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/*
* 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","tree",false,false,true); parameters.push_back(pshared);
CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none","tree",false,false); parameters.push_back(pphylip);
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","",false,false); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "countcolumn","",false,false); parameters.push_back(pcount);
CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName-countcolumn","tree",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,true); parameters.push_back(pcalc);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); 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 similarity 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);
}
}
//**********************************************************************************************************************
string TreeGroupCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "tree") { pattern = "[filename],[calc],[distance],[tag],tre-[filename],tre"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "TreeGroupCommand", "getOutputPattern");
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; }
}
it = parameters.find("count");
//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["count"] = 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); }
countfile = validParameter.validFile(parameters, "count", true);
if (countfile == "not open") { abort = true; countfile = ""; }
else if (countfile == "not found") { countfile = ""; }
else { m->setCountTableFile(countfile); }
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 == "") && (countfile == "")){
namefile = m->getNameFile();
if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
else {
countfile = m->getCountTableFile();
if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
else {
m->mothurOut("You need to provide a namefile or countfile 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 list; }
delete ct;
}
}
//**********************************************************************************************************************
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
ct = new CountTable();
set<string> nameMap;
map<string, string> groupMap;
set<string> gps;
for (int i = 0; i < m->getAllGroups().size(); i++) {
nameMap.insert(m->getAllGroups()[i]);
gps.insert(m->getAllGroups()[i]);
groupMap[m->getAllGroups()[i]] = m->getAllGroups()[i];
}
ct->createTable(nameMap, groupMap, gps);
//clear globaldatas old tree names if any
m->Treenames.clear();
//fills globaldatas tree names
//m->Treenames = m->getGroups();
for (int k = 0; k < lookup.size(); k++) {
m->Treenames.push_back(lookup[k]->getGroup());
}
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;
ReadMatrix* readMatrix;
if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
readMatrix->setCutoff(cutoff);
ct = NULL;
nameMap = NULL;
if(namefile != ""){
nameMap = new NameAssignment(namefile);
nameMap->readMap();
readMatrix->read(nameMap);
}else if (countfile != "") {
ct = new CountTable();
ct->readTable(countfile, true, false);
readMatrix->read(ct);
}else {
readMatrix->read(nameMap);
}
list = readMatrix->getListVector();
SparseDistanceMatrix* dMatrix = readMatrix->getDMatrix();
//clear globaldatas old tree names if any
m->Treenames.clear();
//make treemap
if (ct != NULL) { delete ct; }
ct = new CountTable();
set<string> nameMap;
map<string, string> groupMap;
set<string> gps;
for (int i = 0; i < list->getNumBins(); i++) {
string bin = list->get(i);
nameMap.insert(bin);
gps.insert(bin);
groupMap[bin] = bin;
m->Treenames.push_back(bin);
}
ct->createTable(nameMap, groupMap, gps);
vector<string> namesGroups = ct->getNamesOfGroups();
m->setGroups(namesGroups);
//used in tree constructor
m->runParse = false;
if (m->control_pressed) { return 0; }
vector< vector<double> > matrix = makeSimsDist(dMatrix);
delete readMatrix;
delete dMatrix;
if (m->control_pressed) { return 0; }
//create a new filename
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
string outputFile = getOutputFileName("tree",variables);
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(ct, simMatrix);
if (m->control_pressed) { delete t; t = NULL; return t; }
//assemble tree
t->assembleTree();
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(SparseDistanceMatrix* matrix) {
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 (int i = 0; i < matrix->seqVec.size(); i++) {
for (int j = 0; j < matrix->seqVec[i].size(); j++) {
//already checked everyone else in row
if (i < matrix->seqVec[i][j].index) {
simMatrix[i][matrix->seqVec[i][j].index] = -(matrix->seqVec[i][j].dist -1.0);
simMatrix[matrix->seqVec[i][j].index][i] = -(matrix->seqVec[i][j].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();
m->Treenames.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]);
m->Treenames.push_back(lookup[i]->getGroup());
}
}
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();
//sanity check to make sure processors < numComparisions
int numDists = 0;
for(int i=0;i<numGroups;i++){
for(int j=0;j<i;j++){
numDists++;
if (numDists > processors) { break; }
}
}
if (numDists < processors) { processors = numDists; }
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++){
if (pDataArray[i]->count != (pDataArray[i]->end-pDataArray[i]->start)) {
m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end-pDataArray[i]->start) + " groups assigned to it, quitting. \n"); m->control_pressed = true;
}
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 (m->debug) { m->mothurOut("[DEBUG]: iter = " + toString(thisIter) + ".\n"); }
}
if (m->debug) { m->mothurOut("[DEBUG]: done with iters.\n"); }
if (iters != 1) {
//we need to find the average distance and standard deviation for each groups distance
vector< vector<seqDist> > calcAverages = m->getAverages(calcDistsTotals);
if (m->debug) { m->mothurOut("[DEBUG]: found averages.\n"); }
//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
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
variables["[calc]"] = treeCalculators[i]->getName();
variables["[distance]"] = thisLookup[0]->getLabel();
variables["[tag]"] = "ave";
string outputFile = getOutputFileName("tree",variables);
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); }
}
if (m->debug) { m->mothurOut("[DEBUG]: done averages trees.\n"); }
//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
//create a new filename
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
variables["[calc]"] = treeCalculators[i]->getName();
variables["[distance]"] = thisLookup[0]->getLabel();
variables["[tag]"] = "all";
string outputFile = getOutputFileName("tree",variables);
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]; } }
if (m->debug) { m->mothurOut("[DEBUG]: done all trees.\n"); }
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);
if (m->debug) { m->mothurOut("[DEBUG]: done cons tree.\n"); }
//create a new filename
variables["[tag]"] = "cons";
string conFile = getOutputFileName("tree",variables);
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
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
variables["[calc]"] = treeCalculators[i]->getName();
variables["[distance]"] = thisLookup[0]->getLabel();
variables["[tag]"] = "";
string outputFile = getOutputFileName("tree",variables);
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);
}
}
/***********************************************************/
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