subsamplecommand.cpp

   1 /*
   2  *  subsamplecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 10/27/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "subsamplecommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> SubSampleCommand::getValidParameters(){
  14         try {
  15                 string Array[] =  {"groups","label","outputdir","inputdir"};
  16                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  17                 return myArray;
  18         }
  19         catch(exception& e) {
  20                 m->errorOut(e, "SubSampleCommand", "getValidParameters");
  21                 exit(1);
  22         }
  23 }
  24 //**********************************************************************************************************************
  25 SubSampleCommand::SubSampleCommand(){
  26         try {
  27                 abort = true;
  28                 //initialize outputTypes
  29                 vector<string> tempOutNames;
  30                 outputTypes["shared"] = tempOutNames;
  31                 outputTypes["list"] = tempOutNames;
  32                 outputTypes["rabund"] = tempOutNames;
  33                 outputTypes["sabund"] = tempOutNames;
  34         }
  35         catch(exception& e) {
  36                 m->errorOut(e, "SubSampleCommand", "GetRelAbundCommand");
  37                 exit(1);
  38         }
  39 }
  40 //**********************************************************************************************************************
  41 vector<string> SubSampleCommand::getRequiredParameters(){
  42         try {
  43                 vector<string> myArray;
  44                 return myArray;
  45         }
  46         catch(exception& e) {
  47                 m->errorOut(e, "SubSampleCommand", "getRequiredParameters");
  48                 exit(1);
  49         }
  50 }
  51 //**********************************************************************************************************************
  52 vector<string> SubSampleCommand::getRequiredFiles(){
  53         try {
  54                 string Array[] =  {"shared","list","rabund","sabund","or"};
  55                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  56                 return myArray;
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "SubSampleCommand", "getRequiredFiles");
  60                 exit(1);
  61         }
  62 }
  63 //**********************************************************************************************************************
  64 SubSampleCommand::SubSampleCommand(string option) {
  65         try {
  66                 globaldata = GlobalData::getInstance();
  67                 abort = false;
  68                 allLines = 1;
  69                 labels.clear();
  70
  71                 //allow user to run help
  72                 if(option == "help") { help(); abort = true; }
  73
  74                 else {
  75                         //valid paramters for this command
  76                         string AlignArray[] =  {"groups","label","outputdir","inputdir"};
  77                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  78
  79                         OptionParser parser(option);
  80                         map<string,string> parameters = parser.getParameters();
  81
  82                         ValidParameters validParameter;
  83
  84                         //check to make sure all parameters are valid for command
  85                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  86                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  87                         }
  88
  89                         //initialize outputTypes
  90                         vector<string> tempOutNames;
  91                         outputTypes["shared"] = tempOutNames;
  92                         outputTypes["list"] = tempOutNames;
  93                         outputTypes["rabund"] = tempOutNames;
  94                         outputTypes["sabund"] = tempOutNames;
  95
  96                         //if the user changes the output directory command factory will send this info to us in the output parameter
  97                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  98                                 outputDir = "";
  99                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
 100                         }
 101
 102                         //make sure the user has already run the read.otu command
 103                         if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund, rabund or shared file before you can use the sub.sample command."); m->mothurOutEndLine(); abort = true; }
 104
 105                         //check for optional parameter and set defaults
 106                         // ...at some point should added some additional type checking...
 107                         label = validParameter.validFile(parameters, "label", false);
 108                         if (label == "not found") { label = ""; }
 109                         else {
 110                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 111                                 else { allLines = 1;  }
 112                         }
 113
 114                         //if the user has not specified any labels use the ones from read.otu
 115                         if (label == "") {
 116                                 allLines = globaldata->allLines;
 117                                 labels = globaldata->labels;
 118                         }
 119
 120                         groups = validParameter.validFile(parameters, "groups", false);
 121                         if (groups == "not found") { groups = ""; pickedGroups = false; }
 122                         else {
 123                                 pickedGroups = true;
 124                                 m->splitAtDash(groups, Groups);
 125                                 globaldata->Groups = Groups;
 126                         }
 127
 128                 }
 129
 130         }
 131         catch(exception& e) {
 132                 m->errorOut(e, "SubSampleCommand", "SubSampleCommand");
 133                 exit(1);
 134         }
 135 }
 136
 137 //**********************************************************************************************************************
 138
 139 void SubSampleCommand::help(){
 140         try {
 141                 m->mothurOut("The get.relabund command can only be executed after a successful read.otu command of a list and group or shared file.\n");
 142                 m->mothurOut("The get.relabund command parameters are groups, scale and label.  No parameters are required.\n");
 143                 m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n");
 144                 m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");
 145                 m->mothurOut("The scale parameter allows you to select what scale you would like to use. Choices are totalgroup, totalotu, averagegroup, averageotu, default is totalgroup.\n");
 146                 m->mothurOut("The get.relabund command should be in the following format: get.relabund(groups=yourGroups, label=yourLabels).\n");
 147                 m->mothurOut("Example get.relabund(groups=A-B-C, scale=averagegroup).\n");
 148                 m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
 149                 m->mothurOut("The get.relabund command outputs a .relabund file.\n");
 150                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 151
 152         }
 153         catch(exception& e) {
 154                 m->errorOut(e, "SubSampleCommand", "help");
 155                 exit(1);
 156         }
 157 }
 158
 159 //**********************************************************************************************************************
 160
 161 SubSampleCommand::~SubSampleCommand(){
 162 }
 163
 164 //**********************************************************************************************************************
 165
 166 int SubSampleCommand::execute(){
 167         try {
 168
 169                 if (abort == true) { return 0; }
 170
 171                 string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "subsample" +  m->getExtension(globaldata->inputFileName);
 172                 ofstream out;
 173                 m->openOutputFile(outputFileName, out);
 174                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 175
 176                 string format = globaldata->getFormat();
 177
 178                 read = new ReadOTUFile(globaldata->inputFileName);
 179                 read->read(&*globaldata);
 180                 input = globaldata->ginput;
 181
 182                 if (format == "sharedfile") {
 183                         lookup = input->getSharedRAbundVectors();
 184                         outputTypes["shared"].push_back(outputFileName);
 185                         getSubSampleShared(lookup, out);
 186                 }else if (format == "list") {
 187                         list = globaldata->glist;
 188                         outputTypes["list"].push_back(outputFileName);
 189                         //getSubSamplesList();
 190                 }else if (format == "rabund") {
 191                         rabund = globaldata->rabund;
 192                         outputTypes["rabund"].push_back(outputFileName);
 193                         //getSubSamplesRabund();
 194
 195                 }else if (format == "sabund") {
 196                         sabund = globaldata->sabund;
 197                         outputTypes["sabund"].push_back(outputFileName);
 198                         //getSubSamplesSabund();
 199                 }
 200
 201                 out.close();
 202
 203                 //reset groups parameter
 204                 delete input; globaldata->ginput = NULL;
 205                 delete read;
 206
 207                 if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0;}
 208
 209                 m->mothurOutEndLine();
 210                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 211                 m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName);
 212                 m->mothurOutEndLine();
 213
 214                 return 0;
 215         }
 216         catch(exception& e) {
 217                 m->errorOut(e, "SubSampleCommand", "execute");
 218                 exit(1);
 219         }
 220 }
 221 //**********************************************************************************************************************
 222 int SubSampleCommand::getSubSampleShared(vector<SharedRAbundVector*>& thislookup, ofstream& filename) {
 223         try {
 224
 225                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 226                 set<string> processedLabels;
 227                 set<string> userLabels = labels;
 228
 229                 string lastLabel = lookup[0]->getLabel();
 230
 231                 //as long as you are not at the end of the file or done wih the lines you want
 232                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 233                         if (m->control_pressed) {  return 0;  }
 234
 235                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 236
 237                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 238
 239                                 //process lookup
 240
 241
 242
 243                                 processedLabels.insert(lookup[0]->getLabel());
 244                                 userLabels.erase(lookup[0]->getLabel());
 245                         }
 246
 247                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 248                                 string saveLabel = lookup[0]->getLabel();
 249
 250                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 251
 252                                 lookup = input->getSharedRAbundVectors(lastLabel);
 253                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 254
 255                                 //process lookup
 256                                 processedLabels.insert(lookup[0]->getLabel());
 257                                 userLabels.erase(lookup[0]->getLabel());
 258
 259                                 //restore real lastlabel to save below
 260                                 lookup[0]->setLabel(saveLabel);
 261                         }
 262
 263                         lastLabel = lookup[0]->getLabel();
 264                         //prevent memory leak
 265                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 266
 267                         //get next line to process
 268                         lookup = input->getSharedRAbundVectors();
 269                 }
 270
 271
 272                 if (m->control_pressed) {  return 0;  }
 273
 274                 //output error messages about any remaining user labels
 275                 set<string>::iterator it;
 276                 bool needToRun = false;
 277                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 278                         m->mothurOut("Your file does not include the label " + *it);
 279                         if (processedLabels.count(lastLabel) != 1) {
 280                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 281                                 needToRun = true;
 282                         }else {
 283                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 284                         }
 285                 }
 286
 287                 //run last label if you need to
 288                 if (needToRun == true)  {
 289                         for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 290                         lookup = input->getSharedRAbundVectors(lastLabel);
 291
 292                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 293
 294                         //process lookup
 295
 296
 297
 298                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 299                 }
 300
 301                 //reset groups parameter
 302                 globaldata->Groups.clear();
 303
 304                 return 0;
 305
 306         }
 307         catch(exception& e) {
 308                 m->errorOut(e, "SubSampleCommand", "getSubSampleShared");
 309                 exit(1);
 310         }
 311 }
 312
 313
 314 //**********************************************************************************************************************
 315 int SubSampleCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
 316         try {
 317
 318                 vector<SharedRAbundVector*> newLookup;
 319                 for (int i = 0; i < thislookup.size(); i++) {
 320                         SharedRAbundVector* temp = new SharedRAbundVector();
 321                         temp->setLabel(thislookup[i]->getLabel());
 322                         temp->setGroup(thislookup[i]->getGroup());
 323                         newLookup.push_back(temp);
 324                 }
 325
 326                 //for each bin
 327                 for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
 328                         if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
 329
 330                         //look at each sharedRabund and make sure they are not all zero
 331                         bool allZero = true;
 332                         for (int j = 0; j < thislookup.size(); j++) {
 333                                 if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
 334                         }
 335
 336                         //if they are not all zero add this bin
 337                         if (!allZero) {
 338                                 for (int j = 0; j < thislookup.size(); j++) {
 339                                         newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
 340                                 }
 341                         }
 342                 }
 343
 344                 for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
 345
 346                 thislookup = newLookup;
 347
 348                 return 0;
 349
 350         }
 351         catch(exception& e) {
 352                 m->errorOut(e, "SubSampleCommand", "eliminateZeroOTUS");
 353                 exit(1);
 354         }
 355 }
 356
 357 //**********************************************************************************************************************
 358
 359