rarefactcommand.cpp

   1 /*
   2  *  rarefactcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "rarefactcommand.h"
  11 #include "ace.h"
  12 #include "sobs.h"
  13 #include "nseqs.h"
  14 #include "chao1.h"
  15 #include "bootstrap.h"
  16 #include "simpson.h"
  17 #include "npshannon.h"
  18 #include "shannon.h"
  19 #include "jackknife.h"
  20 #include "coverage.h"
  21
  22 //**********************************************************************************************************************
  23
  24
  25 RareFactCommand::RareFactCommand(string option){
  26         try {
  27                 globaldata = GlobalData::getInstance();
  28                 abort = false;
  29                 allLines = 1;
  30                 labels.clear();
  31                 Estimators.clear();
  32
  33                 //allow user to run help
  34                 if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
  35
  36                 else {
  37                         //valid paramters for this command
  38                         string Array[] =  {"iters","freq","label","calc","abund"};
  39                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  40
  41                         OptionParser parser(option);
  42                         map<string,string> parameters = parser.getParameters();
  43
  44                         ValidParameters validParameter;
  45
  46                         //check to make sure all parameters are valid for command
  47                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  48                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  49                         }
  50
  51                         //make sure the user has already run the read.otu command
  52                         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; }
  53
  54                         //check for optional parameter and set defaults
  55                         // ...at some point should added some additional type checking...
  56                         label = validParameter.validFile(parameters, "label", false);
  57                         if (label == "not found") { label = ""; }
  58                         else {
  59                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  60                                 else { allLines = 1;  }
  61                         }
  62
  63                         //if the user has not specified any labels use the ones from read.otu
  64                         if(label == "") {
  65                                 allLines = globaldata->allLines;
  66                                 labels = globaldata->labels;
  67                         }
  68
  69                         calc = validParameter.validFile(parameters, "calc", false);
  70                         if (calc == "not found") { calc = "sobs";  }
  71                         else {
  72                                  if (calc == "default")  {  calc = "sobs";  }
  73                         }
  74                         splitAtDash(calc, Estimators);
  75
  76                         string temp;
  77                         temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
  78                         convert(temp, freq);
  79
  80                         temp = validParameter.validFile(parameters, "abund", false);                    if (temp == "not found") { temp = "10"; }
  81                         convert(temp, abund);
  82
  83                         temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
  84                         convert(temp, nIters);
  85
  86                         if (abort == false) {
  87
  88                                 string fileNameRoot = getRootName(globaldata->inputFileName);
  89                                 int i;
  90                                 validCalculator = new ValidCalculators();
  91
  92
  93                                 for (i=0; i<Estimators.size(); i++) {
  94                                         if (validCalculator->isValidCalculator("rarefaction", Estimators[i]) == true) {
  95                                                 if (Estimators[i] == "sobs") {
  96                                                         rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
  97                                                 }else if (Estimators[i] == "chao") {
  98                                                         rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
  99                                                 }else if (Estimators[i] == "ace") {
 100                                                         if(abund < 5)
 101                                                                 abund = 10;
 102                                                         rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace")));
 103                                                 }else if (Estimators[i] == "jack") {
 104                                                         rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
 105                                                 }else if (Estimators[i] == "shannon") {
 106                                                         rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
 107                                                 }else if (Estimators[i] == "npshannon") {
 108                                                         rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
 109                                                 }else if (Estimators[i] == "simpson") {
 110                                                         rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
 111                                                 }else if (Estimators[i] == "bootstrap") {
 112                                                         rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
 113                                                 }else if (Estimators[i] == "coverage") {
 114                                                         rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage")));
 115                                                 }else if (Estimators[i] == "nseqs") {
 116                                                         rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
 117                                                 }
 118                                         }
 119                                 }
 120                         }
 121
 122                 }
 123
 124         }
 125         catch(exception& e) {
 126                 errorOut(e, "RareFactCommand", "RareFactCommand");
 127                 exit(1);
 128         }
 129 }
 130 //**********************************************************************************************************************
 131
 132 void RareFactCommand::help(){
 133         try {
 134                 mothurOut("The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
 135                 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");
 136                 mothurOut("The rarefaction.single command parameters are label, iters, freq, calc and abund.  No parameters are required. \n");
 137                 mothurOut("The rarefaction.single command should be in the following format: \n");
 138                 mothurOut("rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
 139                 mothurOut("Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n");
 140                 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");
 141                 validCalculator->printCalc("rarefaction", cout);
 142                 mothurOut("The label parameter is used to analyze specific labels in your input.\n");
 143                 mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
 144         }
 145         catch(exception& e) {
 146                 errorOut(e, "RareFactCommand", "help");
 147                 exit(1);
 148         }
 149 }
 150
 151 //**********************************************************************************************************************
 152
 153 RareFactCommand::~RareFactCommand(){
 154         if (abort == false) {
 155                 globaldata->gorder = NULL;
 156                 delete input;  globaldata->ginput = NULL;
 157                 delete read;
 158                 delete validCalculator;
 159         }
 160 }
 161
 162 //**********************************************************************************************************************
 163
 164 int RareFactCommand::execute(){
 165         try {
 166
 167                 if (abort == true) { return 0; }
 168
 169                 //if the users entered no valid calculators don't execute command
 170                 if (rDisplays.size() == 0) { return 0; }
 171
 172                 read = new ReadOTUFile(globaldata->inputFileName);
 173                 read->read(&*globaldata);
 174
 175                 order = globaldata->gorder;
 176                 string lastLabel = order->getLabel();
 177                 input = globaldata->ginput;
 178
 179                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 180                 set<string> processedLabels;
 181                 set<string> userLabels = labels;
 182
 183                 //as long as you are not at the end of the file or done wih the lines you want
 184                 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 185
 186                         if(allLines == 1 || labels.count(order->getLabel()) == 1){
 187
 188                                 rCurve = new Rarefact(order, rDisplays);
 189                                 rCurve->getCurve(freq, nIters);
 190                                 delete rCurve;
 191
 192                                 mothurOut(order->getLabel()); mothurOutEndLine();
 193                                 processedLabels.insert(order->getLabel());
 194                                 userLabels.erase(order->getLabel());
 195                         }
 196
 197                         if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 198                                 delete order;
 199                                 order = (input->getOrderVector(lastLabel));
 200
 201                                 rCurve = new Rarefact(order, rDisplays);
 202                                 rCurve->getCurve(freq, nIters);
 203                                 delete rCurve;
 204
 205                                 mothurOut(order->getLabel()); mothurOutEndLine();
 206                                 processedLabels.insert(order->getLabel());
 207                                 userLabels.erase(order->getLabel());
 208                         }
 209
 210                         lastLabel = order->getLabel();
 211
 212                         delete order;
 213                         order = (input->getOrderVector());
 214                 }
 215
 216                 //output error messages about any remaining user labels
 217                 set<string>::iterator it;
 218                 bool needToRun = false;
 219                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 220                         mothurOut("Your file does not include the label " + *it);
 221                         if (processedLabels.count(lastLabel) != 1) {
 222                                 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
 223                                 needToRun = true;
 224                         }else {
 225                                 mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
 226                         }
 227                 }
 228
 229                 //run last label if you need to
 230                 if (needToRun == true)  {
 231                         if (order != NULL) {    delete order;   }
 232                         order = (input->getOrderVector(lastLabel));
 233
 234                         rCurve = new Rarefact(order, rDisplays);
 235                         rCurve->getCurve(freq, nIters);
 236                         delete rCurve;
 237
 238                         mothurOut(order->getLabel()); mothurOutEndLine();
 239                         delete order;
 240                 }
 241
 242
 243                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 244                 return 0;
 245         }
 246         catch(exception& e) {
 247                 errorOut(e, "RareFactCommand", "execute");
 248                 exit(1);
 249         }
 250 }
 251
 252 //**********************************************************************************************************************