#include "collectcommand.h"
#include "ace.h"
#include "sobs.h"
+#include "nseqs.h"
#include "chao1.h"
#include "bootstrap.h"
#include "simpson.h"
#include "npshannon.h"
#include "shannon.h"
#include "jackknife.h"
+#include "geom.h"
+#include "qstat.h"
+#include "logsd.h"
+#include "bergerparker.h"
+#include "bstick.h"
+#include "goodscoverage.h"
+#include "efron.h"
+#include "boneh.h"
+#include "solow.h"
+#include "shen.h"
+#include "coverage.h"
//**********************************************************************************************************************
-
-
-CollectCommand::CollectCommand(){
+CollectCommand::CollectCommand(string option){
try {
globaldata = GlobalData::getInstance();
- string fileNameRoot;
- fileNameRoot = getRootName(globaldata->inputFileName);
- int i;
- validCalculator = new ValidCalculators();
-
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("single", globaldata->Estimators[i]) == true) {
- if (globaldata->Estimators[i] == "sobs") {
- cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
- }else if (globaldata->Estimators[i] == "chao") {
- cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
- }else if (globaldata->Estimators[i] == "ace") {
- convert(globaldata->getAbund(), abund);
- cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
- }else if (globaldata->Estimators[i] == "jack") {
- cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
- }else if (globaldata->Estimators[i] == "shannon") {
- cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
- }else if (globaldata->Estimators[i] == "npshannon") {
- cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
- }else if (globaldata->Estimators[i] == "simpson") {
- cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
- }else if (globaldata->Estimators[i] == "bootstrap") {
- cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
- }
+ abort = false;
+ allLines = 1;
+ labels.clear();
+ Estimators.clear();
+
+ //allow user to run help
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"freq","label","calc","abund","size","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ 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; }
+ }
+
+ //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 = ""; }
+
+ //make sure the user has already run the read.otu command
+ if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund, rabund or shared file before you can use the collect.single command."); mothurOutEndLine(); abort = true; }
+
+ //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") { 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-chao-ace-jack-shannon-npshannon-simpson"; }
+ else {
+ if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
}
+ splitAtDash(calc, Estimators);
+
+ string temp;
+ temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
+ convert(temp, freq);
+
+ temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
+ convert(temp, abund);
+
+ temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, size);
}
- //reset calc for next command
- globaldata->setCalc("");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "CollectCommand", "CollectCommand");
exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void CollectCommand::help(){
+ try {
+ mothurOut("The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. \n");
+ mothurOut("The collect.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n");
+ mothurOut("The collect.single command parameters are label, freq, calc and abund. No parameters are required. \n");
+ mothurOut("The collect.single command should be in the following format: \n");
+ mothurOut("collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
+ mothurOut("Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n");
+ mothurOut("The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n");
+ validCalculator->printCalc("single", cout);
+ mothurOut("The label parameter is used to analyze specific labels in your input.\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
}
- catch(...) {
- cout << "An unknown error has occurred in the CollectCommand class function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ catch(exception& e) {
+ errorOut(e, "CollectCommand", "help");
exit(1);
- }
-
+ }
}
//**********************************************************************************************************************
-CollectCommand::~CollectCommand(){
- delete order;
- delete input;
- delete cCurve;
- delete read;
-}
+CollectCommand::~CollectCommand(){}
//**********************************************************************************************************************
int CollectCommand::execute(){
try {
- int count = 1;
- //if the users entered no valid calculators don't execute command
- if (cDisplays.size() == 0) { return 0; }
-
- read = new ReadPhilFile(globaldata->inputFileName);
- read->read(&*globaldata);
+ if (abort == true) { return 0; }
- order = globaldata->gorder;
- input = globaldata->ginput;
- set<string> orderList;
+ if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
+ else { inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); }
- while(order != NULL){
+ for (int p = 0; p < inputFileNames.size(); p++) {
+
+ if (outputDir == "") { outputDir += hasPath(inputFileNames[p]); }
+ string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p]));
+ globaldata->inputFileName = inputFileNames[p];
+
+ if (inputFileNames.size() > 1) {
+ mothurOutEndLine(); mothurOut("Processing group " + groups[p]); mothurOutEndLine(); mothurOutEndLine();
+ }
+
+ validCalculator = new ValidCalculators();
+
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("single", Estimators[i]) == true) {
+ if (Estimators[i] == "sobs") {
+ cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
+ }else if (Estimators[i] == "chao") {
+ cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
+ }else if (Estimators[i] == "nseqs") {
+ cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
+ }else if (Estimators[i] == "coverage") {
+ cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
+ }else if (Estimators[i] == "ace") {
+ cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
+ }else if (Estimators[i] == "jack") {
+ cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
+ }else if (Estimators[i] == "shannon") {
+ cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
+ }else if (Estimators[i] == "npshannon") {
+ cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
+ }else if (Estimators[i] == "simpson") {
+ cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
+ }else if (Estimators[i] == "bootstrap") {
+ cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
+ }else if (Estimators[i] == "geometric") {
+ cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
+ }else if (Estimators[i] == "qstat") {
+ cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
+ }else if (Estimators[i] == "logseries") {
+ cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
+ }else if (Estimators[i] == "bergerparker") {
+ cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
+ }else if (Estimators[i] == "bstick") {
+ cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
+ }else if (Estimators[i] == "goodscoverage") {
+ cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
+ }else if (Estimators[i] == "efron") {
+ cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
+ }else if (Estimators[i] == "boneh") {
+ cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
+ }else if (Estimators[i] == "solow") {
+ cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
+ }else if (Estimators[i] == "shen") {
+ cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+"shen")));
+ }
+ }
+ }
- orderList.insert(order->getLabel());
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+
+ //if the users entered no valid calculators don't execute command
+ if (cDisplays.size() == 0) { return 0; }
+
+ read = new ReadOTUFile(inputFileNames[p]);
+ read->read(&*globaldata);
+
+ order = globaldata->gorder;
+ 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<string> processedLabels;
+ set<string> userLabels = labels;
+
+ while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if(allLines == 1 || labels.count(order->getLabel()) == 1){
+
+ cCurve = new Collect(order, cDisplays);
+ cCurve->getCurve(freq);
+ delete cCurve;
+
+ mothurOut(order->getLabel()); mothurOutEndLine();
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
+
+
+ }
+ //you have a label the user want that is smaller than this label and the last label has not already been processed
+ if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = order->getLabel();
+
+ delete order;
+ order = (input->getOrderVector(lastLabel));
+
+ cCurve = new Collect(order, cDisplays);
+ cCurve->getCurve(freq);
+ delete cCurve;
+
+ mothurOut(order->getLabel()); mothurOutEndLine();
+ 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());
+ }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ needToRun = true;
+ }else {
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ if (order != NULL) { delete order; }
+ order = (input->getOrderVector(lastLabel));
+
+ mothurOut(order->getLabel()); mothurOutEndLine();
+
cCurve = new Collect(order, cDisplays);
- convert(globaldata->getFreq(), freq);
cCurve->getCurve(freq);
-
delete cCurve;
-
- cout << order->getLabel() << '\t' << count << endl;
+ delete order;
}
- order = (input->getOrderVector());
- count++;
+
+ for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
+ cDisplays.clear();
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ globaldata->gorder = NULL;
+ delete validCalculator;
}
- set<string>::iterator i;
- for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
- if(orderList.count(*i) == 0)
- cout << "'" << *i << "'" << " is not a valid label.\n";
- for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
+
+
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "CollectCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the CollectCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
+vector<string> CollectCommand::parseSharedFile(string filename) {
+ try {
+ vector<string> filenames;
+
+ map<string, ofstream*> filehandles;
+ map<string, ofstream*>::iterator it3;
+
+
+ //read first line
+ read = new ReadOTUFile(filename);
+ read->read(&*globaldata);
+
+ input = globaldata->ginput;
+ vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
+
+ string sharedFileRoot = getRootName(filename);
+
+ //clears file before we start to write to it below
+ for (int i=0; i<lookup.size(); i++) {
+ remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
+ 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();
+ 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 read;
+ delete input;
+ globaldata->ginput = NULL;
+
+ return filenames;
+ }
+ catch(exception& e) {
+ errorOut(e, "CollectCommand", "parseSharedFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
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