+++ /dev/null
-/*
- * treegroupscommand.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 4/8/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "treegroupscommand.h"
-#include "subsample.h"
-#include "consensus.h"
-
-//**********************************************************************************************************************
-vector<string> TreeGroupCommand::setParameters(){
- try {
- CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);
- CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
- CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName",false,false); parameters.push_back(pcolumn);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
- CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
- CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
-
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-//CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
- 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, "TreeGroupCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string TreeGroupCommand::getHelpString(){
- try {
- string helpString = "";
- ValidCalculators validCalculator;
- helpString += "The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n";
- helpString += "The tree.shared command parameters are shared, groups, calc, phylip, column, name, cutoff, precision, processors, subsample, iters and label.\n";
- helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
- helpString += "The group names are separated by dashes. The label allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n";
- helpString += "The phylip or column parameter are required if you do not provide a sharedfile, and only one may be used. If you use a column file the name filename is required. \n";
- helpString += "If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n";
- helpString += "The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
- helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
- helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group. The subsample parameter may only be used with a shared file.\n";
- helpString += "Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\n";
- helpString += "The default value for groups is all the groups in your groupfile.\n";
- helpString += "The default value for calc is jclass-thetayc.\n";
- helpString += "The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n";
- helpString += validCalculator.printCalc("treegroup");
- helpString += "Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n";
- helpString += "Example tree.shared(phylip=abrecovery.dist).\n";
- helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "TreeGroupCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-TreeGroupCommand::TreeGroupCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["tree"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-TreeGroupCommand::TreeGroupCommand(string option) {
- try {
- abort = false; calledHelp = false;
- allLines = 1;
-
- //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;
- 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["tree"] = 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;
- it = parameters.find("phylip");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["phylip"] = inputDir + it->second; }
- }
-
- it = parameters.find("column");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["column"] = inputDir + it->second; }
- }
-
- it = parameters.find("name");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["name"] = inputDir + it->second; }
- }
- }
-
- //check for required parameters
- phylipfile = validParameter.validFile(parameters, "phylip", true);
- if (phylipfile == "not open") { phylipfile = ""; abort = true; }
- else if (phylipfile == "not found") { phylipfile = ""; }
- else { inputfile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile); }
-
- columnfile = validParameter.validFile(parameters, "column", true);
- if (columnfile == "not open") { columnfile = ""; abort = true; }
- else if (columnfile == "not found") { columnfile = ""; }
- else { inputfile = columnfile; format = "column"; m->setColumnFile(columnfile); }
-
- sharedfile = validParameter.validFile(parameters, "shared", true);
- if (sharedfile == "not open") { sharedfile = ""; abort = true; }
- else if (sharedfile == "not found") { sharedfile = ""; }
- else { inputfile = sharedfile; format = "sharedfile"; m->setSharedFile(sharedfile); }
-
- namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = true; }
- else if (namefile == "not found") { namefile = ""; }
- else { m->setNameFile(namefile); }
-
- if ((phylipfile == "") && (columnfile == "") && (sharedfile == "")) {
- //is there are current file available for either of these?
- //give priority to shared, then column, then phylip
- sharedfile = m->getSharedFile();
- if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
- else {
- columnfile = m->getColumnFile();
- if (columnfile != "") { inputfile = columnfile; format = "column"; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
- else {
- phylipfile = m->getPhylipFile();
- if (phylipfile != "") { inputfile = phylipfile; format = "phylip"; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
- else {
- m->mothurOut("No valid current files. You must provide a shared, phylip or column file."); m->mothurOutEndLine();
- abort = true;
- }
- }
- }
- }
- else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When running the tree.shared command with a distance file you may not use both the column and the phylip parameters."); m->mothurOutEndLine(); abort = true; }
-
- if (columnfile != "") {
- if (namefile == "") {
- namefile = m->getNameFile();
- if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
- else {
- m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine();
- abort = true;
- }
- }
- }
-
- //check for optional parameter and set defaults
- // ...at some point should added some additional type checking...
- label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { label = ""; }
- else {
- if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
- else { allLines = 1; }
- }
-
- groups = validParameter.validFile(parameters, "groups", false);
- if (groups == "not found") { groups = ""; }
- else {
- m->splitAtDash(groups, Groups);
- m->setGroups(Groups);
- }
-
- calc = validParameter.validFile(parameters, "calc", false);
- if (calc == "not found") { calc = "jclass-thetayc"; }
- else {
- if (calc == "default") { calc = "jclass-thetayc"; }
- }
- m->splitAtDash(calc, Estimators);
- if (m->inUsersGroups("citation", Estimators)) {
- ValidCalculators validCalc; validCalc.printCitations(Estimators);
- //remove citation from list of calcs
- for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
- }
-
- string temp;
- temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
- m->mothurConvert(temp, precision);
-
- temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; }
- m->mothurConvert(temp, cutoff);
- cutoff += (5 / (precision * 10.0));
-
- temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
- m->setProcessors(temp);
- m->mothurConvert(temp, processors);
-
- temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
- m->mothurConvert(temp, iters);
-
- temp = validParameter.validFile(parameters, "subsample", false); if (temp == "not found") { temp = "F"; }
- if (m->isNumeric1(temp)) { m->mothurConvert(temp, subsampleSize); subsample = true; }
- else {
- if (m->isTrue(temp)) { subsample = true; subsampleSize = -1; } //we will set it to smallest group later
- else { subsample = false; }
- }
-
- if (subsample == false) { iters = 1; }
-
- if (subsample && (format != "sharedfile")) { m->mothurOut("[ERROR]: the subsample parameter can only be used with a shared file.\n"); abort=true; }
-
- //if the user changes the output directory command factory will send this info to us in the output parameter
- outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
- outputDir = "";
- outputDir += m->hasPath(inputfile); //if user entered a file with a path then preserve it
- }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-TreeGroupCommand::~TreeGroupCommand(){
- if (abort == false) {
- if (format == "sharedfile") { delete input; }
- else { delete readMatrix; delete matrix; delete list; }
- delete tmap;
- }
-
-}
-
-//**********************************************************************************************************************
-
-int TreeGroupCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- if (format == "sharedfile") {
-
- ValidCalculators validCalculator;
-
- for (int i=0; i<Estimators.size(); i++) {
- if (validCalculator.isValidCalculator("treegroup", Estimators[i]) == true) {
- if (Estimators[i] == "sharedsobs") {
- treeCalculators.push_back(new SharedSobsCS());
- }else if (Estimators[i] == "sharedchao") {
- treeCalculators.push_back(new SharedChao1());
- }else if (Estimators[i] == "sharedace") {
- treeCalculators.push_back(new SharedAce());
- }else if (Estimators[i] == "jabund") {
- treeCalculators.push_back(new JAbund());
- }else if (Estimators[i] == "sorabund") {
- treeCalculators.push_back(new SorAbund());
- }else if (Estimators[i] == "jclass") {
- treeCalculators.push_back(new Jclass());
- }else if (Estimators[i] == "sorclass") {
- treeCalculators.push_back(new SorClass());
- }else if (Estimators[i] == "jest") {
- treeCalculators.push_back(new Jest());
- }else if (Estimators[i] == "sorest") {
- treeCalculators.push_back(new SorEst());
- }else if (Estimators[i] == "thetayc") {
- treeCalculators.push_back(new ThetaYC());
- }else if (Estimators[i] == "thetan") {
- treeCalculators.push_back(new ThetaN());
- }else if (Estimators[i] == "kstest") {
- treeCalculators.push_back(new KSTest());
- }else if (Estimators[i] == "sharednseqs") {
- treeCalculators.push_back(new SharedNSeqs());
- }else if (Estimators[i] == "ochiai") {
- treeCalculators.push_back(new Ochiai());
- }else if (Estimators[i] == "anderberg") {
- treeCalculators.push_back(new Anderberg());
- }else if (Estimators[i] == "kulczynski") {
- treeCalculators.push_back(new Kulczynski());
- }else if (Estimators[i] == "kulczynskicody") {
- treeCalculators.push_back(new KulczynskiCody());
- }else if (Estimators[i] == "lennon") {
- treeCalculators.push_back(new Lennon());
- }else if (Estimators[i] == "morisitahorn") {
- treeCalculators.push_back(new MorHorn());
- }else if (Estimators[i] == "braycurtis") {
- treeCalculators.push_back(new BrayCurtis());
- }else if (Estimators[i] == "whittaker") {
- treeCalculators.push_back(new Whittaker());
- }else if (Estimators[i] == "odum") {
- treeCalculators.push_back(new Odum());
- }else if (Estimators[i] == "canberra") {
- treeCalculators.push_back(new Canberra());
- }else if (Estimators[i] == "structeuclidean") {
- treeCalculators.push_back(new StructEuclidean());
- }else if (Estimators[i] == "structchord") {
- treeCalculators.push_back(new StructChord());
- }else if (Estimators[i] == "hellinger") {
- treeCalculators.push_back(new Hellinger());
- }else if (Estimators[i] == "manhattan") {
- treeCalculators.push_back(new Manhattan());
- }else if (Estimators[i] == "structpearson") {
- treeCalculators.push_back(new StructPearson());
- }else if (Estimators[i] == "soergel") {
- treeCalculators.push_back(new Soergel());
- }else if (Estimators[i] == "spearman") {
- treeCalculators.push_back(new Spearman());
- }else if (Estimators[i] == "structkulczynski") {
- treeCalculators.push_back(new StructKulczynski());
- }else if (Estimators[i] == "speciesprofile") {
- treeCalculators.push_back(new SpeciesProfile());
- }else if (Estimators[i] == "hamming") {
- treeCalculators.push_back(new Hamming());
- }else if (Estimators[i] == "structchi2") {
- treeCalculators.push_back(new StructChi2());
- }else if (Estimators[i] == "gower") {
- treeCalculators.push_back(new Gower());
- }else if (Estimators[i] == "memchi2") {
- treeCalculators.push_back(new MemChi2());
- }else if (Estimators[i] == "memchord") {
- treeCalculators.push_back(new MemChord());
- }else if (Estimators[i] == "memeuclidean") {
- treeCalculators.push_back(new MemEuclidean());
- }else if (Estimators[i] == "mempearson") {
- treeCalculators.push_back(new MemPearson());
- }
- }
- }
-
- //if the users entered no valid calculators don't execute command
- if (treeCalculators.size() == 0) { m->mothurOut("You have given no valid calculators."); m->mothurOutEndLine(); return 0; }
-
- input = new InputData(sharedfile, "sharedfile");
- lookup = input->getSharedRAbundVectors();
- lastLabel = lookup[0]->getLabel();
-
- if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); return 0; }
-
- //used in tree constructor
- m->runParse = false;
-
- //create treemap class from groupmap for tree class to use
- tmap = new TreeMap();
- tmap->makeSim(m->getAllGroups());
-
- //clear globaldatas old tree names if any
- m->Treenames.clear();
-
- //fills globaldatas tree names
- m->Treenames = m->getGroups();
-
- if (m->control_pressed) { return 0; }
-
- //create tree file
- makeSimsShared();
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
- }else{
- //read in dist file
- filename = inputfile;
-
- if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
- else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
-
- readMatrix->setCutoff(cutoff);
-
- if(namefile != ""){
- nameMap = new NameAssignment(namefile);
- nameMap->readMap();
- }
- else{
- nameMap = NULL;
- }
-
- readMatrix->read(nameMap);
- list = readMatrix->getListVector();
- matrix = readMatrix->getMatrix();
-
- //make treemap
- tmap = new TreeMap();
-
- if (m->control_pressed) { return 0; }
-
- tmap->makeSim(list);
-
- vector<string> namesGroups = tmap->getNamesOfGroups();
- m->setGroups(namesGroups);
-
- //clear globaldatas old tree names if any
- m->Treenames.clear();
-
- //fills globaldatas tree names
- m->Treenames = m->getGroups();
-
- //used in tree constructor
- m->runParse = false;
-
- if (m->control_pressed) { return 0; }
-
- vector< vector<double> > matrix = makeSimsDist();
-
- if (m->control_pressed) { return 0; }
-
- //create a new filename
- string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "tre";
- outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
-
- Tree* newTree = createTree(matrix);
-
- if (newTree != NULL) { writeTree(outputFile, newTree); delete newTree; }
-
- if (m->control_pressed) { return 0; }
-
- m->mothurOut("Tree complete. "); m->mothurOutEndLine();
-
- }
-
- //reset groups parameter
- m->clearGroups();
-
- //set tree file as new current treefile
- string current = "";
- itTypes = outputTypes.find("tree");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
- }
-
- m->mothurOutEndLine();
- m->mothurOut("Output File Names: "); 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, "TreeGroupCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-Tree* TreeGroupCommand::createTree(vector< vector<double> >& simMatrix){
- try {
- //create tree
- t = new Tree(tmap, simMatrix);
-
- if (m->control_pressed) { delete t; t = NULL; return t; }
-
- //assemble tree
- map<string, string> empty;
- t->assembleTree(empty);
-
- return t;
- }
- catch(exception& e) {
- m->errorOut(e, "TreeGroupCommand", "createTree");
- exit(1);
- }
-}
-/***********************************************************/
-int TreeGroupCommand::writeTree(string out, Tree* T) {
- try {
-
- //print newick file
- t->createNewickFile(out);
-
- if (m->control_pressed) { m->mothurRemove(out); outputNames.pop_back(); return 1; }
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "TreeGroupCommand", "printSims");
- exit(1);
- }
-}
-
-/***********************************************************/
-void TreeGroupCommand::printSims(ostream& out, vector< vector<double> >& simMatrix) {
- try {
-
- for (int m = 0; m < simMatrix.size(); m++) {
- //out << lookup[m]->getGroup() << '\t';
- for (int n = 0; n < simMatrix.size(); n++) {
- out << simMatrix[m][n] << '\t';
- }
- out << endl;
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "TreeGroupCommand", "printSims");
- exit(1);
- }
-}
-/***********************************************************/
-vector< vector<double> > TreeGroupCommand::makeSimsDist() {
- try {
- numGroups = list->size();
-
- //initialize simMatrix
- vector< vector<double> > simMatrix;
- simMatrix.resize(numGroups);
- for (int k = 0; k < simMatrix.size(); k++) {
- for (int j = 0; j < simMatrix.size(); j++) {
- simMatrix[k].push_back(0.0);
- }
- }
-
- //go through sparse matrix and fill sims
- //go through each cell in the sparsematrix
- for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
- //similairity = -(distance-1)
- simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0);
- simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);
-
- if (m->control_pressed) { return simMatrix; }
-
- }
-
- return simMatrix;
- }
- catch(exception& e) {
- m->errorOut(e, "TreeGroupCommand", "makeSimsDist");
- exit(1);
- }
-}
-
-/***********************************************************/
-int TreeGroupCommand::makeSimsShared() {
- try {
-
- if (subsample) {
- if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
- subsampleSize = lookup[0]->getNumSeqs();
- for (int i = 1; i < lookup.size(); i++) {
- int thisSize = lookup[i]->getNumSeqs();
-
- if (thisSize < subsampleSize) { subsampleSize = thisSize; }
- }
- }else {
- m->clearGroups();
- Groups.clear();
- vector<SharedRAbundVector*> temp;
- for (int i = 0; i < lookup.size(); i++) {
- if (lookup[i]->getNumSeqs() < subsampleSize) {
- m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
- delete lookup[i];
- }else {
- Groups.push_back(lookup[i]->getGroup());
- temp.push_back(lookup[i]);
- }
- }
- lookup = temp;
- m->setGroups(Groups);
- }
-
- if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
- }
-
- numGroups = lookup.size();
- lines.resize(processors);
- for (int i = 0; i < processors; i++) {
- lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
- lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
- }
-
- set<string> processedLabels;
- set<string> userLabels = labels;
-
- //as long as you are not at the end of the file or done wih the lines you want
- while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; } return 1; }
-
- if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- process(lookup);
-
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
- }
-
- if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = lookup[0]->getLabel();
-
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- lookup = input->getSharedRAbundVectors(lastLabel);
-
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- process(lookup);
-
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
-
- //restore real lastlabel to save below
- lookup[0]->setLabel(saveLabel);
- }
-
- lastLabel = lookup[0]->getLabel();
-
- //get next line to process
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- lookup = input->getSharedRAbundVectors();
- }
-
- if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; } return 1; }
-
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
- }
- }
-
- //run last label if you need to
- if (needToRun == true) {
- for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
- lookup = input->getSharedRAbundVectors(lastLabel);
-
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- process(lookup);
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- }
-
- for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TreeGroupCommand", "makeSimsShared");
- exit(1);
- }
-}
-
-/***********************************************************/
-int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
- try{
- vector< vector< vector<seqDist> > > calcDistsTotals; //each iter, one for each calc, then each groupCombos dists. this will be used to make .dist files
- vector< vector<seqDist> > calcDists; calcDists.resize(treeCalculators.size());
-
- for (int thisIter = 0; thisIter < iters; thisIter++) {
-
- vector<SharedRAbundVector*> thisItersLookup = thisLookup;
-
- if (subsample) {
- SubSample sample;
- vector<string> tempLabels; //dont need since we arent printing the sampled sharedRabunds
-
- //make copy of lookup so we don't get access violations
- vector<SharedRAbundVector*> newLookup;
- for (int k = 0; k < thisItersLookup.size(); k++) {
- SharedRAbundVector* temp = new SharedRAbundVector();
- temp->setLabel(thisItersLookup[k]->getLabel());
- temp->setGroup(thisItersLookup[k]->getGroup());
- newLookup.push_back(temp);
- }
-
- //for each bin
- for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) {
- if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
- for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); }
- }
-
- tempLabels = sample.getSample(newLookup, subsampleSize);
- thisItersLookup = newLookup;
- }
-
- if(processors == 1){
- driver(thisItersLookup, 0, numGroups, calcDists);
- }else{
- int process = 1;
- vector<int> processIDS;
-
-#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){
-
- driver(thisItersLookup, lines[process].start, lines[process].end, calcDists);
-
- string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(getpid()) + ".dist";
- ofstream outtemp;
- m->openOutputFile(tempdistFileName, outtemp);
-
- for (int i = 0; i < calcDists.size(); i++) {
- outtemp << calcDists[i].size() << endl;
-
- for (int j = 0; j < calcDists[i].size(); j++) {
- outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl;
- }
- }
- outtemp.close();
-
- exit(0);
- }else {
- m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
- for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
- exit(0);
- }
- }
-
- //parent do your part
- driver(thisItersLookup, lines[0].start, lines[0].end, calcDists);
-
- //force parent to wait until all the processes are done
- for (int i = 0; i < processIDS.size(); i++) {
- int temp = processIDS[i];
- wait(&temp);
- }
-
- for (int i = 0; i < processIDS.size(); i++) {
- string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(processIDS[i]) + ".dist";
- ifstream intemp;
- m->openInputFile(tempdistFileName, intemp);
-
- for (int k = 0; k < calcDists.size(); k++) {
- int size = 0;
- intemp >> size; m->gobble(intemp);
-
- for (int j = 0; j < size; j++) {
- int seq1 = 0;
- int seq2 = 0;
- float dist = 1.0;
-
- intemp >> seq1 >> seq2 >> dist; m->gobble(intemp);
-
- seqDist tempDist(seq1, seq2, dist);
- calcDists[k].push_back(tempDist);
- }
- }
- intemp.close();
- m->mothurRemove(tempdistFileName);
- }
-#else
- //////////////////////////////////////////////////////////////////////////////////////////////////////
- //Windows version shared memory, so be careful when passing variables through the treeSharedData struct.
- //Above fork() will clone, so memory is separate, but that's not the case with windows,
- //Taking advantage of shared memory to pass results vectors.
- //////////////////////////////////////////////////////////////////////////////////////////////////////
-
- vector<treeSharedData*> pDataArray;
- DWORD dwThreadIdArray[processors-1];
- HANDLE hThreadArray[processors-1];
-
- //Create processor worker threads.
- for( int i=1; i<processors; i++ ){
-
- //make copy of lookup so we don't get access violations
- vector<SharedRAbundVector*> newLookup;
- for (int k = 0; k < thisItersLookup.size(); k++) {
- SharedRAbundVector* temp = new SharedRAbundVector();
- temp->setLabel(thisItersLookup[k]->getLabel());
- temp->setGroup(thisItersLookup[k]->getGroup());
- newLookup.push_back(temp);
- }
-
- //for each bin
- for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) {
- if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
- for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); }
- }
-
- // Allocate memory for thread data.
- treeSharedData* tempSum = new treeSharedData(m, lines[i].start, lines[i].end, Estimators, newLookup);
- pDataArray.push_back(tempSum);
- processIDS.push_back(i);
-
- hThreadArray[i-1] = CreateThread(NULL, 0, MyTreeSharedThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
- }
-
- //parent do your part
- driver(thisItersLookup, lines[0].start, lines[0].end, calcDists);
-
- //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++){
- for (int j = 0; j < pDataArray[i]->thisLookup.size(); j++) { delete pDataArray[i]->thisLookup[j]; }
-
- for (int k = 0; k < calcDists.size(); k++) {
- int size = pDataArray[i]->calcDists[k].size();
- for (int j = 0; j < size; j++) { calcDists[k].push_back(pDataArray[i]->calcDists[k][j]); }
- }
-
- CloseHandle(hThreadArray[i]);
- delete pDataArray[i];
- }
-
-#endif
- }
-
- calcDistsTotals.push_back(calcDists);
-
- if (subsample) {
-
- //clean up memory
- for (int i = 0; i < thisItersLookup.size(); i++) { delete thisItersLookup[i]; }
- thisItersLookup.clear();
- for (int i = 0; i < calcDists.size(); i++) { calcDists[i].clear(); }
- }
- }
-
- if (iters != 1) {
- //we need to find the average distance and standard deviation for each groups distance
-
- vector< vector<seqDist> > calcAverages; calcAverages.resize(treeCalculators.size());
- for (int i = 0; i < calcAverages.size(); i++) { //initialize sums to zero.
- calcAverages[i].resize(calcDistsTotals[0][i].size());
-
- for (int j = 0; j < calcAverages[i].size(); j++) {
- calcAverages[i][j].seq1 = calcDists[i][j].seq1;
- calcAverages[i][j].seq2 = calcDists[i][j].seq2;
- calcAverages[i][j].dist = 0.0;
- }
- }
-
- for (int thisIter = 0; thisIter < iters; thisIter++) { //sum all groups dists for each calculator
- for (int i = 0; i < calcAverages.size(); i++) { //initialize sums to zero.
- for (int j = 0; j < calcAverages[i].size(); j++) {
- calcAverages[i][j].dist += calcDistsTotals[thisIter][i][j].dist;
- }
- }
- }
-
- for (int i = 0; i < calcAverages.size(); i++) { //finds average.
- for (int j = 0; j < calcAverages[i].size(); j++) {
- calcAverages[i][j].dist /= (float) iters;
- }
- }
-
- //create average tree for each calc
- for (int i = 0; i < calcDists.size(); i++) {
- vector< vector<double> > matrix; //square matrix to represent the distance
- matrix.resize(thisLookup.size());
- for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); }
-
- for (int j = 0; j < calcAverages[i].size(); j++) {
- int row = calcAverages[i][j].seq1;
- int column = calcAverages[i][j].seq2;
- float dist = calcAverages[i][j].dist;
-
- matrix[row][column] = dist;
- matrix[column][row] = dist;
- }
-
- //create a new filename
- string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".ave.tre";
- outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
-
- //creates tree from similarity matrix and write out file
- Tree* newTree = createTree(matrix);
- if (newTree != NULL) { writeTree(outputFile, newTree); }
- }
-
- //create all trees for each calc and find their consensus tree
- for (int i = 0; i < calcDists.size(); i++) {
- if (m->control_pressed) { break; }
-
- //create a new filename
- string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".all.tre";
- outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
-
- ofstream outAll;
- m->openOutputFile(outputFile, outAll);
-
- vector<Tree*> trees;
- for (int myIter = 0; myIter < iters; myIter++) {
-
- if(m->control_pressed) { break; }
-
- //initialize matrix
- vector< vector<double> > matrix; //square matrix to represent the distance
- matrix.resize(thisLookup.size());
- for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); }
-
- for (int j = 0; j < calcDistsTotals[myIter][i].size(); j++) {
- int row = calcDistsTotals[myIter][i][j].seq1;
- int column = calcDistsTotals[myIter][i][j].seq2;
- double dist = calcDistsTotals[myIter][i][j].dist;
-
- matrix[row][column] = dist;
- matrix[column][row] = dist;
- }
-
- //creates tree from similarity matrix and write out file
- Tree* newTree = createTree(matrix);
- if (newTree != NULL) {
- newTree->print(outAll);
- trees.push_back(newTree);
- }
- }
- outAll.close();
- if (m->control_pressed) { for (int k = 0; k < trees.size(); k++) { delete trees[k]; } }
-
- Consensus consensus;
- //clear old tree names if any
- m->Treenames.clear(); m->Treenames = m->getGroups(); //may have changed if subsample eliminated groups
- Tree* conTree = consensus.getTree(trees);
-
- //create a new filename
- string conFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".cons.tre";
- outputNames.push_back(conFile); outputTypes["tree"].push_back(conFile);
- ofstream outTree;
- m->openOutputFile(conFile, outTree);
-
- if (conTree != NULL) { conTree->print(outTree, "boot"); delete conTree; }
- }
-
- }else {
-
- for (int i = 0; i < calcDists.size(); i++) {
- if (m->control_pressed) { break; }
-
- //initialize matrix
- vector< vector<double> > matrix; //square matrix to represent the distance
- matrix.resize(thisLookup.size());
- for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); }
-
- for (int j = 0; j < calcDists[i].size(); j++) {
- int row = calcDists[i][j].seq1;
- int column = calcDists[i][j].seq2;
- double dist = calcDists[i][j].dist;
-
- matrix[row][column] = dist;
- matrix[column][row] = dist;
- }
-
- //create a new filename
- string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";
- outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
-
- //creates tree from similarity matrix and write out file
- Tree* newTree = createTree(matrix);
- if (newTree != NULL) { writeTree(outputFile, newTree); delete newTree; }
- }
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TreeGroupCommand", "process");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int TreeGroupCommand::driver(vector<SharedRAbundVector*> thisLookup, int start, int end, vector< vector<seqDist> >& calcDists) {
- try {
- vector<SharedRAbundVector*> subset;
- for (int k = start; k < end; k++) { // pass cdd each set of groups to compare
-
- for (int l = 0; l < k; l++) {
-
- if (k != l) { //we dont need to similiarity of a groups to itself
- subset.clear(); //clear out old pair of sharedrabunds
- //add new pair of sharedrabunds
- subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
-
- for(int i=0;i<treeCalculators.size();i++) {
-
- //if this calc needs all groups to calculate the pair load all groups
- if (treeCalculators[i]->getNeedsAll()) {
- //load subset with rest of lookup for those calcs that need everyone to calc for a pair
- for (int w = 0; w < thisLookup.size(); w++) {
- if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
- }
- }
-
- vector<double> tempdata = treeCalculators[i]->getValues(subset); //saves the calculator outputs
-
- if (m->control_pressed) { return 1; }
-
- seqDist temp(l, k, -(tempdata[0]-1.0));
- calcDists[i].push_back(temp);
- }
- }
- }
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "TreeGroupCommand", "driver");
- exit(1);
- }
-}
-/***********************************************************/
-
-
-
projects / mothur.git / blobdiff