X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.cpp;h=473d2db8b473bbef240793c419e6c8beece29ddf;hb=6777912b79eb6d011163da47f3ada09d1a9293c1;hp=01f2fff68b93596a52fc60703bce790559b0fbec;hpb=a8f5a612bba54ceb74e17efc027d3a7f5aa93c9a;p=mothur.git diff --git a/collectcommand.cpp b/collectcommand.cpp index 01f2fff..473d2db 100644 --- a/collectcommand.cpp +++ b/collectcommand.cpp @@ -31,174 +31,325 @@ //********************************************************************************************************************** -CollectCommand::CollectCommand(){ +CollectCommand::CollectCommand(string option){ try { globaldata = GlobalData::getInstance(); - string fileNameRoot; - fileNameRoot = getRootName(globaldata->inputFileName); - convert(globaldata->getFreq(), freq); - int i; - validCalculator = new ValidCalculators(); - - for (i=0; iEstimators.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] == "nseqs") { - cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs"))); - }else if (globaldata->Estimators[i] == "coverage") { - cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage"))); - }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"))); - }else if (globaldata->Estimators[i] == "geometric") { - cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric"))); - }else if (globaldata->Estimators[i] == "qstat") { - cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat"))); - }else if (globaldata->Estimators[i] == "logseries") { - cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries"))); - }else if (globaldata->Estimators[i] == "bergerparker") { - cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker"))); - }else if (globaldata->Estimators[i] == "bstick") { - cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick"))); - }else if (globaldata->Estimators[i] == "goodscoverage") { - cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage"))); - }else if (globaldata->Estimators[i] == "efron") { - convert(globaldata->getSize(), size); - cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron"))); - }else if (globaldata->Estimators[i] == "boneh") { - convert(globaldata->getSize(), size); - cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh"))); - }else if (globaldata->Estimators[i] == "solow") { - convert(globaldata->getSize(), size); - cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow"))); - }else if (globaldata->Estimators[i] == "shen") { - convert(globaldata->getSize(), size); - cDisplays.push_back(new CollectDisplay(new Shen(size), new OneColumnFile(fileNameRoot+"shen"))); - } + 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 myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + + //check to make sure all parameters are valid for command + for (map::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 ReadOTUFile(globaldata->inputFileName); - read->read(&*globaldata); + if (abort == true) { return 0; } - order = globaldata->gorder; - lastOrder = order; - input = globaldata->ginput; + if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); } + else { inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); } + + for (int p = 0; p < inputFileNames.size(); p++) { - //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. - set processedLabels; - set userLabels = globaldata->labels; + if (outputDir == "") { outputDir += hasPath(inputFileNames[p]); } + string fileNameRoot = outputDir + getRootName(getSimpleName(inputFileNames[p])); + globaldata->inputFileName = inputFileNames[p]; - while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) { + if (inputFileNames.size() > 1) { + mothurOutEndLine(); mothurOut("Processing group " + groups[p]); mothurOutEndLine(); mothurOutEndLine(); + } - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ - - cCurve = new Collect(order, cDisplays); - cCurve->getCurve(freq); - delete cCurve; + validCalculator = new ValidCalculators(); + + for (int i=0; iisValidCalculator("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"))); + } + } + } + + //if the users entered no valid calculators don't execute command + if (cDisplays.size() == 0) { return 0; } - cout << order->getLabel() << '\t' << count << endl; - processedLabels.insert(order->getLabel()); - userLabels.erase(order->getLabel()); + read = new ReadOTUFile(inputFileNames[p]); + read->read(&*globaldata); + + order = globaldata->gorder; + string lastLabel = order->getLabel(); + input = globaldata->ginput; - //you have a label the user want that is smaller than this line and the last line has not already been processed + //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. + set processedLabels; + set 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::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 ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) { - cCurve = new Collect(lastOrder, cDisplays); + //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); cCurve->getCurve(freq); delete cCurve; - - cout << lastOrder->getLabel() << '\t' << count << endl; - processedLabels.insert(lastOrder->getLabel()); - userLabels.erase(lastOrder->getLabel()); + delete order; } - if (count != 1) { delete lastOrder; } - lastOrder = order; - order = (input->getOrderVector()); - count++; + for(int i=0;iginput = NULL; + delete read; + globaldata->gorder = NULL; + delete validCalculator; } - //output error messages about any remaining user labels - set::iterator it; - bool needToRun = false; - for (it = userLabels.begin(); it != userLabels.end(); it++) { - cout << "Your file does not include the label "<< *it; - if (processedLabels.count(lastOrder->getLabel()) != 1) { - cout << ". I will use " << lastOrder->getLabel() << "." << endl; - needToRun = true; - }else { - cout << ". Please refer to " << lastOrder->getLabel() << "." << endl; - } - } - //run last line if you need to - if (needToRun == true) { - cCurve = new Collect(lastOrder, cDisplays); - cCurve->getCurve(freq); - delete cCurve; - - cout << lastOrder->getLabel() << '\t' << count << endl; - } - delete lastOrder; - for(int i=0;i CollectCommand::parseSharedFile(string filename) { + try { + vector filenames; + + map filehandles; + map::iterator it3; + + + //read first line + read = new ReadOTUFile(filename); + read->read(&*globaldata); + + input = globaldata->ginput; + vector lookup = input->getSharedRAbundVectors(); + + string sharedFileRoot = getRootName(filename); + + //clears file before we start to write to it below + for (int i=0; igetGroup() + ".rabund").c_str()); + filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund")); + } + + ofstream* temp; + for (int i=0; igetGroup()] = 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); + } +} +//********************************************************************************************************************** +