X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bootstrapsharedcommand.cpp;h=cc0cfb63f37c4adad6c4965f9e419f0733100ef3;hb=e150b0b0664caec517485ee6d69dcdade6dcae77;hp=9e3a82de0bfaff9807c653ce0986f96f59b67cba;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp index 9e3a82d..cc0cfb6 100644 --- a/bootstrapsharedcommand.cpp +++ b/bootstrapsharedcommand.cpp @@ -21,90 +21,144 @@ //********************************************************************************************************************** +vector BootSharedCommand::setParameters(){ + try { + CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared); + CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); + CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); + CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters); + CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); -BootSharedCommand::BootSharedCommand(string option){ + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "BootSharedCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string BootSharedCommand::getHelpString(){ try { - globaldata = GlobalData::getInstance(); - abort = false; - allLines = 1; - lines.clear(); - labels.clear(); - Groups.clear(); - Estimators.clear(); + string helpString = ""; + helpString += "The bootstrap.shared command parameters are shared, groups, calc, iters and label. shared is required.\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 parameter allows you to select what distance levels you would like trees created for, and is also separated by dashes.\n"; + helpString += "The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels, iters=yourIters).\n"; + helpString += "Example bootstrap.shared(groups=A-B-C, calc=jabund-sorabund, iters=100).\n"; + helpString += "The default value for groups is all the groups in your groupfile.\n"; + helpString += "The default value for calc is jclass-thetayc. The default for iters is 1000.\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "BootSharedCommand", "getHelpString"); + exit(1); + } +} +//********************************************************************************************************************** +BootSharedCommand::BootSharedCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["tree"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "BootSharedCommand", "BootSharedCommand"); + exit(1); + } +} +//********************************************************************************************************************** +BootSharedCommand::BootSharedCommand(string option) { + try { + abort = false; calledHelp = false; //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string Array[] = {"line","label","calc","groups","iters"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); - parser = new OptionParser(); - parser->parse(option, parameters); delete parser; + OptionParser parser(option); + map parameters = parser.getParameters(); + map::iterator it; - ValidParameters* validParameter = new ValidParameters(); + ValidParameters validParameter; //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; } + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } - //make sure the user has already run the read.otu command - if (globaldata->getSharedFile() == "") { - if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the bootstrap.shared command." << endl; abort = true; } - else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the bootstrap.shared command." << endl; abort = true; } + //initialize outputTypes + vector 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("shared"); + //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["shared"] = inputDir + it->second; } + } } - //check for optional parameter and set defaults - // ...at some point should added some additional type checking... - line = validParameter->validFile(parameters, "line", false); - if (line == "not found") { line = ""; } - else { - if(line != "all") { splitAtDash(line, lines); allLines = 0; } - else { allLines = 1; } + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not found") { m->mothurOut("shared is a required parameter."); m->mothurOutEndLine(); sharedfile = ""; abort = true; } + else if (sharedfile == "not open") { sharedfile = ""; 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(sharedfile); //if user entered a file with a path then preserve it } - label = validParameter->validFile(parameters, "label", false); + //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; } + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } else { allLines = 1; } } - - //make sure user did not use both the line and label parameters - if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; } - //if the user has not specified any line or labels use the ones from read.otu - else if((line == "") && (label == "")) { - allLines = globaldata->allLines; - labels = globaldata->labels; - lines = globaldata->lines; - } - - groups = validParameter->validFile(parameters, "groups", false); + + groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } else { - splitAtDash(groups, Groups); - globaldata->Groups = Groups; + m->splitAtDash(groups, Groups); + m->Groups = Groups; } - calc = validParameter->validFile(parameters, "calc", false); + calc = validParameter.validFile(parameters, "calc", false); if (calc == "not found") { calc = "jclass-thetayc"; } else { if (calc == "default") { calc = "jclass-thetayc"; } } - splitAtDash(calc, Estimators); + m->splitAtDash(calc, Estimators); string temp; - temp = validParameter->validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } + temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } convert(temp, iters); - - delete validParameter; - + if (abort == false) { + //used in tree constructor + m->runParse = false; + validCalculator = new ValidCalculators(); + + //NOTE: if you add a calc to this if statement you must add it to the setParameters function + //or it will not be visible in the gui int i; for (i=0; iisValidCalculator("boot", Estimators[i]) == true) { @@ -138,71 +192,34 @@ BootSharedCommand::BootSharedCommand(string option){ 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()); } } } 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"; - exit(1); - } } - //********************************************************************************************************************** - -void BootSharedCommand::help(){ - try { - cout << "The bootstrap.shared command can only be executed after a successful read.otu command." << "\n"; - cout << "The bootstrap.shared command parameters are groups, calc, iters, line and label. You may not use line and label at the same time." << "\n"; - cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n"; - cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like trees created for, and are also separated by dashes." << "\n"; - cout << "The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, iters=yourIters)." << "\n"; - cout << "Example bootstrap.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund, iters=100)." << "\n"; - cout << "The default value for groups is all the groups in your groupfile." << "\n"; - cout << "The default value for calc is jclass-thetayc. The default for iters is 1000." << "\n"; - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the BootSharedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } -} - -//********************************************************************************************************************** - -BootSharedCommand::~BootSharedCommand(){ - //made new in execute - if (abort == false) { - delete input; - delete read; - delete util; - } -} - +BootSharedCommand::~BootSharedCommand(){} //********************************************************************************************************************** int BootSharedCommand::execute(){ try { - if (abort == true) { return 0; } - - int count = 1; - util = new SharedUtil(); - + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + m->mothurOut("bootstrap.shared command is no longer available."); m->mothurOutEndLine(); + /* //read first line - read = new ReadOTUFile(globaldata->inputFileName); - read->read(&*globaldata); - input = globaldata->ginput; + input = new InputData(sharedfile, "sharedfile"); 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; } @@ -210,100 +227,132 @@ int BootSharedCommand::execute(){ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. set processedLabels; set userLabels = labels; - set userLines = lines; //set users groups - util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "treegroup"); - numGroups = globaldata->Groups.size(); + util = new SharedUtil(); + util->setGroups(m->Groups, m->namesOfGroups, "treegroup"); + + numGroups = m->Groups.size(); //clear globaldatas old tree names if any globaldata->Treenames.clear(); //fills globaldatas tree names - globaldata->Treenames = globaldata->Groups; + globaldata->Treenames = m->Groups; //create treemap class from groupmap for tree class to use tmap = new TreeMap(); tmap->makeSim(globaldata->gGroupmap); globaldata->gTreemap = tmap; - while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { - - if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){ + while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); delete input;delete util; return 0; } + + 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(); delete input;delete util; return 0; } processedLabels.insert(order->getLabel()); userLabels.erase(order->getLabel()); - userLines.erase(count); } - //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 ((m->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(); delete input;delete util; 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++; } + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); delete input; delete util; return 0; } + //output error messages about any remaining user labels set::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(); } } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); delete input; delete util; return 0; } + //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(); delete input; delete util; return 0; } + + delete order; + } - delete lastOrder; + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear();delete input; delete util; return 0; } //reset groups parameter globaldata->Groups.clear(); + + //set first tree file as new current treefile + string currentTree = ""; + itTypes = outputTypes.find("tree"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { currentTree = (itTypes->second)[0]; m->setTreeFile(currentTree); } + } + + delete input; + delete util; + + 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++) { @@ -336,8 +385,8 @@ void BootSharedCommand::createTree(ostream* out){ 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++) { @@ -345,78 +394,83 @@ void BootSharedCommand::createTree(ostream* out){ 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(); + + if (m->control_pressed) { return 1; } //print newick file - t->print(*out); - - //delete tree - delete t; + t->print(*out);*/ + + 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; + /* EstOutput data; vector 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"; - openOutputFile(outputFile, *(out[z])); + outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre"; + m->openOutputFile(outputFile, *(out[z])); + outputNames.push_back(outputFile); outputTypes["tree"].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++) { - util->getSharedVectorswithReplacement(Groups, lookup, order); //fills group vectors from order vector. + if (m->control_pressed) { return 1; } + + util->getSharedVectorswithReplacement(m->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); } } @@ -439,23 +493,56 @@ void BootSharedCommand::process(SharedOrderVector* order) { } } } - + + 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); + + if (m->control_pressed) { delete tempTree; return 1; } + + //save trees for consensus command. + trees[i].push_back(tempTree); } } + + m->mothurOut("\tDone."); m->mothurOutEndLine(); + + + //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 + m->getRootName(m->getSimpleName(sharedfile)) + 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"); + + } + + + //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); - } } /***********************************************************/