rarefactsharedcommand.cpp

   1 /*
   2  *  rarefactsharedcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/6/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "rarefactsharedcommand.h"
  11 #include "sharedsobs.h"
  12 #include "sharednseqs.h"
  13
  14 //**********************************************************************************************************************
  15
  16 RareFactSharedCommand::RareFactSharedCommand(string option){
  17         try {
  18                 globaldata = GlobalData::getInstance();
  19
  20                 abort = false;
  21                 allLines = 1;
  22                 labels.clear();
  23                 Estimators.clear();
  24                 Groups.clear();
  25
  26                 //allow user to run help
  27                 if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
  28
  29                 else {
  30                         //valid paramters for this command
  31                         string Array[] =  {"iters","label","calc","groups", "jumble","outputdir","inputdir"};
  32                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  33
  34                         OptionParser parser(option);
  35                         map<string,string> parameters = parser.getParameters();
  36
  37                         ValidParameters validParameter;
  38
  39                         //check to make sure all parameters are valid for command
  40                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  41                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  42                         }
  43
  44                         //make sure the user has already run the read.otu command
  45                         if (globaldata->getSharedFile() == "") {
  46                                 if (globaldata->getListFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); mothurOutEndLine(); abort = true; }
  47                                 else if (globaldata->getGroupFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); mothurOutEndLine(); abort = true; }
  48                         }
  49
  50                         //if the user changes the output directory command factory will send this info to us in the output parameter
  51                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  52                                 outputDir = "";
  53                                 outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
  54                         }
  55
  56
  57                         //check for optional parameter and set defaults
  58                         // ...at some point should added some additional type checking...
  59                         label = validParameter.validFile(parameters, "label", false);
  60                         if (label == "not found") { label = ""; }
  61                         else {
  62                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  63                                 else { allLines = 1;  }
  64                         }
  65
  66                         //if the user has not specified any labels use the ones from read.otu
  67                         if(label == "") {
  68                                 allLines = globaldata->allLines;
  69                                 labels = globaldata->labels;
  70                         }
  71
  72                         calc = validParameter.validFile(parameters, "calc", false);
  73                         if (calc == "not found") { calc = "sharedobserved";  }
  74                         else {
  75                                  if (calc == "default")  {  calc = "sharedobserved";  }
  76                         }
  77                         splitAtDash(calc, Estimators);
  78
  79                         groups = validParameter.validFile(parameters, "groups", false);
  80                         if (groups == "not found") { groups = ""; }
  81                         else {
  82                                 splitAtDash(groups, Groups);
  83                         }
  84                         globaldata->Groups = Groups;
  85
  86                         string temp;
  87                         temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
  88                         convert(temp, nIters);
  89
  90                         temp = validParameter.validFile(parameters, "jumble", false);                   if (temp == "not found") { temp = "T"; }
  91                         if (isTrue(temp)) { jumble = true; }
  92                         else { jumble = false; }
  93                         globaldata->jumble = jumble;
  94
  95                         if (abort == false) {
  96
  97                                 string fileNameRoot = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
  98 //                              format = globaldata->getFormat();
  99
 100
 101                                 validCalculator = new ValidCalculators();
 102
 103                                 for (int i=0; i<Estimators.size(); i++) {
 104                                         if (validCalculator->isValidCalculator("sharedrarefaction", Estimators[i]) == true) {
 105                                                 if (Estimators[i] == "sharedobserved") {
 106                                                         rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
 107                                                 }else if (Estimators[i] == "sharednseqs") {
 108                                                         rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
 109                                                 }
 110                                         }
 111                                 }
 112                         }
 113
 114                 }
 115
 116         }
 117         catch(exception& e) {
 118                 errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand");
 119                 exit(1);
 120         }
 121 }
 122
 123 //**********************************************************************************************************************
 124
 125 void RareFactSharedCommand::help(){
 126         try {
 127                 mothurOut("The rarefaction.shared command can only be executed after a successful read.otu command.\n");
 128                 mothurOut("The rarefaction.shared command parameters are label, iters, groups, jumble and calc.  No parameters are required.\n");
 129                 mothurOut("The rarefaction command should be in the following format: \n");
 130                 mothurOut("rarefaction.shared(label=yourLabel, iters=yourIters, calc=yourEstimators, jumble=yourJumble, groups=yourGroups).\n");
 131                 mothurOut("Example rarefaction.shared(label=unique-0.01-0.03,  iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n");
 132                 mothurOut("The default values for iters is 1000, freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness.\n");
 133                 mothurOut("The default value for groups is all the groups in your groupfile, and jumble is true.\n");
 134                 validCalculator->printCalc("sharedrarefaction", cout);
 135                 mothurOut("The label parameter is used to analyze specific labels in your input.\n");
 136                 mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups.\n");
 137                 mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
 138         }
 139         catch(exception& e) {
 140                 errorOut(e, "RareFactSharedCommand", "help");
 141                 exit(1);
 142         }
 143 }
 144
 145 //**********************************************************************************************************************
 146
 147 RareFactSharedCommand::~RareFactSharedCommand(){
 148         if (abort == false) {
 149                 delete input;   globaldata->ginput = NULL;
 150                 delete read;
 151                 delete validCalculator;
 152         }
 153 }
 154
 155 //**********************************************************************************************************************
 156
 157 int RareFactSharedCommand::execute(){
 158         try {
 159
 160                 if (abort == true) { return 0; }
 161
 162                 //if the users entered no valid calculators don't execute command
 163                 if (rDisplays.size() == 0) { return 0; }
 164
 165                 read = new ReadOTUFile(globaldata->inputFileName);
 166                 read->read(&*globaldata);
 167
 168                 input = globaldata->ginput;
 169                 lookup = input->getSharedRAbundVectors();
 170                 string lastLabel = lookup[0]->getLabel();
 171
 172                 if (lookup.size() < 2) {
 173                         mothurOut("I cannot run the command without at least 2 valid groups.");
 174                         for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
 175                         return 0;
 176                 }
 177
 178                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 179                 set<string> processedLabels;
 180                 set<string> userLabels = labels;
 181
 182                 //as long as you are not at the end of the file or done wih the lines you want
 183                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 184
 185                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 186
 187                                 rCurve = new Rarefact(lookup, rDisplays);
 188                                 rCurve->getSharedCurve(freq, nIters);
 189                                 delete rCurve;
 190
 191                                 mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 192                                 processedLabels.insert(lookup[0]->getLabel());
 193                                 userLabels.erase(lookup[0]->getLabel());
 194                         }
 195
 196                         if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 197                                         string saveLabel = lookup[0]->getLabel();
 198
 199                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 200                                         lookup = input->getSharedRAbundVectors(lastLabel);
 201
 202                                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 203                                         rCurve = new Rarefact(lookup, rDisplays);
 204                                         rCurve->getSharedCurve(freq, nIters);
 205                                         delete rCurve;
 206
 207                                         processedLabels.insert(lookup[0]->getLabel());
 208                                         userLabels.erase(lookup[0]->getLabel());
 209
 210                                         //restore real lastlabel to save below
 211                                         lookup[0]->setLabel(saveLabel);
 212                         }
 213
 214
 215                         lastLabel = lookup[0]->getLabel();
 216
 217                         //get next line to process
 218                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 219                         lookup = input->getSharedRAbundVectors();
 220                 }
 221
 222                 //output error messages about any remaining user labels
 223                 set<string>::iterator it;
 224                 bool needToRun = false;
 225                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 226                         mothurOut("Your file does not include the label " + *it);
 227                         if (processedLabels.count(lastLabel) != 1) {
 228                                 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
 229                                 needToRun = true;
 230                         }else {
 231                                 mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
 232                         }
 233                 }
 234
 235                 //run last label if you need to
 236                 if (needToRun == true)  {
 237                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i]; }  }
 238                         lookup = input->getSharedRAbundVectors(lastLabel);
 239
 240                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 241                         rCurve = new Rarefact(lookup, rDisplays);
 242                         rCurve->getSharedCurve(freq, nIters);
 243                         delete rCurve;
 244                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 245                 }
 246
 247                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 248
 249                 //reset groups parameter
 250                 globaldata->Groups.clear();
 251
 252                 return 0;
 253         }
 254         catch(exception& e) {
 255                 errorOut(e, "RareFactSharedCommand", "execute");
 256                 exit(1);
 257         }
 258 }
 259
 260
 261 //**********************************************************************************************************************