//**********************************************************************************************************************
-BootSharedCommand::BootSharedCommand(){
+BootSharedCommand::BootSharedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- format = globaldata->getFormat();
- convert(globaldata->getIters(), iters);
- validCalculator = new ValidCalculators();
- util = new SharedUtil();
+ abort = false;
+ allLines = 1;
+ labels.clear();
+ Groups.clear();
+ Estimators.clear();
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
- int i;
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("boot", globaldata->Estimators[i]) == true) {
- if (globaldata->Estimators[i] == "jabund") {
- treeCalculators.push_back(new JAbund());
- }else if (globaldata->Estimators[i] == "sorabund") {
- treeCalculators.push_back(new SorAbund());
- }else if (globaldata->Estimators[i] == "jclass") {
- treeCalculators.push_back(new Jclass());
- }else if (globaldata->Estimators[i] == "sorclass") {
- treeCalculators.push_back(new SorClass());
- }else if (globaldata->Estimators[i] == "jest") {
- treeCalculators.push_back(new Jest());
- }else if (globaldata->Estimators[i] == "sorest") {
- treeCalculators.push_back(new SorEst());
- }else if (globaldata->Estimators[i] == "thetayc") {
- treeCalculators.push_back(new ThetaYC());
- }else if (globaldata->Estimators[i] == "thetan") {
- treeCalculators.push_back(new ThetaN());
- }else if (globaldata->Estimators[i] == "morisitahorn") {
- treeCalculators.push_back(new MorHorn());
- }else if (globaldata->Estimators[i] == "braycurtis") {
- treeCalculators.push_back(new BrayCurtis());
+ else {
+ //valid paramters for this command
+ string Array[] = {"label","calc","groups","iters","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { 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 += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ }
+
+
+ //make sure the user has already run the read.otu command
+ if (globaldata->getSharedFile() == "") {
+ if (globaldata->getListFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the bootstrap.shared command."); m->mothurOutEndLine(); abort = true; }
+ else if (globaldata->getGroupFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the bootstrap.shared command."); 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") { splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //if the user has not specified any labels use the ones from read.otu
+ if(label == "") {
+ allLines = globaldata->allLines;
+ labels = globaldata->labels;
+ }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
+ calc = validParameter.validFile(parameters, "calc", false);
+ if (calc == "not found") { calc = "jclass-thetayc"; }
+ else {
+ if (calc == "default") { calc = "jclass-thetayc"; }
+ }
+ splitAtDash(calc, Estimators);
+
+ string temp;
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ convert(temp, iters);
+
+ if (abort == false) {
+
+ //used in tree constructor
+ globaldata->runParse = false;
+
+ validCalculator = new ValidCalculators();
+
+ int i;
+ for (i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("boot", Estimators[i]) == true) {
+ 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] == "morisitahorn") {
+ treeCalculators.push_back(new MorHorn());
+ }else if (Estimators[i] == "braycurtis") {
+ treeCalculators.push_back(new BrayCurtis());
+ }
+ }
}
+
+ delete validCalculator;
+
+ ofstream* tempo;
+ for (int i=0; i < treeCalculators.size(); i++) {
+ tempo = new ofstream;
+ out.push_back(tempo);
+ }
+
+ //make a vector of tree* for each calculator
+ trees.resize(treeCalculators.size());
}
}
-
- ofstream* temp;
- for (int i=0; i < treeCalculators.size(); i++) {
- temp = new ofstream;
- out.push_back(temp);
- }
-
- //reset calc for next command
- globaldata->setCalc("");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function BootSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "BootSharedCommand", "BootSharedCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the BootSharedCommand class function BootSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+//**********************************************************************************************************************
+
+void BootSharedCommand::help(){
+ try {
+ m->mothurOut("The bootstrap.shared command can only be executed after a successful read.otu command.\n");
+ m->mothurOut("The bootstrap.shared command parameters are groups, calc, iters and label.\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
+ m->mothurOut("The group names are separated by dashes. The label parameter allows you to select what distance levels you would like trees created for, and is also separated by dashes.\n");
+ m->mothurOut("The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels, iters=yourIters).\n");
+ m->mothurOut("Example bootstrap.shared(groups=A-B-C, calc=jabund-sorabund, iters=100).\n");
+ m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
+ m->mothurOut("The default value for calc is jclass-thetayc. The default for iters is 1000.\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BootSharedCommand", "help");
exit(1);
- }
+ }
}
+
//**********************************************************************************************************************
BootSharedCommand::~BootSharedCommand(){
- delete input;
- delete read;
- delete util;
+ //made new in execute
+ if (abort == false) {
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete util;
+ globaldata->gorder = NULL;
+ }
}
//**********************************************************************************************************************
int BootSharedCommand::execute(){
try {
- int count = 1;
- //if the users entered no valid calculators don't execute command
- if (treeCalculators.size() == 0) { return 0; }
-
+ if (abort == true) { return 0; }
+
+ util = new SharedUtil();
+
//read first line
read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
input = globaldata->ginput;
order = input->getSharedOrderVector();
- SharedOrderVector* lastOrder = order;
+ string lastLabel = order->getLabel();
+ //if the users entered no valid calculators don't execute command
+ if (treeCalculators.size() == 0) { return 0; }
+
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
- set<string> userLabels = globaldata->labels;
+ set<string> userLabels = labels;
//set users groups
util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "treegroup");
tmap->makeSim(globaldata->gGroupmap);
globaldata->gTreemap = tmap;
- while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+ while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+ if(allLines == 1 || labels.count(order->getLabel()) == 1){
- cout << order->getLabel() << '\t' << count << endl;
- process(order);
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+ int error = process(order);
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
-
- //you have a label the user want that is smaller than this line and the last line has not already been processed
}
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
-
- cout << lastOrder->getLabel() << '\t' << count << endl;
- process(lastOrder);
+ //you have a label the user want that is smaller than this label and the last label has not already been processed
+ if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = order->getLabel();
+
+ delete order;
+ order = input->getSharedOrderVector(lastLabel);
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+ int error = process(order);
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
- processedLabels.insert(lastOrder->getLabel());
- userLabels.erase(lastOrder->getLabel());
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
+
+ //restore real lastlabel to save below
+ order->setLabel(saveLabel);
}
- if (count != 1) { delete lastOrder; }
- lastOrder = order;
+
+ lastLabel = order->getLabel();
//get next line to process
+ delete order;
order = input->getSharedOrderVector();
- count++;
}
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastOrder->getLabel()) != 1) {
- cout << ". I will use " << lastOrder->getLabel() << "." << endl;
+ 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 {
- cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
//run last line if you need to
if (needToRun == true) {
- process(lastOrder);
- cout << lastOrder->getLabel() << '\t' << count << endl;
+ if (order != NULL) { delete order; }
+ order = input->getSharedOrderVector(lastLabel);
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+ int error = process(order);
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
+
+ delete order;
+
}
- delete lastOrder;
-
//reset groups parameter
- globaldata->Groups.clear(); globaldata->setGroups("");
+ globaldata->Groups.clear();
+
+ 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) {
- cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "BootSharedCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the BootSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
-void BootSharedCommand::createTree(ostream* out){
+int BootSharedCommand::createTree(ostream* out, Tree* t){
try {
- //create tree
- t = new Tree();
//do merges and create tree structure by setting parents and children
//there are numGroups - 1 merges to do
for (int i = 0; i < (numGroups - 1); i++) {
- float largest = -1.0;
+ if (m->control_pressed) { return 1; }
+
+ float largest = -1000.0;
int row, column;
//find largest value in sims matrix by searching lower triangle
for (int j = 1; j < simMatrix.size(); j++) {
index[column] = numGroups+i;
//zero out highest value that caused the merge.
- simMatrix[row][column] = -1.0;
- simMatrix[column][row] = -1.0;
+ simMatrix[row][column] = -1000.0;
+ simMatrix[column][row] = -1000.0;
//merge values in simsMatrix
for (int n = 0; n < simMatrix.size(); n++) {
simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
simMatrix[n][row] = simMatrix[row][n];
//delete column
- simMatrix[column][n] = -1.0;
- simMatrix[n][column] = -1.0;
+ simMatrix[column][n] = -1000.0;
+ simMatrix[n][column] = -1000.0;
}
}
+
+ //adjust tree to make sure root to tip length is .5
+ int root = t->findRoot();
+ t->tree[root].setBranchLength((0.5 - t->tree[root].getLengthToLeaves()));
//assemble tree
t->assembleTree();
//print newick file
t->print(*out);
-
- //delete tree
- delete t;
+
+ return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the BootSharedCommand class function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "BootSharedCommand", "createTree");
exit(1);
}
}
/***********************************************************/
void BootSharedCommand::printSims() {
try {
- cout << "simsMatrix" << endl;
- for (int m = 0; m < simMatrix.size(); m++) {
+ m->mothurOut("simsMatrix"); m->mothurOutEndLine();
+ for (int k = 0; k < simMatrix.size(); k++) {
for (int n = 0; n < simMatrix.size(); n++) {
- cout << simMatrix[m][n] << '\t';
+ m->mothurOut(toString(simMatrix[k][n])); m->mothurOut("\t");
}
- cout << endl;
+ m->mothurOutEndLine();
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "BootSharedCommand", "printSims");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the BootSharedCommand class function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************/
-void BootSharedCommand::process(SharedOrderVector* order) {
+int BootSharedCommand::process(SharedOrderVector* order) {
try{
EstOutput data;
vector<SharedRAbundVector*> subset;
-
+
//open an ostream for each calc to print to
for (int z = 0; z < treeCalculators.size(); z++) {
//create a new filename
- outputFile = getRootName(globaldata->inputFileName) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre";
+ outputFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre";
openOutputFile(outputFile, *(out[z]));
+ outputNames.push_back(outputFile);
}
+ m->mothurOut("Generating bootstrap trees..."); cout.flush();
+
//create a file for each calculator with the 1000 trees in it.
for (int p = 0; p < iters; p++) {
+ if (m->control_pressed) { return 1; }
+
util->getSharedVectorswithReplacement(globaldata->Groups, lookup, order); //fills group vectors from order vector.
+
//for each calculator
for(int i = 0 ; i < treeCalculators.size(); i++) {
-
+
+ if (m->control_pressed) { return 1; }
+
//initialize simMatrix
simMatrix.clear();
simMatrix.resize(numGroups);
- for (int m = 0; m < simMatrix.size(); m++) {
+ for (int o = 0; o < simMatrix.size(); o++) {
for (int j = 0; j < simMatrix.size(); j++) {
- simMatrix[m].push_back(0.0);
+ simMatrix[o].push_back(0.0);
}
}
}
}
}
-
+
+ tempTree = new Tree();
+
+ if (m->control_pressed) { delete tempTree; return 1; }
+
//creates tree from similarity matrix and write out file
- createTree(out[i]);
+ createTree(out[i], tempTree);
+
+ //save trees for consensus command.
+ trees[i].push_back(tempTree);
}
}
+
+ m->mothurOut("\tDone."); m->mothurOutEndLine();
+ //delete globaldata's tree
+ //for (int m = 0; m < globaldata->gTree.size(); m++) { delete globaldata->gTree[m]; }
+ //globaldata->gTree.clear();
+
+
+ //create consensus trees for each bootstrapped tree set
+ for (int k = 0; k < trees.size(); k++) {
+
+ m->mothurOut("Generating consensus tree for " + treeCalculators[k]->getName()); m->mothurOutEndLine();
+
+ if (m->control_pressed) { return 1; }
+
+ //set global data to calc trees
+ globaldata->gTree = trees[k];
+
+ string filename = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + treeCalculators[k]->getName() + ".boot" + order->getLabel();
+ consensus = new ConcensusCommand(filename);
+ consensus->execute();
+ delete consensus;
+
+ outputNames.push_back(filename + ".cons.pairs");
+ outputNames.push_back(filename + ".cons.tre");
+
+ //delete globaldata's tree
+ //for (int m = 0; m < globaldata->gTree.size(); m++) { delete globaldata->gTree[m]; }
+ //globaldata->gTree.clear();
+
+ }
+
+
+
//close ostream for each calc
for (int z = 0; z < treeCalculators.size(); z++) { out[z]->close(); }
-
+
+ return 0;
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "BootSharedCommand", "process");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the BootSharedCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************/
projects / mothur.git / blobdiff