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[] = {"line","label","calc","abund","size"};
+ string Array[] = {"label","calc","abund","size","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
}
//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 summary.single command."); mothurOutEndLine(); abort = true; }
+ 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 summary.single command."); 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 = "";
+ outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ }
+
//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, "size", false); if (temp == "not found") { temp = "0"; }
convert(temp, size);
- if (abort == false) {
-
- validCalculator = new ValidCalculators();
- int i;
-
- for (i=0; i<Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("summary", Estimators[i]) == true) {
- if(Estimators[i] == "sobs"){
- sumCalculators.push_back(new Sobs());
- }else if(Estimators[i] == "chao"){
- sumCalculators.push_back(new Chao1());
- }else if(Estimators[i] == "coverage"){
- sumCalculators.push_back(new Coverage());
- }else if(Estimators[i] == "geometric"){
- sumCalculators.push_back(new Geom());
- }else if(Estimators[i] == "logseries"){
- sumCalculators.push_back(new LogSD());
- }else if(Estimators[i] == "qstat"){
- sumCalculators.push_back(new QStat());
- }else if(Estimators[i] == "bergerparker"){
- sumCalculators.push_back(new BergerParker());
- }else if(Estimators[i] == "bstick"){
- sumCalculators.push_back(new BStick());
- }else if(Estimators[i] == "ace"){
- if(abund < 5)
- abund = 10;
- sumCalculators.push_back(new Ace(abund));
- }else if(Estimators[i] == "jack"){
- sumCalculators.push_back(new Jackknife());
- }else if(Estimators[i] == "shannon"){
- sumCalculators.push_back(new Shannon());
- }else if(Estimators[i] == "npshannon"){
- sumCalculators.push_back(new NPShannon());
- }else if(Estimators[i] == "simpson"){
- sumCalculators.push_back(new Simpson());
- }else if(Estimators[i] == "bootstrap"){
- sumCalculators.push_back(new Bootstrap());
- }else if (Estimators[i] == "nseqs") {
- sumCalculators.push_back(new NSeqs());
- }else if (Estimators[i] == "goodscoverage") {
- sumCalculators.push_back(new GoodsCoverage());
- }else if (Estimators[i] == "efron") {
- sumCalculators.push_back(new Efron(size));
- }else if (Estimators[i] == "boneh") {
- sumCalculators.push_back(new Boneh(size));
- }else if (Estimators[i] == "solow") {
- sumCalculators.push_back(new Solow(size));
- }else if (Estimators[i] == "shen") {
- sumCalculators.push_back(new Shen(size, abund));
- }
- }
- }
- }
}
-
-
}
catch(exception& e) {
errorOut(e, "SummaryCommand", "SummaryCommand");
try {
mothurOut("The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
mothurOut("The summary.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 summary.single command parameters are label, line, calc, abund. No parameters are required, but you may not use \n");
- mothurOut("both the line and label parameters at the same time. The summary.single command should be in the following format: \n");
- mothurOut("summary.single(label=yourLabel, line=yourLines, calc=yourEstimators).\n");
- mothurOut("Example summary.single(label=unique-.01-.03, line=0,5,10, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n");
+ mothurOut("The summary.single command parameters are label, calc, abund. No parameters are required.\n");
+ mothurOut("The summary.single command should be in the following format: \n");
+ mothurOut("summary.single(label=yourLabel, calc=yourEstimators).\n");
+ mothurOut("Example summary.single(label=unique-.01-.03, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n");
validCalculator->printCalc("summary", cout);
mothurOut("The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n");
- 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. line), '=' and parameters (i.e.yourLines).\n\n");
+ mothurOut("The label parameter is used to analyze specific labels in your input.\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
}
catch(exception& e) {
errorOut(e, "SummaryCommand", "help");
//**********************************************************************************************************************
-SummaryCommand::~SummaryCommand(){
- if (abort == false) {
- delete input; globaldata->ginput = NULL;
- delete read;
- delete validCalculator;
- globaldata->sabund = NULL;
- }
-}
+SummaryCommand::~SummaryCommand(){}
//**********************************************************************************************************************
if (abort == true) { return 0; }
- int count = 1;
-
- //if the users entered no valid calculators don't execute command
- if (sumCalculators.size() == 0) { return 0; }
-
- outputFileName = ((getRootName(globaldata->inputFileName)) + "summary");
- openOutputFile(outputFileName, outputFileHandle);
- outputFileHandle << "label";
-
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- sabund = globaldata->sabund;
- string lastLabel = sabund->getLabel();
- input = globaldata->ginput;
+ if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
+ else { inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); }
- for(int i=0;i<sumCalculators.size();i++){
- if(sumCalculators[i]->getCols() == 1){
- outputFileHandle << '\t' << sumCalculators[i]->getName();
+ for (int p = 0; p < inputFileNames.size(); p++) {
+
+ string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p])) + "summary";
+ globaldata->inputFileName = inputFileNames[p];
+
+ if (inputFileNames.size() > 1) {
+ mothurOutEndLine(); mothurOut("Processing group " + groups[p]); mothurOutEndLine(); mothurOutEndLine();
}
- else{
- outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
+
+ sumCalculators.clear();
+
+ validCalculator = new ValidCalculators();
+
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("summary", Estimators[i]) == true) {
+ if(Estimators[i] == "sobs"){
+ sumCalculators.push_back(new Sobs());
+ }else if(Estimators[i] == "chao"){
+ sumCalculators.push_back(new Chao1());
+ }else if(Estimators[i] == "coverage"){
+ sumCalculators.push_back(new Coverage());
+ }else if(Estimators[i] == "geometric"){
+ sumCalculators.push_back(new Geom());
+ }else if(Estimators[i] == "logseries"){
+ sumCalculators.push_back(new LogSD());
+ }else if(Estimators[i] == "qstat"){
+ sumCalculators.push_back(new QStat());
+ }else if(Estimators[i] == "bergerparker"){
+ sumCalculators.push_back(new BergerParker());
+ }else if(Estimators[i] == "bstick"){
+ sumCalculators.push_back(new BStick());
+ }else if(Estimators[i] == "ace"){
+ if(abund < 5)
+ abund = 10;
+ sumCalculators.push_back(new Ace(abund));
+ }else if(Estimators[i] == "jack"){
+ sumCalculators.push_back(new Jackknife());
+ }else if(Estimators[i] == "shannon"){
+ sumCalculators.push_back(new Shannon());
+ }else if(Estimators[i] == "npshannon"){
+ sumCalculators.push_back(new NPShannon());
+ }else if(Estimators[i] == "simpson"){
+ sumCalculators.push_back(new Simpson());
+ }else if(Estimators[i] == "bootstrap"){
+ sumCalculators.push_back(new Bootstrap());
+ }else if (Estimators[i] == "nseqs") {
+ sumCalculators.push_back(new NSeqs());
+ }else if (Estimators[i] == "goodscoverage") {
+ sumCalculators.push_back(new GoodsCoverage());
+ }else if (Estimators[i] == "efron") {
+ sumCalculators.push_back(new Efron(size));
+ }else if (Estimators[i] == "boneh") {
+ sumCalculators.push_back(new Boneh(size));
+ }else if (Estimators[i] == "solow") {
+ sumCalculators.push_back(new Solow(size));
+ }else if (Estimators[i] == "shen") {
+ sumCalculators.push_back(new Shen(size, abund));
+ }
+ }
}
- }
- outputFileHandle << endl;
-
- //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;
-
- while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
- if(allLines == 1 || lines.count(count) == 1 || labels.count(sabund->getLabel()) == 1){
-
- mothurOut(sabund->getLabel()); mothurOutEndLine();
- processedLabels.insert(sabund->getLabel());
- userLabels.erase(sabund->getLabel());
- userLines.erase(count);
-
-
- outputFileHandle << sabund->getLabel();
- for(int i=0;i<sumCalculators.size();i++){
- vector<double> data = sumCalculators[i]->getValues(sabund);
- outputFileHandle << '\t';
- sumCalculators[i]->print(outputFileHandle);
+ //if the users entered no valid calculators don't execute command
+ if (sumCalculators.size() == 0) { return 0; }
+
+ ofstream outputFileHandle;
+ openOutputFile(fileNameRoot, outputFileHandle);
+ outputFileHandle << "label";
+
+ read = new ReadOTUFile(globaldata->inputFileName);
+ read->read(&*globaldata);
+
+ sabund = globaldata->sabund;
+ string lastLabel = sabund->getLabel();
+ input = globaldata->ginput;
+
+ for(int i=0;i<sumCalculators.size();i++){
+ if(sumCalculators[i]->getCols() == 1){
+ outputFileHandle << '\t' << sumCalculators[i]->getName();
+ }
+ else{
+ outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
}
- outputFileHandle << endl;
}
+ outputFileHandle << endl;
+
+ //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 ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
+
+ mothurOut(sabund->getLabel()); mothurOutEndLine();
+ processedLabels.insert(sabund->getLabel());
+ userLabels.erase(sabund->getLabel());
+
+ outputFileHandle << sabund->getLabel();
+ for(int i=0;i<sumCalculators.size();i++){
+ vector<double> data = sumCalculators[i]->getValues(sabund);
+ outputFileHandle << '\t';
+ sumCalculators[i]->print(outputFileHandle);
+ }
+ outputFileHandle << endl;
+ }
+
+ if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = sabund->getLabel();
+
+ delete sabund;
+ sabund = input->getSAbundVector(lastLabel);
+
+ mothurOut(sabund->getLabel()); mothurOutEndLine();
+ processedLabels.insert(sabund->getLabel());
+ userLabels.erase(sabund->getLabel());
+
+ outputFileHandle << sabund->getLabel();
+ for(int i=0;i<sumCalculators.size();i++){
+ vector<double> data = sumCalculators[i]->getValues(sabund);
+ outputFileHandle << '\t';
+ sumCalculators[i]->print(outputFileHandle);
+ }
+ outputFileHandle << endl;
+
+ //restore real lastlabel to save below
+ sabund->setLabel(saveLabel);
+ }
+
+ lastLabel = sabund->getLabel();
+
delete sabund;
+ sabund = input->getSAbundVector();
+ }
+
+ //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 (sabund != NULL) { delete sabund; }
sabund = input->getSAbundVector(lastLabel);
mothurOut(sabund->getLabel()); mothurOutEndLine();
- processedLabels.insert(sabund->getLabel());
- userLabels.erase(sabund->getLabel());
-
outputFileHandle << sabund->getLabel();
for(int i=0;i<sumCalculators.size();i++){
vector<double> data = sumCalculators[i]->getValues(sabund);
sumCalculators[i]->print(outputFileHandle);
}
outputFileHandle << endl;
- }
-
- lastLabel = sabund->getLabel();
+ delete sabund;
+ }
- delete sabund;
- sabund = input->getSAbundVector();
- count++;
+ outputFileHandle.close();
+
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete validCalculator;
+ globaldata->sabund = NULL;
}
- //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();
- }
- }
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "SummaryCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SummaryCommand::parseSharedFile(string filename) {
+ try {
+ vector<string> filenames;
- //run last line if you need to
- if (needToRun == true) {
- if (sabund != NULL) { delete sabund; }
- sabund = input->getSAbundVector(lastLabel);
+ map<string, ofstream*> filehandles;
+ map<string, ofstream*>::iterator it3;
+
+
+ //read first line
+ read = new ReadOTUFile(filename);
+ read->read(&*globaldata);
- mothurOut(sabund->getLabel()); mothurOutEndLine();
- outputFileHandle << sabund->getLabel();
- for(int i=0;i<sumCalculators.size();i++){
- vector<double> data = sumCalculators[i]->getValues(sabund);
- outputFileHandle << '\t';
- sumCalculators[i]->print(outputFileHandle);
- }
- outputFileHandle << endl;
- delete sabund;
+ 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"));
}
- outputFileHandle.close();
+ 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) {
- return 0;
+ 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, "SummaryCommand", "execute");
+ errorOut(e, "SummaryCommand", "parseSharedFile");
exit(1);
}
}
-
//**********************************************************************************************************************
projects / mothur.git / blobdiff