+++ /dev/null
-/*
- * summarycommand.cpp
- * Dotur
- *
- * Created by Sarah Westcott on 1/2/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "summarycommand.h"
-#include "ace.h"
-#include "sobs.h"
-#include "nseqs.h"
-#include "chao1.h"
-#include "bootstrap.h"
-#include "simpson.h"
-#include "simpsoneven.h"
-#include "invsimpson.h"
-#include "npshannon.h"
-#include "shannon.h"
-#include "heip.h"
-#include "smithwilson.h"
-#include "shannoneven.h"
-#include "jackknife.h"
-#include "geom.h"
-#include "logsd.h"
-#include "qstat.h"
-#include "bergerparker.h"
-#include "bstick.h"
-#include "goodscoverage.h"
-#include "coverage.h"
-#include "efron.h"
-#include "boneh.h"
-#include "solow.h"
-#include "shen.h"
-
-//**********************************************************************************************************************
-vector<string> SummaryCommand::setParameters(){
- try {
- CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); 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); parameters.push_back(pshared);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
- CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
- CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
- 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);
-
- vector<string> myArray;
- for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "SummaryCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string SummaryCommand::getHelpString(){
- try {
- string helpString = "";
- ValidCalculators validCalculator;
- helpString += "The summary.single command parameters are list, sabund, rabund, shared, label, calc, abund and groupmode. list, sabund, rabund or shared is required unless you have a valid current file.\n";
- helpString += "The summary.single command should be in the following format: \n";
- helpString += "summary.single(label=yourLabel, calc=yourEstimators).\n";
- helpString += "Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n";
- helpString += validCalculator.printCalc("summary");
- helpString += "The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n";
- helpString += "If you are running summary.single with a shared file and would like your summary 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. label), '=' and parameters (i.e.yourLabels).\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "SummaryCommand", "getHelpString");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-SummaryCommand::SummaryCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["summary"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "SummaryCommand", "SummaryCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-SummaryCommand::SummaryCommand(string option) {
- try {
- abort = false; calledHelp = false;
- allLines = 1;
-
- //allow user to run help
- if(option == "help") { help(); abort = true; calledHelp = true; }
- else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
- vector<string> myArray = setParameters();
-
- OptionParser parser(option);
- map<string,string> parameters = parser.getParameters();
- map<string,string>::iterator it;
-
- 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; }
- }
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["summary"] = 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); }
-
- //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-chao-ace-jack-shannon-npshannon-simpson"; }
- else {
- if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
- }
- m->splitAtDash(calc, Estimators);
- if (m->inUsersGroups("citation", Estimators)) {
- ValidCalculators validCalc; validCalc.printCitations(Estimators);
- //remove citation from list of calcs
- for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
- }
-
- string temp;
- temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
- m->mothurConvert(temp, abund);
-
- temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }
- m->mothurConvert(temp, size);
-
- temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "T"; }
- groupMode = m->isTrue(temp);
-
-
- }
- }
- catch(exception& e) {
- m->errorOut(e, "SummaryCommand", "SummaryCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int SummaryCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- if ((format != "sharedfile")) { inputFileNames.push_back(inputfile); }
- else { inputFileNames = parseSharedFile(sharedfile); format = "rabund"; }
-
- if (m->control_pressed) { return 0; }
-
- int numLines = 0;
- int numCols = 0;
-
- for (int p = 0; p < inputFileNames.size(); p++) {
-
- numLines = 0;
- numCols = 0;
-
- string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + "summary";
- outputNames.push_back(fileNameRoot); outputTypes["summary"].push_back(fileNameRoot);
-
- if (inputFileNames.size() > 1) {
- m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
- }
-
- sumCalculators.clear();
-
- ValidCalculators validCalculator;
-
- for (int i=0; i<Estimators.size(); i++) {
- if (validCalculator.isValidCalculator("summary", Estimators[i]) == true) {
- if(Estimators[i] == "sobs"){
- sumCalculators.push_back(new Sobs());
- }else if(Estimators[i] == "chao"){
- sumCalculators.push_back(new Chao1());
- }else if(Estimators[i] == "coverage"){
- sumCalculators.push_back(new Coverage());
- }else if(Estimators[i] == "geometric"){
- sumCalculators.push_back(new Geom());
- }else if(Estimators[i] == "logseries"){
- sumCalculators.push_back(new LogSD());
- }else if(Estimators[i] == "qstat"){
- sumCalculators.push_back(new QStat());
- }else if(Estimators[i] == "bergerparker"){
- sumCalculators.push_back(new BergerParker());
- }else if(Estimators[i] == "bstick"){
- sumCalculators.push_back(new BStick());
- }else if(Estimators[i] == "ace"){
- if(abund < 5)
- abund = 10;
- sumCalculators.push_back(new Ace(abund));
- }else if(Estimators[i] == "jack"){
- sumCalculators.push_back(new Jackknife());
- }else if(Estimators[i] == "shannon"){
- sumCalculators.push_back(new Shannon());
- }else if(Estimators[i] == "shannoneven"){
- sumCalculators.push_back(new ShannonEven());
- }else if(Estimators[i] == "npshannon"){
- sumCalculators.push_back(new NPShannon());
- }else if(Estimators[i] == "heip"){
- sumCalculators.push_back(new Heip());
- }else if(Estimators[i] == "smithwilson"){
- sumCalculators.push_back(new SmithWilson());
- }else if(Estimators[i] == "simpson"){
- sumCalculators.push_back(new Simpson());
- }else if(Estimators[i] == "simpsoneven"){
- sumCalculators.push_back(new SimpsonEven());
- }else if(Estimators[i] == "invsimpson"){
- sumCalculators.push_back(new InvSimpson());
- }else if(Estimators[i] == "bootstrap"){
- sumCalculators.push_back(new Bootstrap());
- }else if (Estimators[i] == "nseqs") {
- sumCalculators.push_back(new NSeqs());
- }else if (Estimators[i] == "goodscoverage") {
- sumCalculators.push_back(new GoodsCoverage());
- }else if (Estimators[i] == "efron") {
- sumCalculators.push_back(new Efron(size));
- }else if (Estimators[i] == "boneh") {
- sumCalculators.push_back(new Boneh(size));
- }else if (Estimators[i] == "solow") {
- sumCalculators.push_back(new Solow(size));
- }else if (Estimators[i] == "shen") {
- sumCalculators.push_back(new Shen(size, abund));
- }
- }
- }
-
- //if the users entered no valid calculators don't execute command
- if (sumCalculators.size() == 0) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
-
- ofstream outputFileHandle;
- m->openOutputFile(fileNameRoot, outputFileHandle);
- outputFileHandle << "label";
-
- input = new InputData(inputFileNames[p], format);
- sabund = input->getSAbundVector();
- string lastLabel = sabund->getLabel();
-
- for(int i=0;i<sumCalculators.size();i++){
- if(sumCalculators[i]->getCols() == 1){
- outputFileHandle << '\t' << sumCalculators[i]->getName();
- numCols++;
- }
- else{
- outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
- numCols += 3;
- }
- }
- outputFileHandle << endl;
-
- //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 = labels;
-
- if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
-
- while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
- if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
-
- if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
-
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- processedLabels.insert(sabund->getLabel());
- userLabels.erase(sabund->getLabel());
-
- outputFileHandle << sabund->getLabel();
- for(int i=0;i<sumCalculators.size();i++){
- vector<double> data = sumCalculators[i]->getValues(sabund);
-
- if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
-
- outputFileHandle << '\t';
- sumCalculators[i]->print(outputFileHandle);
- }
- outputFileHandle << endl;
- numLines++;
- }
-
- if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = sabund->getLabel();
-
- delete sabund;
- sabund = input->getSAbundVector(lastLabel);
-
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- processedLabels.insert(sabund->getLabel());
- userLabels.erase(sabund->getLabel());
-
- outputFileHandle << sabund->getLabel();
- for(int i=0;i<sumCalculators.size();i++){
- vector<double> data = sumCalculators[i]->getValues(sabund);
-
- if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
-
- outputFileHandle << '\t';
- sumCalculators[i]->print(outputFileHandle);
- }
- outputFileHandle << endl;
- numLines++;
-
- //restore real lastlabel to save below
- sabund->setLabel(saveLabel);
- }
-
- lastLabel = sabund->getLabel();
-
- delete sabund;
- sabund = input->getSAbundVector();
- }
-
- if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete input; return 0; }
-
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
- }
- }
-
- //run last label if you need to
- if (needToRun == true) {
- if (sabund != NULL) { delete sabund; }
- sabund = input->getSAbundVector(lastLabel);
-
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- outputFileHandle << sabund->getLabel();
- for(int i=0;i<sumCalculators.size();i++){
- vector<double> data = sumCalculators[i]->getValues(sabund);
-
- if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete sabund; delete input; return 0; }
-
- outputFileHandle << '\t';
- sumCalculators[i]->print(outputFileHandle);
- }
- outputFileHandle << endl;
- numLines++;
- delete sabund;
- }
-
- outputFileHandle.close();
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; } delete input; return 0; }
-
-
- delete input;
- for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
- }
-
- if (m->control_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.push_back(createGroupSummaryFile(numLines, numCols, outputNames)); }
-
- 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, "SummaryCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> SummaryCommand::parseSharedFile(string filename) {
- try {
- vector<string> filenames;
-
- map<string, ofstream*> filehandles;
- map<string, ofstream*>::iterator it3;
-
- input = new InputData(filename, "sharedfile");
- vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
-
- string sharedFileRoot = m->getRootName(filename);
-
- //clears file before we start to write to it below
- for (int i=0; i<lookup.size(); i++) {
- m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
- filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
- }
-
- ofstream* temp;
- for (int i=0; i<lookup.size(); i++) {
- temp = new ofstream;
- filehandles[lookup[i]->getGroup()] = temp;
- groups.push_back(lookup[i]->getGroup());
- }
-
- while(lookup[0] != NULL) {
-
- for (int i = 0; i < lookup.size(); i++) {
- RAbundVector rav = lookup[i]->getRAbundVector();
- m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
- rav.print(*(filehandles[lookup[i]->getGroup()]));
- (*(filehandles[lookup[i]->getGroup()])).close();
- }
-
- 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;
-
- return filenames;
- }
- catch(exception& e) {
- m->errorOut(e, "SummaryCommand", "parseSharedFile");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<string>& outputNames) {
- try {
-
- ofstream out;
- string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups.summary";
-
- //open combined file
- m->openOutputFile(combineFileName, out);
-
- //open each groups summary file
- string newLabel = "";
- map<string, vector<string> > files;
- for (int i=0; i<outputNames.size(); i++) {
- vector<string> thisFilesLines;
-
- ifstream temp;
- m->openInputFile(outputNames[i], temp);
-
- //read through first line - labels
- string tempLabel;
- if (i == 0) { //we want to save the labels to output below
- for (int j = 0; j < numCols+1; j++) {
- temp >> tempLabel;
-
- if (j == 1) { newLabel += "group\t" + tempLabel + '\t';
- }else{ newLabel += tempLabel + '\t'; }
- }
- }else{ for (int j = 0; j < numCols+1; j++) { temp >> tempLabel; } }
-
- m->gobble(temp);
-
- //for each label
- for (int k = 0; k < numLines; k++) {
-
- string thisLine = "";
- string tempLabel;
-
- for (int j = 0; j < numCols+1; j++) {
- temp >> tempLabel;
-
- //save for later
- if (j == 1) { thisLine += groups[i] + "\t" + tempLabel + "\t"; }
- else{ thisLine += tempLabel + "\t"; }
- }
-
- thisLine += "\n";
-
- thisFilesLines.push_back(thisLine);
-
- m->gobble(temp);
- }
-
- files[outputNames[i]] = thisFilesLines;
-
- temp.close();
- m->mothurRemove(outputNames[i]);
- }
-
- //output label line to new file
- out << newLabel << endl;
-
- //for each label
- for (int k = 0; k < numLines; k++) {
-
- //grab summary data for each group
- for (int i=0; i<outputNames.size(); i++) {
- out << files[outputNames[i]][k];
- }
- }
-
- outputNames.clear();
-
- out.close();
-
- //return combine file name
- return combineFileName;
-
- }
- catch(exception& e) {
- m->errorOut(e, "SummaryCommand", "createGroupSummaryFile");
- exit(1);
- }
-}
-//**********************************************************************************************************************