getrabundcommand.cpp

   1 /*
   2  *  getrabundcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 6/2/09.
   6  *  Copyright 2009 Schloss Lab Umass Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "getrabundcommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> GetRAbundCommand::getValidParameters(){
  14         try {
  15                 string Array[] =  {"label","sorted","outputdir","inputdir"};
  16                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  17                 return myArray;
  18         }
  19         catch(exception& e) {
  20                 m->errorOut(e, "GetRAbundCommand", "getValidParameters");
  21                 exit(1);
  22         }
  23 }
  24 //**********************************************************************************************************************
  25 GetRAbundCommand::GetRAbundCommand(){
  26         try {
  27                 abort = true; calledHelp = true;
  28                 vector<string> tempOutNames;
  29                 outputTypes["rabund"] = tempOutNames;
  30         }
  31         catch(exception& e) {
  32                 m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
  33                 exit(1);
  34         }
  35 }
  36 //**********************************************************************************************************************
  37 vector<string> GetRAbundCommand::getRequiredParameters(){
  38         try {
  39                 vector<string> myArray;
  40                 return myArray;
  41         }
  42         catch(exception& e) {
  43                 m->errorOut(e, "GetRAbundCommand", "getRequiredParameters");
  44                 exit(1);
  45         }
  46 }
  47 //**********************************************************************************************************************
  48 vector<string> GetRAbundCommand::getRequiredFiles(){
  49         try {
  50                 string Array[] =  {"list"};
  51                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  52
  53                 return myArray;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "GetRAbundCommand", "getRequiredFiles");
  57                 exit(1);
  58         }
  59 }
  60 //**********************************************************************************************************************
  61 GetRAbundCommand::GetRAbundCommand(string option)  {
  62         try {
  63                 globaldata = GlobalData::getInstance();
  64                 abort = false; calledHelp = false;
  65                 allLines = 1;
  66                 labels.clear();
  67
  68                 //allow user to run help
  69                 if(option == "help") { help(); abort = true; calledHelp = true; }
  70
  71                 else {
  72                         //valid paramters for this command
  73                         string Array[] =  {"label","sorted","outputdir","inputdir"};
  74                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  75
  76                         OptionParser parser(option);
  77                         map<string,string> parameters = parser.getParameters();
  78
  79                         ValidParameters validParameter;
  80
  81                         //check to make sure all parameters are valid for command
  82                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  83                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  84                         }
  85
  86                         //if the user changes the output directory command factory will send this info to us in the output parameter
  87                         string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found"){
  88                                 outputDir = "";
  89                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
  90                         }
  91
  92                         //initialize outputTypes
  93                         vector<string> tempOutNames;
  94                         outputTypes["rabund"] = tempOutNames;
  95
  96                         //make sure the user has already run the read.otu command
  97                         if (globaldata->getListFile() == "") { m->mothurOut("You must read a listfile before you can use the get.rabund command."); m->mothurOutEndLine(); abort = true; }
  98
  99                         //check for optional parameter and set defaults
 100                         // ...at some point should added some additional type checking...
 101
 102                         string temp;
 103                         temp = validParameter.validFile(parameters, "sorted", false);                   if (temp == "not found") { temp = "T"; }
 104                         sorted = m->isTrue(temp);
 105
 106                         label = validParameter.validFile(parameters, "label", false);
 107                         if (label == "not found") { label = ""; }
 108                         else {
 109                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 110                                 else { allLines = 1;  }
 111                         }
 112
 113                         //if the user has not specified any labels use the ones from read.otu
 114                         if(label == "") {
 115                                 allLines = globaldata->allLines;
 116                                 labels = globaldata->labels;
 117                         }
 118
 119                         if (abort == false) {
 120                                 filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "rabund";
 121                                 m->openOutputFile(filename, out);
 122                         }
 123                 }
 124
 125         }
 126         catch(exception& e) {
 127                 m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
 128                 exit(1);
 129         }
 130 }
 131 //**********************************************************************************************************************
 132
 133 void GetRAbundCommand::help(){
 134         try {
 135                 m->mothurOut("The get.rabund command can only be executed after a successful read.otu of a listfile.\n");
 136                 m->mothurOut("The get.rabund command parameters are label and sorted.  No parameters are required.\n");
 137                 m->mothurOut("The label parameter allows you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n");
 138                 m->mothurOut("The sorted parameters allows you to print the rabund results sorted by abundance or not.  The default is sorted.\n");
 139                 m->mothurOut("The get.rabund command should be in the following format: get.rabund(label=yourLabels, sorted=yourSorted).\n");
 140                 m->mothurOut("Example get.rabund(sorted=F).\n");
 141                 m->mothurOut("The default value for label is all labels in your inputfile.\n");
 142                 m->mothurOut("The get.rabund command outputs a .rabund file containing the lines you selected.\n");
 143                 m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
 144         }
 145         catch(exception& e) {
 146                 m->errorOut(e, "GetRAbundCommand", "help");
 147                 exit(1);
 148         }
 149 }
 150
 151 //**********************************************************************************************************************
 152
 153 GetRAbundCommand::~GetRAbundCommand(){}
 154
 155 //**********************************************************************************************************************
 156
 157 int GetRAbundCommand::execute(){
 158         try {
 159
 160                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 161
 162                 //read first line
 163                 read = new ReadOTUFile(globaldata->inputFileName);
 164                 read->read(&*globaldata);
 165
 166                 input = globaldata->ginput;
 167                 list = globaldata->gListVector;
 168                 string lastLabel = list->getLabel();
 169
 170                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 171                 set<string> processedLabels;
 172                 set<string> userLabels = labels;
 173
 174                 if (m->control_pressed) {  outputTypes.clear();  out.close(); remove(filename.c_str());  delete list; globaldata->gListVector = NULL;  return 0; }
 175
 176                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 177
 178                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
 179                                         m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 180                                         rabund = new RAbundVector();
 181                                         *rabund = (list->getRAbundVector());
 182
 183                                         if (m->control_pressed) {   outputTypes.clear(); out.close(); remove(filename.c_str());  delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
 184
 185
 186                                         if(sorted)      {   rabund->print(out);                         }
 187                                         else            {       rabund->nonSortedPrint(out);    }
 188
 189                                         delete rabund;
 190
 191                                         processedLabels.insert(list->getLabel());
 192                                         userLabels.erase(list->getLabel());
 193                         }
 194
 195                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 196                                         string saveLabel = list->getLabel();
 197
 198                                         delete list;
 199                                         list = input->getListVector(lastLabel);
 200
 201                                         m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 202                                         rabund = new RAbundVector();
 203                                         *rabund = (list->getRAbundVector());
 204
 205                                         if (m->control_pressed) {   outputTypes.clear(); out.close(); remove(filename.c_str());  delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
 206
 207                                         if(sorted)      {   rabund->print(out);                         }
 208                                         else            {       rabund->nonSortedPrint(out);    }
 209
 210                                         delete rabund;
 211
 212                                         processedLabels.insert(list->getLabel());
 213                                         userLabels.erase(list->getLabel());
 214
 215                                         //restore real lastlabel to save below
 216                                         list->setLabel(saveLabel);
 217                         }
 218
 219                         lastLabel = list->getLabel();
 220
 221                         delete list;
 222                         list = input->getListVector();
 223                 }
 224
 225                 //output error messages about any remaining user labels
 226                 set<string>::iterator it;
 227                 bool needToRun = false;
 228                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 229                         m->mothurOut("Your file does not include the label " + *it);
 230                         if (processedLabels.count(lastLabel) != 1) {
 231                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 232                                 needToRun = true;
 233                         }else {
 234                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 235                         }
 236                 }
 237
 238                 //run last label if you need to
 239                 if (needToRun == true)  {
 240                         if (list != NULL) {     delete list;    }
 241                         list = input->getListVector(lastLabel);
 242
 243                         m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 244                         rabund = new RAbundVector();
 245                         *rabund = (list->getRAbundVector());
 246
 247                         if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
 248
 249                         if(sorted)      {   rabund->print(out);                         }
 250                         else            {       rabund->nonSortedPrint(out);    }
 251
 252                         delete rabund;
 253                         delete list;
 254                 }
 255
 256                 m->mothurOutEndLine();
 257                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 258                 m->mothurOut(filename); m->mothurOutEndLine();  outputNames.push_back(filename); outputTypes["rabund"].push_back(filename);
 259                 m->mothurOutEndLine();
 260
 261                 out.close();
 262
 263                 globaldata->gListVector = NULL;
 264
 265                 //set rabund file as new current rabundfile
 266                 string current = "";
 267                 itTypes = outputTypes.find("rabund");
 268                 if (itTypes != outputTypes.end()) {
 269                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 270                 }
 271
 272                 return 0;
 273         }
 274
 275         catch(exception& e) {
 276                 m->errorOut(e, "GetRAbundCommand", "execute");
 277                 exit(1);
 278         }
 279 }
 280
 281 //**********************************************************************************************************************
 282
 283