X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactcommand.cpp;h=82ff7faef0d8886d21fc6b642f34c88c1b143ea1;hb=d2390ede25cc211f95f99e377d5654bad7e6950e;hp=cb377273ebf711d1c7ef41363178a30a4add2e31;hpb=191ae1be0679d5cf4eda950b3b1bf26fb7dd503d;p=mothur.git diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp index cb37727..82ff7fa 100644 --- a/rarefactcommand.cpp +++ b/rarefactcommand.cpp @@ -24,46 +24,62 @@ #include "jackknife.h" #include "coverage.h" + //********************************************************************************************************************** -vector RareFactCommand::getValidParameters(){ - try { - string Array[] = {"iters","freq","label","calc","abund","processors","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "RareFactCommand", "getValidParameters"); - exit(1); - } -} -//********************************************************************************************************************** -vector RareFactCommand::getRequiredParameters(){ +vector RareFactCommand::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 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); parameters.push_back(pcalc); + CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); 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); + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } return myArray; } catch(exception& e) { - m->errorOut(e, "RareFactCommand", "getRequiredParameters"); + m->errorOut(e, "RareFactCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -vector RareFactCommand::getRequiredFiles(){ +string RareFactCommand::getHelpString(){ try { - string AlignArray[] = {"shared","list","rabund","sabund","or"}; - vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); - return myArray; + ValidCalculators validCalculator; + string helpString = ""; + helpString += "The rarefaction.single command parameters are list, sabund, rabund, shared, label, iters, freq, calc, processors 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", "getRequiredFiles"); + m->errorOut(e, "RareFactCommand", "getHelpString"); exit(1); } } + //********************************************************************************************************************** RareFactCommand::RareFactCommand(){ try { - abort = true; - //initialize outputTypes + abort = true; calledHelp = true; + setParameters(); vector tempOutNames; outputTypes["rarefaction"] = tempOutNames; outputTypes["r_chao"] = tempOutNames; @@ -89,27 +105,24 @@ RareFactCommand::RareFactCommand(){ //********************************************************************************************************************** RareFactCommand::RareFactCommand(string option) { try { - globaldata = GlobalData::getInstance(); - abort = false; + abort = false; calledHelp = false; allLines = 1; - labels.clear(); - Estimators.clear(); - + //allow user to run help - if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; 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[] = {"iters","freq","label","calc","abund","processors","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + 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 (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } @@ -131,15 +144,92 @@ RareFactCommand::RareFactCommand(string option) { outputTypes["r_coverage"] = tempOutNames; outputTypes["r_nseqs"] = 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 + //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; } + } } - - //make sure the user has already run the read.otu command - if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund, rabund or shared file before you can use the rarefact.single command."); m->mothurOutEndLine(); abort = true; } + //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); @@ -148,12 +238,6 @@ RareFactCommand::RareFactCommand(string option) { if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } else { allLines = 1; } } - - //if the user has not specified any labels use the ones from read.otu - if(label == "") { - allLines = globaldata->allLines; - labels = globaldata->labels; - } calc = validParameter.validFile(parameters, "calc", false); if (calc == "not found") { calc = "sobs"; } @@ -161,19 +245,28 @@ RareFactCommand::RareFactCommand(string option) { 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; } } + } string temp; temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; } - convert(temp, freq); + m->mothurConvert(temp, freq); temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; } - convert(temp, abund); + m->mothurConvert(temp, abund); temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } - convert(temp, nIters); + 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, "processors", false); if (temp == "not found"){ temp = "1"; } - convert(temp, processors); + temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "T"; } + groupMode = m->isTrue(temp); } } @@ -184,60 +277,32 @@ RareFactCommand::RareFactCommand(string option) { } //********************************************************************************************************************** -void RareFactCommand::help(){ - try { - m->mothurOut("The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n"); - m->mothurOut("The rarefaction.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n"); - m->mothurOut("The rarefaction.single command parameters are label, iters, freq, calc, processors and abund. No parameters are required. \n"); - m->mothurOut("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"); - m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n"); - m->mothurOut("The rarefaction.single command should be in the following format: \n"); - m->mothurOut("rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n"); - m->mothurOut("Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n"); - m->mothurOut("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", cout); - m->mothurOut("The label parameter is used to analyze specific labels in your input.\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "RareFactCommand", "help"); - exit(1); - } -} - -//********************************************************************************************************************** - -RareFactCommand::~RareFactCommand(){} - -//********************************************************************************************************************** - int RareFactCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } - string hadShared = ""; - if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); } - else { hadShared = globaldata->getSharedFile(); inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); } + if ((format != "sharedfile")) { inputFileNames.push_back(inputfile); } + else { inputFileNames = parseSharedFile(sharedfile); format = "rabund"; } - if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; } + if (m->control_pressed) { return 0; } + map file2Group; //index in outputNames[i] -> group for (int p = 0; p < inputFileNames.size(); p++) { string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])); - globaldata->inputFileName = inputFileNames[p]; - - if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } return 0; } + + if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; } if (inputFileNames.size() > 1) { m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine(); } int i; - validCalculator = new ValidCalculators(); - + ValidCalculators validCalculator; + for (i=0; iisValidCalculator("rarefaction", Estimators[i]) == true) { + if (validCalculator.isValidCalculator("rarefaction", Estimators[i]) == true) { if (Estimators[i] == "sobs") { rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction"))); outputNames.push_back(fileNameRoot+"rarefaction"); outputTypes["rarefaction"].push_back(fileNameRoot+"rarefaction"); @@ -286,30 +351,28 @@ int RareFactCommand::execute(){ rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs"))); outputNames.push_back(fileNameRoot+"r_nseqs"); outputTypes["r_nseqs"].push_back(fileNameRoot+"r_nseqs"); } + if (inputFileNames.size() > 1) { file2Group[outputNames.size()-1] = groups[p]; } } } //if the users entered no valid calculators don't execute command - if (rDisplays.size() == 0) { for(int i=0;iinputFileName); - read->read(&*globaldata); + if (rDisplays.size() == 0) { for(int i=0;igorder; + input = new InputData(inputFileNames[p], format); + order = input->getOrderVector(); string lastLabel = order->getLabel(); - input = globaldata->ginput; //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) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } for(int i=0;iginput = NULL; delete order; globaldata->gorder = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + 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) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } for(int i=0;iginput = NULL; delete order; globaldata->gorder = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { for(int i=0;imothurRemove(outputNames[i]); } return 0; } if(allLines == 1 || labels.count(order->getLabel()) == 1){ @@ -347,7 +410,7 @@ int RareFactCommand::execute(){ order = (input->getOrderVector()); } - if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } for(int i=0;iginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { for(int i=0;imothurRemove(outputNames[i]); } return 0; } //output error messages about any remaining user labels set::iterator it; @@ -362,7 +425,7 @@ int RareFactCommand::execute(){ } } - if (m->control_pressed) { if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } for(int i=0;iginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { for(int i=0;imothurRemove(outputNames[i]); } return 0; } //run last label if you need to if (needToRun == true) { @@ -380,16 +443,16 @@ int RareFactCommand::execute(){ for(int i=0;igorder = NULL; - delete input; globaldata->ginput = NULL; - delete read; - delete validCalculator; - + delete input; } - if (hadShared != "") { globaldata->setSharedFile(hadShared); globaldata->setFormat("sharedfile"); } - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + 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 = createGroupFile(outputNames, file2Group); } + + 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(); @@ -404,6 +467,136 @@ int RareFactCommand::execute(){ } } //********************************************************************************************************************** +vector RareFactCommand::createGroupFile(vector& outputNames, map file2Group) { + try { + + vector newFileNames; + + //find different types of files + map > typesFiles; + for (int i = 0; i < outputNames.size(); i++) { + string extension = m->getExtension(outputNames[i]); + + ifstream in; + m->openInputFile(outputNames[i], in); + + string labels = m->getline(in); + string newLine = labels.substr(0, labels.find_first_of('\t')); + + newLine += "\tGroup" + labels.substr(labels.find_first_of('\t')); + + 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; + } + + string combineFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "groups" + extension; + + //print headers + ofstream out; + m->openOutputFile(combineFileName, out); + out << newLine << endl; + out.close(); + + } + + //for each type create a combo file + map lineToNumber; + 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; + + //open each type summary file + map > files; //maps file name to lines in file + int maxLines = 0; + int numColumns = 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); + + vector thisFilesLines; + + thisFilesLines.push_back(group); + int count = 1; + while (!temp.eof()){ + + string thisLine = m->getline(temp); + + string numSampled = thisLine.substr(0, thisLine.find_first_of('\t')); + int num = 0; + convert(numSampled, num); + numColumns = m->getNumChar(thisLine, '\t'); + lineToNumber[count] = num; + count++; + + thisFilesLines.push_back(thisLine); + m->gobble(temp); + } + + files[thisfilename] = thisFilesLines; + + //save longest file for below + if (maxLines < thisFilesLines.size()) { maxLines = thisFilesLines.size(); } + + temp.close(); + m->mothurRemove(thisfilename); + } + + + //for each label + for (int k = 1; k < maxLines; k++) { + + //grab data for each group + for (map::iterator itFileNameGroup = thisTypesFiles.begin(); itFileNameGroup != thisTypesFiles.end(); itFileNameGroup++) { + + string thisfilename = itFileNameGroup->first; + map::iterator itLine = lineToNumber.find(k); + if (itLine != lineToNumber.end()) { + string output = toString(itLine->second); + if (k < files[thisfilename].size()) { + string line = files[thisfilename][k]; + output = line.substr(0, line.find_first_of('\t')); + output += '\t' + files[thisfilename][0] + '\t' + line.substr(line.find_first_of('\t')); + }else{ + output += '\t' + files[thisfilename][0] + '\t'; + for (int h = 0; h < numColumns; h++) { + output += "NA\t"; + } + } + out << output << endl; + }else { m->mothurOut("[ERROR]: parsing results, cant find " + toString(k)); m->mothurOutEndLine(); } + } + } + + out.close(); + + } + + //return combine file name + return newFileNames; + + } + catch(exception& e) { + m->errorOut(e, "RareFactCommand", "createGroupFile"); + exit(1); + } +} +//********************************************************************************************************************** vector RareFactCommand::parseSharedFile(string filename) { try { vector filenames; @@ -411,19 +604,14 @@ vector RareFactCommand::parseSharedFile(string filename) { map filehandles; map::iterator it3; - - //read first line - read = new ReadOTUFile(filename); - read->read(&*globaldata); - - input = globaldata->ginput; + 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; igetGroup() + ".rabund").c_str()); + m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund")); filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund")); } @@ -451,9 +639,9 @@ vector RareFactCommand::parseSharedFile(string filename) { for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; } - delete read; + delete input; - globaldata->ginput = NULL; + m->clearGroups(); return filenames; }