X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=rarefactcommand.cpp;h=75a87efa3a2f95259488b0abf15887fb39ee1955;hp=752ff62298ed183f18e033982b1e0c20513bd963;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=a8f5a612bba54ceb74e17efc027d3a7f5aa93c9a diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp index 752ff62..75a87ef 100644 --- a/rarefactcommand.cpp +++ b/rarefactcommand.cpp @@ -14,163 +14,713 @@ #include "chao1.h" #include "bootstrap.h" #include "simpson.h" +#include "simpsoneven.h" +#include "heip.h" +#include "smithwilson.h" +#include "invsimpson.h" #include "npshannon.h" +#include "shannoneven.h" #include "shannon.h" #include "jackknife.h" #include "coverage.h" -//********************************************************************************************************************** - -RareFactCommand::RareFactCommand(){ +//********************************************************************************************************************** +vector RareFactCommand::setParameters(){ try { - globaldata = GlobalData::getInstance(); - string fileNameRoot; - fileNameRoot = getRootName(globaldata->inputFileName); - convert(globaldata->getFreq(), freq); - convert(globaldata->getIters(), nIters); - validCalculator = new ValidCalculators(); - - int i; - for (i=0; iEstimators.size(); i++) { - if (validCalculator->isValidCalculator("rarefaction", globaldata->Estimators[i]) == true) { - if (globaldata->Estimators[i] == "sobs") { - rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction"))); - }else if (globaldata->Estimators[i] == "chao") { - rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao"))); - }else if (globaldata->Estimators[i] == "ace") { - convert(globaldata->getAbund(), abund); - if(abund < 5) - abund = 10; - rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace"))); - }else if (globaldata->Estimators[i] == "jack") { - rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack"))); - }else if (globaldata->Estimators[i] == "shannon") { - rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon"))); - }else if (globaldata->Estimators[i] == "npshannon") { - rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon"))); - }else if (globaldata->Estimators[i] == "simpson") { - rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson"))); - }else if (globaldata->Estimators[i] == "bootstrap") { - rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap"))); - }else if (globaldata->Estimators[i] == "coverage") { - rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage"))); - }else if (globaldata->Estimators[i] == "nseqs") { - rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs"))); - } - } - } + CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(plist); + CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false); parameters.push_back(prabund); + CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false); parameters.push_back(psabund); + CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(pshared); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq); + CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters); + CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap", "sobs", "", "", "","",true,false,true); parameters.push_back(pcalc); + CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); + CommandParameter pgroupmode("groupmode", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pgroupmode); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); - //reset calc for next command - globaldata->setCalc(""); - + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the RareFactCommand class Function RareFactCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "RareFactCommand", "setParameters"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the RareFactCommand class function RareFactCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +//********************************************************************************************************************** +string RareFactCommand::getHelpString(){ + try { + ValidCalculators validCalculator; + string helpString = ""; + helpString += "The rarefaction.single command parameters are list, sabund, rabund, shared, label, iters, freq, calc, processors, groupmode and abund. list, sabund, rabund or shared is required unless you have a valid current file. \n"; + helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n"; + helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n"; + helpString += "The rarefaction.single command should be in the following format: \n"; + helpString += "rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n"; + helpString += "Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n"; + helpString += "The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness.\n"; + validCalculator.printCalc("rarefaction"); + helpString += "If you are running rarefaction.single with a shared file and would like your results collated in one file, set groupmode=t. (Default=true).\n"; + helpString += "The label parameter is used to analyze specific labels in your input.\n"; + helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "RareFactCommand", "getHelpString"); exit(1); - } - + } } - //********************************************************************************************************************** - -RareFactCommand::~RareFactCommand(){ - delete order; - delete input; - delete rCurve; - delete read; +string RareFactCommand::getOutputPattern(string type) { + try { + string pattern = ""; + if (type == "rarefaction") { pattern = "[filename],rarefaction"; } + else if (type == "r_chao") { pattern = "[filename],r_chao"; } + else if (type == "r_ace") { pattern = "[filename],r_ace"; } + else if (type == "r_jack") { pattern = "[filename],r_jack"; } + else if (type == "r_shannon") { pattern = "[filename],r_shannon"; } + else if (type == "r_shannoneven") { pattern = "[filename],r_shannoneven"; } + else if (type == "r_smithwilson") { pattern = "[filename],r_smithwilson"; } + else if (type == "r_npshannon") { pattern = "[filename],r_npshannon"; } + else if (type == "r_simpson") { pattern = "[filename],r_simpson"; } + else if (type == "r_simpsoneven") { pattern = "[filename],r_simpsoneven"; } + else if (type == "r_invsimpson") { pattern = "[filename],r_invsimpson"; } + else if (type == "r_bootstrap") { pattern = "[filename],r_bootstrap"; } + else if (type == "r_coverage") { pattern = "[filename],r_coverage"; } + else if (type == "r_nseqs") { pattern = "[filename],r_nseqs"; } + else if (type == "r_heip") { pattern = "[filename],r_heip"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "RareFactCommand", "getOutputPattern"); + exit(1); + } } - //********************************************************************************************************************** - -int RareFactCommand::execute(){ +RareFactCommand::RareFactCommand(){ + try { + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["rarefaction"] = tempOutNames; + outputTypes["r_chao"] = tempOutNames; + outputTypes["r_ace"] = tempOutNames; + outputTypes["r_jack"] = tempOutNames; + outputTypes["r_shannon"] = tempOutNames; + outputTypes["r_shannoneven"] = tempOutNames; + outputTypes["r_heip"] = tempOutNames; + outputTypes["r_smithwilson"] = tempOutNames; + outputTypes["r_npshannon"] = tempOutNames; + outputTypes["r_simpson"] = tempOutNames; + outputTypes["r_simpsoneven"] = tempOutNames; + outputTypes["r_invsimpson"] = tempOutNames; + outputTypes["r_bootstrap"] = tempOutNames; + outputTypes["r_coverage"] = tempOutNames; + outputTypes["r_nseqs"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "RareFactCommand", "RareFactCommand"); + exit(1); + } +} +//********************************************************************************************************************** +RareFactCommand::RareFactCommand(string option) { try { - int count = 1; + 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;} - //if the users entered no valid calculators don't execute command - if (rDisplays.size() == 0) { return 0; } + else { + vector myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + map::iterator it; + + 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; } + } + + //initialize outputTypes + vector tempOutNames; + outputTypes["rarefaction"] = tempOutNames; + outputTypes["r_chao"] = tempOutNames; + outputTypes["r_ace"] = tempOutNames; + outputTypes["r_jack"] = tempOutNames; + outputTypes["r_shannon"] = tempOutNames; + outputTypes["r_shannoneven"] = tempOutNames; + outputTypes["r_heip"] = tempOutNames; + outputTypes["r_smithwilson"] = tempOutNames; + outputTypes["r_npshannon"] = tempOutNames; + outputTypes["r_simpson"] = tempOutNames; + outputTypes["r_simpsoneven"] = tempOutNames; + outputTypes["r_invsimpson"] = tempOutNames; + outputTypes["r_bootstrap"] = tempOutNames; + outputTypes["r_coverage"] = tempOutNames; + outputTypes["r_nseqs"] = 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; } + } + + it = parameters.find("rabund"); + //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["rabund"] = inputDir + it->second; } + } + + it = parameters.find("sabund"); + //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["sabund"] = inputDir + it->second; } + } + + it = parameters.find("list"); + //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["list"] = inputDir + it->second; } + } + } + + //check for required parameters + listfile = validParameter.validFile(parameters, "list", true); + if (listfile == "not open") { listfile = ""; abort = true; } + else if (listfile == "not found") { listfile = ""; } + else { format = "list"; inputfile = listfile; m->setListFile(listfile); } + + sabundfile = validParameter.validFile(parameters, "sabund", true); + if (sabundfile == "not open") { sabundfile = ""; abort = true; } + else if (sabundfile == "not found") { sabundfile = ""; } + else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); } + + rabundfile = validParameter.validFile(parameters, "rabund", true); + if (rabundfile == "not open") { rabundfile = ""; abort = true; } + else if (rabundfile == "not found") { rabundfile = ""; } + else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); } + + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { sharedfile = ""; abort = true; } + else if (sharedfile == "not found") { sharedfile = ""; } + else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); } + + if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) { + //is there are current file available for any of these? + //give priority to shared, then list, then rabund, then sabund + //if there is a current shared file, use it + sharedfile = m->getSharedFile(); + if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } + else { + listfile = m->getListFile(); + if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); } + else { + rabundfile = m->getRabundFile(); + if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); } + else { + sabundfile = m->getSabundFile(); + if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file before you can use the collect.single command."); m->mothurOutEndLine(); + 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 = m->hasPath(inputfile); } - read = new ReadOTUFile(globaldata->inputFileName); - read->read(&*globaldata); + //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; } + } + + calc = validParameter.validFile(parameters, "calc", false); + if (calc == "not found") { calc = "sobs"; } + else { + if (calc == "default") { calc = "sobs"; } + } + 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; } } + } - order = globaldata->gorder; - OrderVector* lastOrder = order; - input = globaldata->ginput; + string temp; + temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; } + m->mothurConvert(temp, freq); + + temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; } + m->mothurConvert(temp, abund); + + temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } + m->mothurConvert(temp, nIters); + + temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); } + m->setProcessors(temp); + m->mothurConvert(temp, processors); + + temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "T"; } + groupMode = m->isTrue(temp); + } - //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 = globaldata->labels; + } + catch(exception& e) { + m->errorOut(e, "RareFactCommand", "RareFactCommand"); + exit(1); + } +} +//********************************************************************************************************************** + +int RareFactCommand::execute(){ + try { - //as long as you are not at the end of the file or done wih the lines you want - while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) { + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + map > labelToEnds; + if ((format != "sharedfile")) { inputFileNames.push_back(inputfile); } + else { inputFileNames = parseSharedFile(sharedfile, labelToEnds); format = "rabund"; } + + if (m->control_pressed) { return 0; } + + map file2Group; //index in outputNames[i] -> group + for (int p = 0; p < inputFileNames.size(); p++) { - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ + string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])); + + if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; } - rCurve = new Rarefact(order, rDisplays); - rCurve->getCurve(freq, nIters); - delete rCurve; + if (inputFileNames.size() > 1) { + m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine(); + } + int i; + ValidCalculators validCalculator; - cout << order->getLabel() << '\t' << count << endl; - processedLabels.insert(order->getLabel()); - userLabels.erase(order->getLabel()); + map variables; + variables["[filename]"] = fileNameRoot; + + for (i=0; i 1) { file2Group[outputNames.size()-1] = groups[p]; } + } } - if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) { - rCurve = new Rarefact(lastOrder, rDisplays); + + //if the users entered no valid calculators don't execute command + if (rDisplays.size() == 0) { for(int i=0;igetOrderVector(); + string lastLabel = order->getLabel(); + + //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; + + if (m->control_pressed) { for(int i=0;imothurRemove(outputNames[i]); } return 0; } + + //as long as you are not at the end of the file or done wih the lines you want + while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + + if (m->control_pressed) { for(int i=0;imothurRemove(outputNames[i]); } return 0; } + + + if(allLines == 1 || labels.count(order->getLabel()) == 1){ + + m->mothurOut(order->getLabel()); m->mothurOutEndLine(); + map >::iterator itEndings = labelToEnds.find(order->getLabel()); + set ends; + if (itEndings != labelToEnds.end()) { ends = itEndings->second; } + rCurve = new Rarefact(order, rDisplays, processors, ends); + rCurve->getCurve(freq, nIters); + delete rCurve; + + processedLabels.insert(order->getLabel()); + userLabels.erase(order->getLabel()); + } + + if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = order->getLabel(); + + delete order; + order = (input->getOrderVector(lastLabel)); + + m->mothurOut(order->getLabel()); m->mothurOutEndLine(); + map >::iterator itEndings = labelToEnds.find(order->getLabel()); + set ends; + if (itEndings != labelToEnds.end()) { ends = itEndings->second; } + rCurve = new Rarefact(order, rDisplays, processors, ends); + + rCurve->getCurve(freq, nIters); + delete rCurve; + + processedLabels.insert(order->getLabel()); + userLabels.erase(order->getLabel()); + + //restore real lastlabel to save below + order->setLabel(saveLabel); + } + + lastLabel = order->getLabel(); + + delete order; + order = (input->getOrderVector()); + } + + if (m->control_pressed) { for(int i=0;imothurRemove(outputNames[i]); } return 0; } + + //output error messages about any remaining user labels + set::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(); + } + } + + if (m->control_pressed) { for(int i=0;imothurRemove(outputNames[i]); } return 0; } + + //run last label if you need to + if (needToRun == true) { + if (order != NULL) { delete order; } + order = (input->getOrderVector(lastLabel)); + + m->mothurOut(order->getLabel()); m->mothurOutEndLine(); + map >::iterator itEndings = labelToEnds.find(order->getLabel()); + set ends; + if (itEndings != labelToEnds.end()) { ends = itEndings->second; } + rCurve = new Rarefact(order, rDisplays, processors, ends); + rCurve->getCurve(freq, nIters); delete rCurve; - - cout << lastOrder->getLabel() << '\t' << count << endl; - processedLabels.insert(lastOrder->getLabel()); - userLabels.erase(lastOrder->getLabel()); + + delete order; } - if (count != 1) { delete lastOrder; } - lastOrder = order; + + for(int i=0;icontrol_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + //create summary file containing all the groups data for each label - this function just combines the info from the files already created. + if ((sharedfile != "") && (groupMode)) { outputNames = createGroupFile(outputNames, file2Group); } - order = (input->getOrderVector()); - count++; + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } + + 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, "RareFactCommand", "execute"); + exit(1); + } +} +//********************************************************************************************************************** +vector RareFactCommand::createGroupFile(vector& outputNames, map file2Group) { + try { + + vector newFileNames; + + //find different types of files + map > typesFiles; + map > > fileLabels; //combofile name to labels. each label is a vector because it may be unique lci hci. + vector groupNames; + for (int i = 0; i < outputNames.size(); i++) { + + string extension = m->getExtension(outputNames[i]); + string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension; + m->mothurRemove(combineFileName); //remove old file + + ifstream in; + m->openInputFile(outputNames[i], in); + + string labels = m->getline(in); + + istringstream iss (labels,istringstream::in); + string newLabel = ""; vector theseLabels; + while(!iss.eof()) { iss >> newLabel; m->gobble(iss); theseLabels.push_back(newLabel); } + vector< vector > allLabels; + vector thisSet; thisSet.push_back(theseLabels[0]); allLabels.push_back(thisSet); thisSet.clear(); //makes "numSampled" its own grouping + for (int j = 1; j < theseLabels.size()-1; j++) { + if (theseLabels[j+1] == "lci") { + thisSet.push_back(theseLabels[j]); + thisSet.push_back(theseLabels[j+1]); + thisSet.push_back(theseLabels[j+2]); + j++; j++; + }else{ //no lci or hci for this calc. + thisSet.push_back(theseLabels[j]); + } + allLabels.push_back(thisSet); + thisSet.clear(); + } + fileLabels[combineFileName] = allLabels; + + map >::iterator itfind = typesFiles.find(extension); + if (itfind != typesFiles.end()) { + (itfind->second)[outputNames[i]] = file2Group[i]; + }else { + map temp; + temp[outputNames[i]] = file2Group[i]; + typesFiles[extension] = temp; + } + if (!(m->inUsersGroups(file2Group[i], groupNames))) { groupNames.push_back(file2Group[i]); } } - //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; - needToRun = true; - }else { - cout << ". Please refer to " << lastOrder->getLabel() << "." << endl; + //for each type create a combo file + + for (map >::iterator it = typesFiles.begin(); it != typesFiles.end(); it++) { + + ofstream out; + string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + it->first; + m->openOutputFileAppend(combineFileName, out); + newFileNames.push_back(combineFileName); + map thisTypesFiles = it->second; //it->second maps filename to group + set numSampledSet; + + //open each type summary file + map > > > files; //maps file name to lines in file + int maxLines = 0; + for (map::iterator itFileNameGroup = thisTypesFiles.begin(); itFileNameGroup != thisTypesFiles.end(); itFileNameGroup++) { + + string thisfilename = itFileNameGroup->first; + string group = itFileNameGroup->second; + + ifstream temp; + m->openInputFile(thisfilename, temp); + + //read through first line - labels + m->getline(temp); m->gobble(temp); + + map > > thisFilesLines; + while (!temp.eof()){ + int numSampled = 0; + temp >> numSampled; m->gobble(temp); + + vector< vector > theseReads; + vector thisSet; thisSet.push_back(toString(numSampled)); theseReads.push_back(thisSet); thisSet.clear(); + for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //output thing like 0.03-A lci-A hci-A + vector reads; + string next = ""; + for (int l = 0; l < fileLabels[combineFileName][k].size(); l++) { //output modified labels + temp >> next; m->gobble(temp); + reads.push_back(next); + } + theseReads.push_back(reads); + } + thisFilesLines[numSampled] = theseReads; + m->gobble(temp); + + numSampledSet.insert(numSampled); + } + + files[group] = thisFilesLines; + + //save longest file for below + if (maxLines < thisFilesLines.size()) { maxLines = thisFilesLines.size(); } + + temp.close(); + m->mothurRemove(thisfilename); } + + //output new labels line + out << fileLabels[combineFileName][0][0] << '\t'; + for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //output thing like 0.03-A lci-A hci-A + for (int n = 0; n < groupNames.size(); n++) { // for each group + for (int l = 0; l < fileLabels[combineFileName][k].size(); l++) { //output modified labels + out << fileLabels[combineFileName][k][l] << '-' << groupNames[n] << '\t'; + } + } + } + out << endl; + + //for each label + for (set::iterator itNumSampled = numSampledSet.begin(); itNumSampled != numSampledSet.end(); itNumSampled++) { + + out << (*itNumSampled) << '\t'; + + if (m->control_pressed) { break; } + + for (int k = 1; k < fileLabels[combineFileName].size(); k++) { //each chunk + //grab data for each group + for (map > > >::iterator itFileNameGroup = files.begin(); itFileNameGroup != files.end(); itFileNameGroup++) { + + string group = itFileNameGroup->first; + + map > >::iterator itLine = files[group].find(*itNumSampled); + if (itLine != files[group].end()) { + for (int l = 0; l < (itLine->second)[k].size(); l++) { + out << (itLine->second)[k][l] << '\t'; + + } + }else { + for (int l = 0; l < fileLabels[combineFileName][k].size(); l++) { + out << "NA" << '\t'; + } + } + } + } + out << endl; + } + out.close(); } - //run last line if you need to - if (needToRun == true) { - rCurve = new Rarefact(lastOrder, rDisplays); - rCurve->getCurve(freq, nIters); - delete rCurve; - - cout << lastOrder->getLabel() << '\t' << count << endl; + //return combine file name + return newFileNames; + + } + catch(exception& e) { + m->errorOut(e, "RareFactCommand", "createGroupFile"); + exit(1); + } +} +//********************************************************************************************************************** +vector RareFactCommand::parseSharedFile(string filename, map >& label2Ends) { + try { + vector filenames; + + map filehandles; + map::iterator it3; + + input = new InputData(filename, "sharedfile"); + vector lookup = input->getSharedRAbundVectors(); + + string sharedFileRoot = m->getRootName(filename); + + //clears file before we start to write to it below + for (int i=0; imothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund")); + filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund")); } - delete lastOrder; + ofstream* temp; + for (int i=0; igetGroup()] = temp; + groups.push_back(lookup[i]->getGroup()); + } - for(int i=0;igetRAbundVector(); + m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()])); + rav.print(*(filehandles[lookup[i]->getGroup()])); + (*(filehandles[lookup[i]->getGroup()])).close(); + label2Ends[lookup[i]->getLabel()].insert(rav.getNumSeqs()); + } + + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + lookup = input->getSharedRAbundVectors(); + } + + //free memory + for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { + delete it3->second; + } + + delete input; + m->clearGroups(); + + return filenames; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the RareFactCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "RareFactCommand", "parseSharedFile"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the RareFactCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } - //********************************************************************************************************************** + + +