#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"
-RareFactCommand::RareFactCommand(){
+//**********************************************************************************************************************
+vector<string> RareFactCommand::setParameters(){
try {
- globaldata = GlobalData::getInstance();
- string fileNameRoot;
- fileNameRoot = getRootName(globaldata->inputFileName);
- validCalculator = new ValidCalculators();
-
- int i;
- for (i=0; i<globaldata->Estimators.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")));
- }
- }
- }
+ 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<string> 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);
+ }
}
+//**********************************************************************************************************************
+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 {
- int count = 1;
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
- //if the users entered no valid calculators don't execute command
- if (rDisplays.size() == 0) { return 0; }
+ map<string, set<int> > labelToEnds;
+ if ((format != "sharedfile")) { inputFileNames.push_back(inputfile); }
+ else { inputFileNames = parseSharedFile(sharedfile, labelToEnds); 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;
+
+ map<string, string> variables;
+ variables["[filename]"] = fileNameRoot;
+
+ 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(getOutputFileName("rarefaction",variables))));
+ outputNames.push_back(getOutputFileName("rarefaction",variables)); outputTypes["rarefaction"].push_back(getOutputFileName("rarefaction",variables));
+ }else if (Estimators[i] == "chao") {
+ rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(getOutputFileName("r_chao",variables))));
+ outputNames.push_back(getOutputFileName("r_chao",variables)); outputTypes["r_chao"].push_back(getOutputFileName("r_chao",variables));
+ }else if (Estimators[i] == "ace") {
+ if(abund < 5)
+ abund = 10;
+ rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(getOutputFileName("r_ace",variables))));
+ outputNames.push_back(getOutputFileName("r_ace",variables)); outputTypes["r_ace"].push_back(getOutputFileName("r_ace",variables));
+ }else if (Estimators[i] == "jack") {
+ rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(getOutputFileName("r_jack",variables))));
+ outputNames.push_back(getOutputFileName("r_jack",variables)); outputTypes["r_jack"].push_back(getOutputFileName("r_jack",variables));
+ }else if (Estimators[i] == "shannon") {
+ rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(getOutputFileName("r_shannon",variables))));
+ outputNames.push_back(getOutputFileName("r_shannon",variables)); outputTypes["r_shannon"].push_back(getOutputFileName("r_shannon",variables));
+ }else if (Estimators[i] == "shannoneven") {
+ rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(getOutputFileName("r_shannoneven",variables))));
+ outputNames.push_back(getOutputFileName("r_shannoneven",variables)); outputTypes["r_shannoneven"].push_back(getOutputFileName("r_shannoneven",variables));
+ }else if (Estimators[i] == "heip") {
+ rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(getOutputFileName("r_heip",variables))));
+ outputNames.push_back(getOutputFileName("r_heip",variables)); outputTypes["r_heip"].push_back(getOutputFileName("r_heip",variables));
+ }else if (Estimators[i] == "smithwilson") {
+ rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(getOutputFileName("r_smithwilson",variables))));
+ outputNames.push_back(getOutputFileName("r_smithwilson",variables)); outputTypes["r_smithwilson"].push_back(getOutputFileName("r_smithwilson",variables));
+ }else if (Estimators[i] == "npshannon") {
+ rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(getOutputFileName("r_npshannon",variables))));
+ outputNames.push_back(getOutputFileName("r_npshannon",variables)); outputTypes["r_npshannon"].push_back(getOutputFileName("r_npshannon",variables));
+ }else if (Estimators[i] == "simpson") {
+ rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(getOutputFileName("r_simpson",variables))));
+ outputNames.push_back(getOutputFileName("r_simpson",variables)); outputTypes["r_simpson"].push_back(getOutputFileName("r_simpson",variables));
+ }else if (Estimators[i] == "simpsoneven") {
+ rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(getOutputFileName("r_simpsoneven",variables))));
+ outputNames.push_back(getOutputFileName("r_simpsoneven",variables)); outputTypes["r_simpsoneven"].push_back(getOutputFileName("r_simpsoneven",variables));
+ }else if (Estimators[i] == "invsimpson") {
+ rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(getOutputFileName("r_invsimpson",variables))));
+ outputNames.push_back(getOutputFileName("r_invsimpson",variables)); outputTypes["r_invsimpson"].push_back(getOutputFileName("r_invsimpson",variables));
+ }else if (Estimators[i] == "bootstrap") {
+ rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(getOutputFileName("r_bootstrap",variables))));
+ outputNames.push_back(getOutputFileName("r_bootstrap",variables)); outputTypes["r_bootstrap"].push_back(getOutputFileName("r_bootstrap",variables));
+ }else if (Estimators[i] == "coverage") {
+ rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(getOutputFileName("r_coverage",variables))));
+ outputNames.push_back(getOutputFileName("r_coverage",variables)); outputTypes["r_coverage"].push_back(getOutputFileName("r_coverage",variables));
+ }else if (Estimators[i] == "nseqs") {
+ rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(getOutputFileName("r_nseqs",variables))));
+ outputNames.push_back(getOutputFileName("r_nseqs",variables)); outputTypes["r_nseqs"].push_back(getOutputFileName("r_nseqs",variables));
+ }
+ 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; }
- read = new ReadPhilFile(globaldata->inputFileName);
- read->read(&*globaldata);
+
+ if(allLines == 1 || labels.count(order->getLabel()) == 1){
+
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+ map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
+ set<int> 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<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
+ set<int> ends;
+ if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
+ rCurve = new Rarefact(order, rDisplays, processors, ends);
- order = globaldata->gorder;
- input = globaldata->ginput;
-
- while(order != NULL){
-
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+ 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());
+ }
- rCurve = new Rarefact(order, rDisplays);
- convert(globaldata->getFreq(), freq);
- convert(globaldata->getIters(), nIters);
- rCurve->getCurve(freq, nIters);
+ 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();
+ map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
+ set<int> ends;
+ if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
+ rCurve = new Rarefact(order, rDisplays, processors, ends);
+
+ rCurve->getCurve(freq, nIters);
delete rCurve;
-
- cout << order->getLabel() << '\t' << count << endl;
+
+ delete order;
}
+
+
+ for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
+ rDisplays.clear();
+ delete input;
+ }
- order = (input->getOrderVector());
- count++;
- }
-
- for(int i=0;i<rDisplays.size();i++){ delete rDisplays[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 = 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) {
- 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", "execute");
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";
+}
+//**********************************************************************************************************************
+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;
+ map<string, vector< vector<string> > > fileLabels; //combofile name to labels. each label is a vector because it may be unique lci hci.
+ vector<string> 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<string> theseLabels;
+ while(!iss.eof()) { iss >> newLabel; m->gobble(iss); theseLabels.push_back(newLabel); }
+ vector< vector<string> > allLabels;
+ vector<string> 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<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;
+ }
+ if (!(m->inUsersGroups(file2Group[i], groupNames))) { groupNames.push_back(file2Group[i]); }
+ }
+
+ //for each type create a combo file
+
+ 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; //it->second maps filename to group
+ set<int> numSampledSet;
+
+ //open each type summary file
+ map<string, map<int, vector< vector<string> > > > files; //maps file name to lines in file
+ int maxLines = 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);
+
+ map<int, vector< vector<string> > > thisFilesLines;
+ while (!temp.eof()){
+ int numSampled = 0;
+ temp >> numSampled; m->gobble(temp);
+
+ vector< vector<string> > theseReads;
+ vector<string> 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<string> 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<int>::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<string, map<int, vector< vector<string> > > >::iterator itFileNameGroup = files.begin(); itFileNameGroup != files.end(); itFileNameGroup++) {
+
+ string group = itFileNameGroup->first;
+
+ map<int, vector< vector<string> > >::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();
+ }
+
+ //return combine file name
+ return newFileNames;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactCommand", "createGroupFile");
exit(1);
- }
+ }
}
+//**********************************************************************************************************************
+vector<string> RareFactCommand::parseSharedFile(string filename, map<string, set<int> >& label2Ends) {
+ 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();
+ 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) {
+ m->errorOut(e, "RareFactCommand", "parseSharedFile");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
+
+
+
projects / mothur.git / blobdiff