X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bootstrapsharedcommand.cpp;h=afc3cf1533475b6bf78b8127ba34086193612371;hb=d0954e27635712cdbd8b86e3c4510670803a2665;hp=12c0b5e647fefccded7b826e23efb7d019e1b703;hpb=71b2121662daae3f9044252887d1c16eeddd85bb;p=mothur.git diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp index 12c0b5e..afc3cf1 100644 --- a/bootstrapsharedcommand.cpp +++ b/bootstrapsharedcommand.cpp @@ -19,25 +19,69 @@ #include "sharedmorisitahorn.h" #include "sharedbraycurtis.h" - //********************************************************************************************************************** - -BootSharedCommand::BootSharedCommand(string option){ +vector BootSharedCommand::getValidParameters(){ + try { + string AlignArray[] = {"label","calc","groups","iters","outputdir","inputdir"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "BootSharedCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +BootSharedCommand::BootSharedCommand(){ + try { + abort = true; calledHelp = true; + vector tempOutNames; + outputTypes["tree"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "BootSharedCommand", "BootSharedCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector BootSharedCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "BootSharedCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector BootSharedCommand::getRequiredFiles(){ + try { + string AlignArray[] = {"shared"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "BootSharedCommand", "getRequiredFiles"); + exit(1); + } +} +//********************************************************************************************************************** +BootSharedCommand::BootSharedCommand(string option) { try { globaldata = GlobalData::getInstance(); - abort = false; + abort = false; calledHelp = false; allLines = 1; - lines.clear(); labels.clear(); Groups.clear(); Estimators.clear(); //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } else { //valid paramters for this command - string Array[] = {"line","label","calc","groups","iters"}; + string Array[] = {"label","calc","groups","iters","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); @@ -50,41 +94,42 @@ BootSharedCommand::BootSharedCommand(string option){ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["tree"] = tempOutNames; + + //if the user changes the output directory command factory will send this info to us in the output parameter + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ + outputDir = ""; + outputDir += m->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() == "") { mothurOut("You must read a list and a group, or a shared before you can use the bootstrap.shared command."); mothurOutEndLine(); abort = true; } - else if (globaldata->getGroupFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the bootstrap.shared command."); mothurOutEndLine(); abort = true; } + 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... - line = validParameter.validFile(parameters, "line", false); - if (line == "not found") { line = ""; } - else { - if(line != "all") { splitAtDash(line, lines); allLines = 0; } - else { allLines = 1; } - } - 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 != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; } - //if the user has not specified any line or labels use the ones from read.otu - else if((line == "") && (label == "")) { + //if the user has not specified any labels use the ones from read.otu + if(label == "") { allLines = globaldata->allLines; labels = globaldata->labels; - lines = globaldata->lines; } groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } else { - splitAtDash(groups, Groups); + m->splitAtDash(groups, Groups); globaldata->Groups = Groups; } @@ -93,7 +138,7 @@ BootSharedCommand::BootSharedCommand(string option){ 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"; } @@ -148,7 +193,7 @@ BootSharedCommand::BootSharedCommand(string option){ } catch(exception& e) { - errorOut(e, "BootSharedCommand", "BootSharedCommand"); + m->errorOut(e, "BootSharedCommand", "BootSharedCommand"); exit(1); } } @@ -157,17 +202,17 @@ BootSharedCommand::BootSharedCommand(string option){ void BootSharedCommand::help(){ try { - mothurOut("The bootstrap.shared command can only be executed after a successful read.otu command.\n"); - mothurOut("The bootstrap.shared command parameters are groups, calc, iters, line and label. You may not use line and label at the same time.\n"); - mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n"); - mothurOut("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"); - mothurOut("The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, iters=yourIters).\n"); - mothurOut("Example bootstrap.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund, iters=100).\n"); - mothurOut("The default value for groups is all the groups in your groupfile.\n"); - mothurOut("The default value for calc is jclass-thetayc. The default for iters is 1000.\n"); + 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) { - errorOut(e, "BootSharedCommand", "help"); + m->errorOut(e, "BootSharedCommand", "help"); exit(1); } } @@ -189,9 +234,8 @@ BootSharedCommand::~BootSharedCommand(){ int BootSharedCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } - int count = 1; util = new SharedUtil(); //read first line @@ -207,7 +251,6 @@ 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"); @@ -224,28 +267,34 @@ int BootSharedCommand::execute(){ 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(); return 0; } + + if(allLines == 1 || labels.count(order->getLabel()) == 1){ - mothurOut(order->getLabel()); mothurOutEndLine(); - 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()); - 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(lastLabel) != 1)) { + //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); - mothurOut(order->getLabel()); mothurOutEndLine(); - 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()); + + //restore real lastlabel to save below + order->setLabel(saveLabel); } @@ -254,53 +303,74 @@ int BootSharedCommand::execute(){ //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(); return 0; } + //output error messages about any remaining user labels set::iterator it; bool needToRun = false; for (it = userLabels.begin(); it != userLabels.end(); it++) { - mothurOut("Your file does not include the label " + *it); + m->mothurOut("Your file does not include the label " + *it); if (processedLabels.count(lastLabel) != 1) { - mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine(); + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); needToRun = true; }else { - mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine(); + 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(); return 0; } + //run last line if you need to if (needToRun == true) { - delete order; + if (order != NULL) { delete order; } order = input->getSharedOrderVector(lastLabel); - mothurOut(order->getLabel()); mothurOutEndLine(); - 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; } + delete order; } - - + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); 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); } + } + + 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) { - errorOut(e, "BootSharedCommand", "execute"); + m->errorOut(e, "BootSharedCommand", "execute"); exit(1); } } //********************************************************************************************************************** -void BootSharedCommand::createTree(ostream* out, Tree* t){ +int BootSharedCommand::createTree(ostream* out, Tree* t){ try { //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++) { + if (m->control_pressed) { return 1; } + float largest = -1000.0; int row, column; //find largest value in sims matrix by searching lower triangle @@ -354,64 +424,72 @@ void BootSharedCommand::createTree(ostream* out, Tree* t){ //assemble tree t->assembleTree(); + + if (m->control_pressed) { return 1; } //print newick file t->print(*out); + + return 0; } catch(exception& e) { - errorOut(e, "BootSharedCommand", "createTree"); + m->errorOut(e, "BootSharedCommand", "createTree"); exit(1); } } /***********************************************************/ void BootSharedCommand::printSims() { try { - mothurOut("simsMatrix"); mothurOutEndLine(); - 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++) { - mothurOut(simMatrix[m][n]); mothurOut("\t"); + m->mothurOut(toString(simMatrix[k][n])); m->mothurOut("\t"); } - mothurOutEndLine(); + m->mothurOutEndLine(); } } catch(exception& e) { - errorOut(e, "BootSharedCommand", "printSims"); + m->errorOut(e, "BootSharedCommand", "printSims"); exit(1); } } /***********************************************************/ -void BootSharedCommand::process(SharedOrderVector* order) { +int BootSharedCommand::process(SharedOrderVector* order) { try{ 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(globaldata->inputFileName)) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre"; + m->openOutputFile(outputFile, *(out[z])); + outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); } - mothurOut("Generating bootstrap trees..."); cout.flush(); + 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); } } @@ -437,15 +515,19 @@ 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], tempTree); + if (m->control_pressed) { delete tempTree; return 1; } + //save trees for consensus command. trees[i].push_back(tempTree); } } - mothurOut("\tDone."); mothurOutEndLine(); + 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(); @@ -454,16 +536,21 @@ void BootSharedCommand::process(SharedOrderVector* order) { //create consensus trees for each bootstrapped tree set for (int k = 0; k < trees.size(); k++) { - mothurOut("Generating consensus tree for " + treeCalculators[k]->getName()); mothurOutEndLine(); + 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 = getRootName(globaldata->inputFileName) + treeCalculators[k]->getName() + ".boot" + order->getLabel(); + string filename = outputDir + m->getRootName(m->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(); @@ -474,10 +561,12 @@ void BootSharedCommand::process(SharedOrderVector* order) { //close ostream for each calc for (int z = 0; z < treeCalculators.size(); z++) { out[z]->close(); } + + return 0; } catch(exception& e) { - errorOut(e, "BootSharedCommand", "process"); + m->errorOut(e, "BootSharedCommand", "process"); exit(1); } }