 0; i < fastaFileNames.size(); i++) {
-
- bool ignore = false;
- if (fastaFileNames[i] == "current") {
- fastaFileNames[i] = m->getFastaFile();
- if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
- else {
- m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
- //erase from file list
- fastaFileNames.erase(fastaFileNames.begin()+i);
- i--;
- }
- }
-
- if (!ignore) {
-
- if (inputDir != "") {
- string path = m->hasPath(fastaFileNames[i]);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
- }
-
- int ableToOpen;
- ifstream in;
-
- ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
-
- //if you can't open it, try default location
- if (ableToOpen == 1) {
- if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
- m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- fastaFileNames[i] = tryPath;
- }
- }
-
- //if you can't open it, try output location
- if (ableToOpen == 1) {
- if (m->getOutputDir() != "") { //default path is set
- string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
- m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- fastaFileNames[i] = tryPath;
- }
- }
-
- in.close();
-
- if (ableToOpen == 1) {
- m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
- //erase from file list
- fastaFileNames.erase(fastaFileNames.begin()+i);
- i--;
- }else {
- m->setFastaFile(fastaFileNames[i]);
- }
- }
- }
-
- //make sure there is at least one valid file left
- if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
- }
-
- //check for optional parameter and set defaults
- // ...at some point should added some additional type checking...
- string temp;
- temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
- m->mothurConvert(temp, match);
-
- temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
- m->mothurConvert(temp, misMatch);
- if (misMatch > 0) { m->mothurOut("[ERROR]: mismatch must be negative.\n"); abort=true; }
-
- temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; }
- m->mothurConvert(temp, gapOpen);
- if (gapOpen > 0) { m->mothurOut("[ERROR]: gapopen must be negative.\n"); abort=true; }
-
- temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
- m->mothurConvert(temp, gapExtend);
- if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
-
- temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
- m->setProcessors(temp);
- m->mothurConvert(temp, processors);
-
- temp = validParameter.validFile(parameters, "cutoff", false); if(temp == "not found"){ temp = "1.0"; }
- m->mothurConvert(temp, cutoff);
-
- temp = validParameter.validFile(parameters, "countends", false); if(temp == "not found"){ temp = "T"; }
- countends = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "compress", false); if(temp == "not found"){ temp = "F"; }
- compress = m->isTrue(temp);
-
- align = validParameter.validFile(parameters, "align", false); if (align == "not found"){ align = "needleman"; }
-
- output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "column"; }
- 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"; }
-
- calc = validParameter.validFile(parameters, "calc", false);
- if (calc == "not found") { calc = "onegap"; }
- else {
- if (calc == "default") { calc = "onegap"; }
- }
- m->splitAtDash(calc, Estimators);
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "PairwiseSeqsCommand", "PairwiseSeqsCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int PairwiseSeqsCommand::execute(){
- try {
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- longestBase = 2000; //will need to update this in driver if we find sequences with more bases. hardcoded so we don't have the pre-read user fasta file.
-
- cutoff += 0.005;
-
- for (int s = 0; s < fastaFileNames.size(); s++) {
- if (m->control_pressed) { outputTypes.clear(); return 0; }
-
- m->mothurOut("Processing sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
-
- if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
-
- ifstream inFASTA;
- m->openInputFile(fastaFileNames[s], inFASTA);
- alignDB = SequenceDB(inFASTA);
- inFASTA.close();
-
- int numSeqs = alignDB.getNumSeqs();
- int startTime = time(NULL);
- string outputFile = "";
-
- if (output == "lt") { //does the user want lower triangle phylip formatted file
- outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "phylip.dist";
- m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
- }else if (output == "column") { //user wants column format
- outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "dist";
- outputTypes["column"].push_back(outputFile);
- m->mothurRemove(outputFile);
- }else { //assume square
- outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "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[1024];
- strcpy(filename, outputFile.c_str());
-
- MPI_File_open(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, &outMPI);
-
- 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); m->mothurRemove(outputFile); return 0; }
-
- //wait on chidren
- for(int i = 1; i < processors; i++) {
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); 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); m->mothurRemove(outputFile); 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(); m->mothurRemove(outputFile); return 0; }
-
- int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
- MPI_File outMPI;
- MPI_File inMPI;
-
- char filename[1024];
- strcpy(filename, outputFile.c_str());
-
- MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
-
- //wait on chidren
- for(int b = 1; b < processors; b++) {
- unsigned long long fileSize;
-
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); 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
-
- 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
-
- 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(); }
- }
-
- if (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); }
-
- #ifdef USE_MPI
- }
- #endif
-
- m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
-
- 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();
- for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
- m->mothurOutEndLine();
-
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "PairwiseSeqsCommand", "execute");
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-void PairwiseSeqsCommand::createProcesses(string filename) {
- try {
- int process = 1;
- processIDS.clear();
-
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-
-
- //loop through and create all the processes you want
- while (process != processors) {
- int pid = fork();
-
- if (pid > 0) {
- processIDS.push_back(pid);
- 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."); m->mothurOutEndLine();
- for (int i=0;i<processIDS.size();i++) { int temp = processIDS[i]; kill (temp, SIGINT); }
- exit(0);
- }
- }
-
- //parent do my 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<pairwiseData*> pDataArray; //[processors-1];
- DWORD dwThreadIdArray[processors-1];
- HANDLE hThreadArray[processors-1];
-
- //Create processor-1 worker threads.
- for( int i=0; i<processors-1; i++ ){
- string extension = toString(i) + ".temp";
-
- // Allocate memory for thread data.
- pairwiseData* tempDist = new pairwiseData((filename+extension), align, "square", Estimators[0], countends, output, alignDB, m, lines[i+1].start, lines[i+1].end, match, misMatch, gapOpen, gapExtend, longestBase, i);
- pDataArray.push_back(tempDist);
- processIDS.push_back(i);
-
- if (output != "square") { hThreadArray[i] = CreateThread(NULL, 0, MyPairwiseThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]); }
- else { hThreadArray[i] = CreateThread(NULL, 0, MyPairwiseSquareThreadFunction, 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, "PairwiseSeqsCommand", "createProcesses");
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-/////// need to fix to work with calcs and sequencedb
-int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
- try {
-
- int startTime = time(NULL);
-
- Alignment* alignment;
- if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
- else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
- else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
- else if(align == "noalign") { alignment = new NoAlign(); }
- else {
- m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
- m->mothurOutEndLine();
- alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
- }
-
- ValidCalculators validCalculator;
- Dist* distCalculator;
- if (countends) {
- if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
- if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
- else if (Estimators[0] == "eachgap") { distCalculator = new eachGapDist(); }
- else if (Estimators[0] == "onegap") { distCalculator = new oneGapDist(); }
- }
- }else {
- if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
- if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
- else if (Estimators[0] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
- else if (Estimators[0] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
- }
- }
-
- //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) { outFile.close(); delete alignment; delete distCalculator; return 0; }
-
- if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
- alignment->resize(alignDB.get(i).getUnaligned().length()+1);
- }
-
- if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
- alignment->resize(alignDB.get(j).getUnaligned().length()+1);
- }
-
- Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
- Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
-
- alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
- seqI.setAligned(alignment->getSeqAAln());
- seqJ.setAligned(alignment->getSeqBAln());
-
-
- distCalculator->calcDist(seqI, seqJ);
- 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 alignment;
- delete distCalculator;
-
- return 1;
- }
- catch(exception& e) {
- m->errorOut(e, "PairwiseSeqsCommand", "driver");
- exit(1);
- }
-}
-/**************************************************************************************************/
-/////// need to fix to work with calcs and sequencedb
-int PairwiseSeqsCommand::driver(int startLine, int endLine, string dFileName, string square){
- try {
-
- int startTime = time(NULL);
-
- Alignment* alignment;
- if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
- else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
- else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
- else if(align == "noalign") { alignment = new NoAlign(); }
- else {
- m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
- m->mothurOutEndLine();
- alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
- }
-
- ValidCalculators validCalculator;
- Dist* distCalculator;
- if (countends) {
- if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
- if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
- else if (Estimators[0] == "eachgap") { distCalculator = new eachGapDist(); }
- else if (Estimators[0] == "onegap") { distCalculator = new oneGapDist(); }
- }
- }else {
- if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
- if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
- else if (Estimators[0] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
- else if (Estimators[0] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
- }
- }
-
- //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) { outFile.close(); delete alignment; delete distCalculator; return 0; }
-
- if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
- alignment->resize(alignDB.get(i).getUnaligned().length()+1);
- }
-
- if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
- alignment->resize(alignDB.get(j).getUnaligned().length()+1);
- }
-
- Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
- Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
-
- alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
- seqI.setAligned(alignment->getSeqAAln());
- seqJ.setAligned(alignment->getSeqBAln());
-
- distCalculator->calcDist(seqI, seqJ);
- 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 alignment;
- delete distCalculator;
-
- return 1;
- }
- catch(exception& e) {
- m->errorOut(e, "PairwiseSeqsCommand", "driver");
- exit(1);
- }
-}
-#ifdef USE_MPI
-/**************************************************************************************************/
-/////// need to fix to work with calcs and sequencedb
-int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
- try {
- MPI_Status status;
- int startTime = time(NULL);
-
- Alignment* alignment;
- if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
- else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
- else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
- else if(align == "noalign") { alignment = new NoAlign(); }
- else {
- m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
- m->mothurOutEndLine();
- alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
- }
-
- ValidCalculators validCalculator;
- Dist* distCalculator;
- if (countends) {
- if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
- if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
- else if (Estimators[0] == "eachgap") { distCalculator = new eachGapDist(); }
- else if (Estimators[0] == "onegap") { distCalculator = new oneGapDist(); }
- }
- }else {
- if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
- if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
- else if (Estimators[0] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
- else if (Estimators[0] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
- }
- }
-
- string outputString = "";
-
- for(int i=startLine;i<endLine;i++){
-
- for(int j=0;j<i;j++){
-
- if (m->control_pressed) { delete alignment; delete distCalculator; return 0; }
-
- if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
- alignment->resize(alignDB.get(i).getUnaligned().length()+1);
- }
-
- if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
- alignment->resize(alignDB.get(j).getUnaligned().length()+1);
- }
-
- Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
- Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
-
- alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
- seqI.setAligned(alignment->getSeqAAln());
- seqJ.setAligned(alignment->getSeqBAln());
-
- distCalculator->calcDist(seqI, seqJ);
- 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;
-
- }
- delete alignment;
- delete distCalculator;
- return 1;
- }
- catch(exception& e) {
- m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
- exit(1);
- }
-}
-/**************************************************************************************************/
-/////// need to fix to work with calcs and sequencedb
-int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size){
- try {
- MPI_Status status;
-
- MPI_File outMPI;
- int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
-
- char filename[1024];
- strcpy(filename, file.c_str());
-
- MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
-
- Alignment* alignment;
- if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
- else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
- else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
- else if(align == "noalign") { alignment = new NoAlign(); }
- else {
- m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
- m->mothurOutEndLine();
- alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
- }
-
- ValidCalculators validCalculator;
- Dist* distCalculator;
- if (countends) {
- if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
- if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
- else if (Estimators[0] == "eachgap") { distCalculator = new eachGapDist(); }
- else if (Estimators[0] == "onegap") { distCalculator = new oneGapDist(); }
- }
- }else {
- if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
- if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
- else if (Estimators[0] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
- else if (Estimators[0] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
- }
- }
-
-
- 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 alignment; delete distCalculator; return 0; }
-
- if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
- alignment->resize(alignDB.get(i).getUnaligned().length()+1);
- }
-
- if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
- alignment->resize(alignDB.get(j).getUnaligned().length()+1);
- }
-
- Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
- Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
-
- alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
- seqI.setAligned(alignment->getSeqAAln());
- seqJ.setAligned(alignment->getSeqBAln());
-
- distCalculator->calcDist(seqI, seqJ);
- double dist = distCalculator->getDist();
-
- outputString += toString(dist) + "\t";
- }
-
- outputString += "\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;
- }
-
- MPI_File_close(&outMPI);
- delete alignment;
- delete distCalculator;
-
- return 1;
- }
- catch(exception& e) {
- m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
- exit(1);
- }
-}
-/**************************************************************************************************/
-/////// need to fix to work with calcs and sequencedb
-int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size, string square){
- try {
- MPI_Status status;
-
- MPI_File outMPI;
- int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
-
- char filename[1024];
- strcpy(filename, file.c_str());
-
- MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
-
- Alignment* alignment;
- if(align == "gotoh") { alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase); }
- else if(align == "needleman") { alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase); }
- else if(align == "blast") { alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch); }
- else if(align == "noalign") { alignment = new NoAlign(); }
- else {
- m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
- m->mothurOutEndLine();
- alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
- }
-
- ValidCalculators validCalculator;
- Dist* distCalculator;
- if (countends) {
- if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
- if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
- else if (Estimators[0] == "eachgap") { distCalculator = new eachGapDist(); }
- else if (Estimators[0] == "onegap") { distCalculator = new oneGapDist(); }
- }
- }else {
- if (validCalculator.isValidCalculator("distance", Estimators[0]) == true) {
- if (Estimators[0] == "nogaps") { distCalculator = new ignoreGaps(); }
- else if (Estimators[0] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
- else if (Estimators[0] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
- }
- }
-
- 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 alignment; return 0; }
-
- if (alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
- alignment->resize(alignDB.get(i).getUnaligned().length()+1);
- }
-
- if (alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
- alignment->resize(alignDB.get(j).getUnaligned().length()+1);
- }
-
- Sequence seqI(alignDB.get(i).getName(), alignDB.get(i).getAligned());
- Sequence seqJ(alignDB.get(j).getName(), alignDB.get(j).getAligned());
-
- alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
- seqI.setAligned(alignment->getSeqAAln());
- seqJ.setAligned(alignment->getSeqBAln());
-
- distCalculator->calcDist(seqI, seqJ);
- double dist = distCalculator->getDist();
-
- outputString += toString(dist) + "\t";
- }
-
- outputString += "\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;
- }
-
- MPI_File_close(&outMPI);
-
- delete alignment;
- return 1;
- }
- catch(exception& e) {
- m->errorOut(e, "PairwiseSeqsCommand", "driverMPI");
- exit(1);
- }
-}
-#endif
-/**************************************************************************************************/
-
projects / mothur.git / blobdiff