X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefactcommand.cpp;h=41c38e86899f35d0dfc93e6f54a6f63b6f845254;hb=71b2121662daae3f9044252887d1c16eeddd85bb;hp=7e4ced55244665b4c3540f71491ce6dd4f003517;hpb=09a01fb51eea9e81409d367410c831394193fd86;p=mothur.git diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp index 7e4ced5..41c38e8 100644 --- a/rarefactcommand.cpp +++ b/rarefactcommand.cpp @@ -10,115 +10,259 @@ #include "rarefactcommand.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 "coverage.h" //********************************************************************************************************************** -RareFactCommand::RareFactCommand(){ +RareFactCommand::RareFactCommand(string option){ try { globaldata = GlobalData::getInstance(); - string fileNameRoot; - fileNameRoot = getRootName(globaldata->inputFileName); - validCalculator = new ValidCalculators(); + abort = false; + allLines = 1; + lines.clear(); + labels.clear(); + Estimators.clear(); - int i; - for (i=0; iEstimators.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") { - rDisplays.push_back(new RareDisplay(new Ace(), 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"))); + //allow user to run help + if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; } + + else { + //valid paramters for this command + string Array[] = {"iters","freq","line","label","calc","abund"}; + 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; } + } + + //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; } + + //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 { + if(label != "all") { splitAtDash(label, labels); allLines = 0; } + 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 == "")) { + allLines = globaldata->allLines; + labels = globaldata->labels; + lines = globaldata->lines; + } + + calc = validParameter.validFile(parameters, "calc", false); + if (calc == "not found") { calc = "sobs"; } + else { + if (calc == "default") { calc = "sobs"; } + } + 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, "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; iisValidCalculator("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"))); + } + } } } + } - //reset calc for next command - globaldata->setCalc(""); - } 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"; + errorOut(e, "RareFactCommand", "RareFactCommand"); 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"; +} +//********************************************************************************************************************** + +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"); + 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"); + } + catch(exception& e) { + errorOut(e, "RareFactCommand", "help"); exit(1); - } - + } } //********************************************************************************************************************** RareFactCommand::~RareFactCommand(){ - delete order; - delete input; - delete rCurve; - delete read; + if (abort == false) { + globaldata->gorder = NULL; + delete input; globaldata->ginput = NULL; + delete read; + delete validCalculator; + } } //********************************************************************************************************************** int RareFactCommand::execute(){ try { + + if (abort == true) { return 0; } + int count = 1; //if the users entered no valid calculators don't execute command if (rDisplays.size() == 0) { return 0; } - read = new ReadPhilFile(globaldata->inputFileName); + read = new ReadOTUFile(globaldata->inputFileName); read->read(&*globaldata); order = globaldata->gorder; + string lastLabel = order->getLabel(); input = globaldata->ginput; - - while(order != NULL){ - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ + //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; + set 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(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){ rCurve = new Rarefact(order, rDisplays); - convert(globaldata->getFreq(), freq); - convert(globaldata->getIters(), nIters); rCurve->getCurve(freq, nIters); + delete rCurve; + + mothurOut(order->getLabel()); mothurOutEndLine(); + processedLabels.insert(order->getLabel()); + userLabels.erase(order->getLabel()); + userLines.erase(count); + } + if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + delete order; + order = (input->getOrderVector(lastLabel)); + + rCurve = new Rarefact(order, rDisplays); + rCurve->getCurve(freq, nIters); delete rCurve; - cout << order->getLabel() << '\t' << count << endl; + mothurOut(order->getLabel()); mothurOutEndLine(); + processedLabels.insert(order->getLabel()); + userLabels.erase(order->getLabel()); } - + + lastLabel = order->getLabel(); + + delete order; order = (input->getOrderVector()); count++; + } + //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(); + } } - + + //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; + + mothurOut(order->getLabel()); mothurOutEndLine(); + delete order; + } + + for(int i=0;i