--- /dev/null
+/*
+ * rarefactcommand.cpp
+ * Dotur
+ *
+ * Created by Sarah Westcott on 1/2/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "rarefactcommand.h"
+#include "ace.h"
+#include "sobs.h"
+#include "nseqs.h"
+#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"
+
+
+//**********************************************************************************************************************
+vector<string> 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<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string RareFactCommand::getHelpString(){
+ try {
+ 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", "getHelpString");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+RareFactCommand::RareFactCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> 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 {
+ 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 (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> 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); }
+
+ //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; } }
+ }
+
+ 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);
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactCommand", "RareFactCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int RareFactCommand::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; }
+
+ map<int, string> file2Group; //index in outputNames[i] -> group
+ for (int p = 0; p < inputFileNames.size(); p++) {
+
+ 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; }
+
+ if (inputFileNames.size() > 1) {
+ m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
+ }
+ int i;
+ ValidCalculators validCalculator;
+
+
+ for (i=0; i<Estimators.size(); i++) {
+ 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");
+ }else if (Estimators[i] == "chao") {
+ rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
+ outputNames.push_back(fileNameRoot+"r_chao"); outputTypes["r_chao"].push_back(fileNameRoot+"r_chao");
+ }else if (Estimators[i] == "ace") {
+ if(abund < 5)
+ abund = 10;
+ rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace")));
+ outputNames.push_back(fileNameRoot+"r_ace"); outputTypes["r_ace"].push_back(fileNameRoot+"r_ace");
+ }else if (Estimators[i] == "jack") {
+ rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
+ outputNames.push_back(fileNameRoot+"r_jack"); outputTypes["r_jack"].push_back(fileNameRoot+"r_jack");
+ }else if (Estimators[i] == "shannon") {
+ rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
+ outputNames.push_back(fileNameRoot+"r_shannon"); outputTypes["r_shannon"].push_back(fileNameRoot+"r_shannon");
+ }else if (Estimators[i] == "shannoneven") {
+ rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(fileNameRoot+"r_shannoneven")));
+ outputNames.push_back(fileNameRoot+"r_shannoneven"); outputTypes["r_shannoneven"].push_back(fileNameRoot+"r_shannoneven");
+ }else if (Estimators[i] == "heip") {
+ rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(fileNameRoot+"r_heip")));
+ outputNames.push_back(fileNameRoot+"r_heip"); outputTypes["r_heip"].push_back(fileNameRoot+"r_heip");
+ }else if (Estimators[i] == "smithwilson") {
+ rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(fileNameRoot+"r_smithwilson")));
+ outputNames.push_back(fileNameRoot+"r_smithwilson"); outputTypes["r_smithwilson"].push_back(fileNameRoot+"r_smithwilson");
+ }else if (Estimators[i] == "npshannon") {
+ rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
+ outputNames.push_back(fileNameRoot+"r_npshannon"); outputTypes["r_npshannon"].push_back(fileNameRoot+"r_npshannon");
+ }else if (Estimators[i] == "simpson") {
+ rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
+ outputNames.push_back(fileNameRoot+"r_simpson"); outputTypes["r_simpson"].push_back(fileNameRoot+"r_simpson");
+ }else if (Estimators[i] == "simpsoneven") {
+ rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(fileNameRoot+"r_simpsoneven")));
+ outputNames.push_back(fileNameRoot+"r_simpsoneven"); outputTypes["r_simpsoneven"].push_back(fileNameRoot+"r_simpsoneven");
+ }else if (Estimators[i] == "invsimpson") {
+ rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"r_invsimpson")));
+ outputNames.push_back(fileNameRoot+"r_invsimpson"); outputTypes["r_invsimpson"].push_back(fileNameRoot+"r_invsimpson");
+ }else if (Estimators[i] == "bootstrap") {
+ rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
+ outputNames.push_back(fileNameRoot+"r_bootstrap"); outputTypes["r_bootstrap"].push_back(fileNameRoot+"r_bootstrap");
+ }else if (Estimators[i] == "coverage") {
+ rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage")));
+ outputNames.push_back(fileNameRoot+"r_coverage"); outputTypes["r_coverage"].push_back(fileNameRoot+"r_coverage");
+ }else if (Estimators[i] == "nseqs") {
+ 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;i<rDisplays.size();i++){ delete rDisplays[i]; } return 0; }
+
+ input = new InputData(inputFileNames[p], format);
+ order = input->getOrderVector();
+ 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<string> processedLabels;
+ set<string> userLabels = labels;
+
+ if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; } delete input; delete order; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(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;i<rDisplays.size();i++){ delete rDisplays[i]; } delete input; delete order; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+
+ if(allLines == 1 || labels.count(order->getLabel()) == 1){
+
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+ rCurve = new Rarefact(order, rDisplays, processors);
+ 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();
+ rCurve = new Rarefact(order, rDisplays, processors);
+ 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;i<rDisplays.size();i++){ delete rDisplays[i]; } delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } 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();
+ }
+ }
+
+ if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; } delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(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();
+ rCurve = new Rarefact(order, rDisplays, processors);
+ rCurve->getCurve(freq, nIters);
+ delete rCurve;
+
+ delete order;
+ }
+
+
+ for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
+ rDisplays.clear();
+ delete input;
+ }
+
+
+ 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();
+ 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<string> RareFactCommand::createGroupFile(vector<string>& outputNames, map<int, string> file2Group) {
+ try {
+
+ vector<string> newFileNames;
+
+ //find different types of files
+ map<string, map<string, string> > 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<string, map<string, string> >::iterator itfind = typesFiles.find(extension);
+ if (itfind != typesFiles.end()) {
+ (itfind->second)[outputNames[i]] = file2Group[i];
+ }else {
+ map<string, string> 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<int, int> lineToNumber;
+ for (map<string, map<string, string> >::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<string, string> thisTypesFiles = it->second;
+
+ //open each type summary file
+ map<string, vector<string> > files; //maps file name to lines in file
+ int maxLines = 0;
+ int numColumns = 0;
+ for (map<string, string>::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<string> 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<string, string>::iterator itFileNameGroup = thisTypesFiles.begin(); itFileNameGroup != thisTypesFiles.end(); itFileNameGroup++) {
+
+ string thisfilename = itFileNameGroup->first;
+ map<int, int>::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<string> RareFactCommand::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;
+ m->clearGroups();
+
+ return filenames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactCommand", "parseSharedFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
+
projects / mothur.git / blobdiff