//**********************************************************************************************************************
-RareFactCommand::RareFactCommand(string option){
+RareFactCommand::RareFactCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
- lines.clear();
labels.clear();
Estimators.clear();
-
+
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
else {
//valid paramters for this command
- string Array[] = {"iters","freq","line","label","calc","abund"};
+ string Array[] = {"iters","freq","label","calc","abund","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
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 = "";
+ outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ }
+
//make sure the user has already run the read.otu command
- if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund or rabund before you can use the rarefaction.single command."); mothurOutEndLine(); abort = true; }
+ 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 optional parameter and set defaults
// ...at some point should added some additional type checking...
- line = validParameter.validFile(parameters, "line", false);
- if (line == "not found") { line = ""; }
- else {
- if(line != "all") { splitAtDash(line, lines); allLines = 0; }
- else { allLines = 1; }
- }
-
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
else { allLines = 1; }
}
- //make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
- //if the user has not specified any line or labels use the ones from read.otu
- else if((line == "") && (label == "")) {
+ //if the user has not specified any labels use the ones from read.otu
+ if(label == "") {
allLines = globaldata->allLines;
labels = globaldata->labels;
- lines = globaldata->lines;
}
calc = validParameter.validFile(parameters, "calc", false);
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
convert(temp, nIters);
-
- if (abort == false) {
-
- string fileNameRoot = getRootName(globaldata->inputFileName);
- int i;
- validCalculator = new ValidCalculators();
-
-
- 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")));
- }else if (Estimators[i] == "chao") {
- rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(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")));
- }else if (Estimators[i] == "jack") {
- rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
- }else if (Estimators[i] == "shannon") {
- rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
- }else if (Estimators[i] == "npshannon") {
- rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
- }else if (Estimators[i] == "simpson") {
- rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
- }else if (Estimators[i] == "bootstrap") {
- rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
- }else if (Estimators[i] == "coverage") {
- rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage")));
- }else if (Estimators[i] == "nseqs") {
- rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
- }
- }
- }
- }
-
}
}
catch(exception& e) {
- errorOut(e, "RareFactCommand", "RareFactCommand");
+ m->errorOut(e, "RareFactCommand", "RareFactCommand");
exit(1);
}
}
void RareFactCommand::help(){
try {
- mothurOut("The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
- 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");
- mothurOut("The rarefaction.single command parameters are label, line, iters, freq, calc and abund. No parameters are required, but you may not use \n");
- mothurOut("both the line and label parameters at the same time. The rarefaction.single command should be in the following format: \n");
- mothurOut("rarefaction.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
- mothurOut("Example rarefaction.single(label=unique-.01-.03, line=0-5-10, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n");
- 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");
+ 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 and abund. No parameters are required. \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);
- mothurOut("The label and line parameters are used to analyze specific lines in your input.\n");
- mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
+ 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) {
- errorOut(e, "RareFactCommand", "help");
+ m->errorOut(e, "RareFactCommand", "help");
exit(1);
}
}
//**********************************************************************************************************************
-RareFactCommand::~RareFactCommand(){
- if (abort == false) {
- globaldata->gorder = NULL;
- delete input; globaldata->ginput = NULL;
- delete read;
- delete validCalculator;
- }
-}
+RareFactCommand::~RareFactCommand(){}
//**********************************************************************************************************************
if (abort == true) { return 0; }
- int count = 1;
+ vector<string> outputNames;
- //if the users entered no valid calculators don't execute command
- if (rDisplays.size() == 0) { return 0; }
-
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- order = globaldata->gorder;
- string lastLabel = order->getLabel();
- input = globaldata->ginput;
+ if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
+ else { inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); }
- //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;
- set<int> userLines = lines;
-
- //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) || (userLines.size() != 0))) {
+ if (m->control_pressed) { return 0; }
+
+ for (int p = 0; p < inputFileNames.size(); p++) {
- if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){
+ string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p]));
+ globaldata->inputFileName = inputFileNames[p];
- rCurve = new Rarefact(order, rDisplays);
- rCurve->getCurve(freq, nIters);
- delete rCurve;
+ if (m->control_pressed) { return 0; }
- mothurOut(order->getLabel()); mothurOutEndLine();
- processedLabels.insert(order->getLabel());
- userLabels.erase(order->getLabel());
- userLines.erase(count);
+ if (inputFileNames.size() > 1) {
+ m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
}
+ int i;
+ validCalculator = new ValidCalculators();
+
+
+ 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");
+ }else if (Estimators[i] == "chao") {
+ rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
+ outputNames.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");
+ }else if (Estimators[i] == "jack") {
+ rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
+ outputNames.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");
+ }else if (Estimators[i] == "npshannon") {
+ rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
+ outputNames.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");
+ }else if (Estimators[i] == "bootstrap") {
+ rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
+ outputNames.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");
+ }else if (Estimators[i] == "nseqs") {
+ rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
+ outputNames.push_back(fileNameRoot+"r_nseqs");
+ }
+ }
+ }
+
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ //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]; } delete validCalculator; return 0; }
+
+ read = new ReadOTUFile(globaldata->inputFileName);
+ 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;
+
+ if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; } delete validCalculator; delete read; delete input; globaldata->ginput = NULL; delete order; globaldata->gorder = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } 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 validCalculator; delete read; delete input; globaldata->ginput = NULL; delete order; globaldata->gorder = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+
+ if(allLines == 1 || labels.count(order->getLabel()) == 1){
+
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+ rCurve = new Rarefact(order, rDisplays);
+ rCurve->getCurve(freq, nIters);
+ delete rCurve;
+
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
+ }
+
+ if ((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);
+ 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 validCalculator; delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } 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 validCalculator; delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } 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);
rCurve->getCurve(freq, nIters);
delete rCurve;
-
- mothurOut(order->getLabel()); mothurOutEndLine();
- processedLabels.insert(order->getLabel());
- userLabels.erase(order->getLabel());
+
+ delete order;
}
- lastLabel = order->getLabel();
- delete order;
- order = (input->getOrderVector());
- count++;
+ for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
+ rDisplays.clear();
+ globaldata->gorder = NULL;
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete validCalculator;
+
}
- //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();
- }
- }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } 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::parseSharedFile(string filename) {
+ try {
+ vector<string> filenames;
+
+ map<string, ofstream*> filehandles;
+ map<string, ofstream*>::iterator it3;
- //run last line if you need to
- if (needToRun == true) {
- delete order;
- order = (input->getOrderVector(lastLabel));
- rCurve = new Rarefact(order, rDisplays);
- rCurve->getCurve(freq, nIters);
- delete rCurve;
+ //read first line
+ read = new ReadOTUFile(filename);
+ read->read(&*globaldata);
- mothurOut(order->getLabel()); mothurOutEndLine();
- delete order;
+ 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());
+ }
- for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
- return 0;
+ 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, "RareFactCommand", "execute");
+ m->errorOut(e, "RareFactCommand", "parseSharedFile");
exit(1);
}
}
-
//**********************************************************************************************************************
+
+
+
projects / mothur.git / blobdiff