getrelabundcommand.cpp

   1 /*
   2  *  getrelabundcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 6/21/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "getrelabundcommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> GetRelAbundCommand::setParameters(){
  14         try {
  15                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","relabund",false,true, true); parameters.push_back(pshared);
  16                 CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
  17                 CommandParameter pscale("scale", "Multiple", "totalgroup-totalotu-averagegroup-averageotu", "totalgroup", "", "", "","",false,false); parameters.push_back(pscale);
  18                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  19                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  20                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  21
  22                 vector<string> myArray;
  23                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  24                 return myArray;
  25         }
  26         catch(exception& e) {
  27                 m->errorOut(e, "GetRelAbundCommand", "setParameters");
  28                 exit(1);
  29         }
  30 }
  31 //**********************************************************************************************************************
  32 string GetRelAbundCommand::getHelpString(){
  33         try {
  34                 string helpString = "";
  35                 helpString += "The get.relabund command parameters are shared, groups, scale and label.  shared is required, unless you have a valid current file.\n";
  36                 helpString += "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";
  37                 helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";
  38                 helpString += "The scale parameter allows you to select what scale you would like to use. Choices are totalgroup, totalotu, averagegroup, averageotu, default is totalgroup.\n";
  39                 helpString += "The get.relabund command should be in the following format: get.relabund(groups=yourGroups, label=yourLabels).\n";
  40                 helpString += "Example get.relabund(groups=A-B-C, scale=averagegroup).\n";
  41                 helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
  42                 helpString += "The get.relabund command outputs a .relabund file.\n";
  43                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  44                 return helpString;
  45         }
  46         catch(exception& e) {
  47                 m->errorOut(e, "GetRelAbundCommand", "getHelpString");
  48                 exit(1);
  49         }
  50 }
  51 //**********************************************************************************************************************
  52 string GetRelAbundCommand::getOutputPattern(string type) {
  53     try {
  54         string pattern = "";
  55
  56         if (type == "relabund")      {   pattern = "[filename],relabund";    }
  57         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  58
  59         return pattern;
  60     }
  61     catch(exception& e) {
  62         m->errorOut(e, "GetRelAbundCommand", "getOutputPattern");
  63         exit(1);
  64     }
  65 }
  66 //**********************************************************************************************************************
  67 GetRelAbundCommand::GetRelAbundCommand(){
  68         try {
  69                 abort = true; calledHelp = true;
  70                 setParameters();
  71                 vector<string> tempOutNames;
  72                 outputTypes["relabund"] = tempOutNames;
  73         }
  74         catch(exception& e) {
  75                 m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
  76                 exit(1);
  77         }
  78 }
  79 //**********************************************************************************************************************
  80 GetRelAbundCommand::GetRelAbundCommand(string option) {
  81         try {
  82                 abort = false; calledHelp = false;
  83                 allLines = 1;
  84
  85                 //allow user to run help
  86                 if(option == "help") { help(); abort = true; calledHelp = true; }
  87                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  88
  89                 else {
  90                         vector<string> myArray = setParameters();
  91
  92                         OptionParser parser(option);
  93                         map<string,string> parameters = parser.getParameters();
  94                         map<string,string>::iterator it;
  95
  96                         ValidParameters validParameter;
  97
  98                         //check to make sure all parameters are valid for command
  99                         for (it = parameters.begin(); it != parameters.end(); it++) {
 100                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 101                         }
 102
 103                         //initialize outputTypes
 104                         vector<string> tempOutNames;
 105                         outputTypes["relabund"] = tempOutNames;
 106
 107                         //if the user changes the input directory command factory will send this info to us in the output parameter
 108                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 109                         if (inputDir == "not found"){   inputDir = "";          }
 110                         else {
 111                                 string path;
 112                                 it = parameters.find("shared");
 113                                 //user has given a template file
 114                                 if(it != parameters.end()){
 115                                         path = m->hasPath(it->second);
 116                                         //if the user has not given a path then, add inputdir. else leave path alone.
 117                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 118                                 }
 119                         }
 120
 121                         //get shared file
 122                         sharedfile = validParameter.validFile(parameters, "shared", true);
 123                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 124                         else if (sharedfile == "not found") {
 125                                 //if there is a current shared file, use it
 126                                 sharedfile = m->getSharedFile();
 127                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 128                                 else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
 129                         }else { m->setSharedFile(sharedfile); }
 130
 131
 132                         //if the user changes the output directory command factory will send this info to us in the output parameter
 133                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(sharedfile);             }
 134
 135                         //check for optional parameter and set defaults
 136                         // ...at some point should added some additional type checking...
 137                         label = validParameter.validFile(parameters, "label", false);
 138                         if (label == "not found") { label = ""; }
 139                         else {
 140                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 141                                 else { allLines = 1;  }
 142                         }
 143
 144                         groups = validParameter.validFile(parameters, "groups", false);
 145                         if (groups == "not found") { groups = ""; pickedGroups = false; }
 146                         else {
 147                                 pickedGroups = true;
 148                                 m->splitAtDash(groups, Groups);
 149                                 m->setGroups(Groups);
 150                         }
 151
 152                         scale = validParameter.validFile(parameters, "scale", false);                           if (scale == "not found") { scale = "totalgroup"; }
 153
 154                         if ((scale != "totalgroup") && (scale != "totalotu") && (scale != "averagegroup") && (scale != "averageotu")) {
 155                                 m->mothurOut(scale + " is not a valid scaling option for the get.relabund command. Choices are totalgroup, totalotu, averagegroup, averageotu."); m->mothurOutEndLine(); abort = true;
 156                         }
 157                 }
 158
 159         }
 160         catch(exception& e) {
 161                 m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
 162                 exit(1);
 163         }
 164 }
 165 //**********************************************************************************************************************
 166
 167 int GetRelAbundCommand::execute(){
 168         try {
 169
 170                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 171
 172         map<string, string> variables;
 173                 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
 174                 string outputFileName = getOutputFileName("relabund", variables);
 175                 ofstream out;
 176                 m->openOutputFile(outputFileName, out);
 177                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 178
 179                 input = new InputData(sharedfile, "sharedfile");
 180                 lookup = input->getSharedRAbundVectors();
 181                 string lastLabel = lookup[0]->getLabel();
 182
 183                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 184                 set<string> processedLabels;
 185                 set<string> userLabels = labels;
 186
 187                 //as long as you are not at the end of the file or done wih the lines you want
 188                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 189
 190                         if (m->control_pressed) {  outputTypes.clear();  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups(); delete input;  out.close(); m->mothurRemove(outputFileName); return 0; }
 191
 192                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 193
 194                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 195                                 if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 196                                 getRelAbundance(lookup, out);
 197
 198                                 processedLabels.insert(lookup[0]->getLabel());
 199                                 userLabels.erase(lookup[0]->getLabel());
 200                         }
 201
 202                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 203                                 string saveLabel = lookup[0]->getLabel();
 204
 205                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 206                                 lookup = input->getSharedRAbundVectors(lastLabel);
 207                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 208                                 if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 209                                 getRelAbundance(lookup, out);
 210
 211                                 processedLabels.insert(lookup[0]->getLabel());
 212                                 userLabels.erase(lookup[0]->getLabel());
 213
 214                                 //restore real lastlabel to save below
 215                                 lookup[0]->setLabel(saveLabel);
 216                         }
 217
 218                         lastLabel = lookup[0]->getLabel();
 219                         //prevent memory leak
 220                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 221
 222                         if (m->control_pressed) {  outputTypes.clear();  m->clearGroups(); delete input;  out.close(); m->mothurRemove(outputFileName); return 0; }
 223
 224                         //get next line to process
 225                         lookup = input->getSharedRAbundVectors();
 226                 }
 227
 228                 if (m->control_pressed) { outputTypes.clear(); m->clearGroups(); delete input;  out.close(); m->mothurRemove(outputFileName);  return 0; }
 229
 230                 //output error messages about any remaining user labels
 231                 set<string>::iterator it;
 232                 bool needToRun = false;
 233                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 234                         m->mothurOut("Your file does not include the label " + *it);
 235                         if (processedLabels.count(lastLabel) != 1) {
 236                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 237                                 needToRun = true;
 238                         }else {
 239                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 240                         }
 241                 }
 242
 243                 //run last label if you need to
 244                 if (needToRun == true)  {
 245                         for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 246                         lookup = input->getSharedRAbundVectors(lastLabel);
 247
 248                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 249                         if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
 250                         getRelAbundance(lookup, out);
 251
 252                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 253                 }
 254
 255                 //reset groups parameter
 256                 m->clearGroups();
 257                 delete input;
 258                 out.close();
 259
 260                 if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0;}
 261
 262                 m->mothurOutEndLine();
 263                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 264                 m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["relabund"].push_back(outputFileName);
 265                 m->mothurOutEndLine();
 266
 267                 //set relabund file as new current relabundfile
 268                 string current = "";
 269                 itTypes = outputTypes.find("relabund");
 270                 if (itTypes != outputTypes.end()) {
 271                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRelAbundFile(current); }
 272                 }
 273
 274                 return 0;
 275         }
 276         catch(exception& e) {
 277                 m->errorOut(e, "GetRelAbundCommand", "execute");
 278                 exit(1);
 279         }
 280 }
 281 //**********************************************************************************************************************
 282
 283 int GetRelAbundCommand::getRelAbundance(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
 284         try {
 285
 286                  for (int i = 0; i < thisLookUp.size(); i++) {
 287                         out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t' << thisLookUp[i]->getNumBins() << '\t';
 288
 289                         for (int j = 0; j < thisLookUp[i]->getNumBins(); j++) {
 290
 291                                 if (m->control_pressed) { return 0; }
 292
 293                                 int abund = thisLookUp[i]->getAbundance(j);
 294
 295                                 float relabund = 0.0;
 296
 297                                 if (scale == "totalgroup") {
 298                                         relabund = abund / (float) thisLookUp[i]->getNumSeqs();
 299                                 }else if (scale == "totalotu") {
 300                                         //calc the total in this otu
 301                                         int totalOtu = 0;
 302                                         for (int l = 0; l < thisLookUp.size(); l++) {  totalOtu += thisLookUp[l]->getAbundance(j); }
 303                                         relabund = abund / (float) totalOtu;
 304                                 }else if (scale == "averagegroup") {
 305                                         relabund = abund / (float) (thisLookUp[i]->getNumSeqs() / (float) thisLookUp[i]->getNumBins());
 306                                 }else if (scale == "averageotu") {
 307                                         //calc the total in this otu
 308                                         int totalOtu = 0;
 309                                         for (int l = 0; l < thisLookUp.size(); l++) {  totalOtu += thisLookUp[l]->getAbundance(j); }
 310                                         float averageOtu = totalOtu / (float) thisLookUp.size();
 311
 312                                         relabund = abund / (float) averageOtu;
 313                                 }else{ m->mothurOut(scale + " is not a valid scaling option."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
 314
 315                                 out << relabund << '\t';
 316                         }
 317                         out << endl;
 318                  }
 319
 320                  return 0;
 321         }
 322         catch(exception& e) {
 323                 m->errorOut(e, "GetRelAbundCommand", "getRelAbundance");
 324                 exit(1);
 325         }
 326 }
 327 //**********************************************************************************************************************
 328
 329