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",false,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 GetRelAbundCommand::GetRelAbundCommand(){
  53         try {
  54                 abort = true; calledHelp = true;
  55                 setParameters();
  56                 vector<string> tempOutNames;
  57                 outputTypes["relabund"] = tempOutNames;
  58         }
  59         catch(exception& e) {
  60                 m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
  61                 exit(1);
  62         }
  63 }
  64 //**********************************************************************************************************************
  65 GetRelAbundCommand::GetRelAbundCommand(string option) {
  66         try {
  67                 abort = false; calledHelp = false;
  68                 allLines = 1;
  69
  70                 //allow user to run help
  71                 if(option == "help") { help(); abort = true; calledHelp = true; }
  72
  73                 else {
  74                         vector<string> myArray = setParameters();
  75
  76                         OptionParser parser(option);
  77                         map<string,string> parameters = parser.getParameters();
  78                         map<string,string>::iterator it;
  79
  80                         ValidParameters validParameter;
  81
  82                         //check to make sure all parameters are valid for command
  83                         for (it = parameters.begin(); it != parameters.end(); it++) {
  84                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  85                         }
  86
  87                         //initialize outputTypes
  88                         vector<string> tempOutNames;
  89                         outputTypes["relabund"] = tempOutNames;
  90
  91                         //if the user changes the input directory command factory will send this info to us in the output parameter
  92                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  93                         if (inputDir == "not found"){   inputDir = "";          }
  94                         else {
  95                                 string path;
  96                                 it = parameters.find("shared");
  97                                 //user has given a template file
  98                                 if(it != parameters.end()){
  99                                         path = m->hasPath(it->second);
 100                                         //if the user has not given a path then, add inputdir. else leave path alone.
 101                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 102                                 }
 103                         }
 104
 105                         //get shared file
 106                         sharedfile = validParameter.validFile(parameters, "shared", true);
 107                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 108                         else if (sharedfile == "not found") {
 109                                 //if there is a current shared file, use it
 110                                 sharedfile = m->getSharedFile();
 111                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 112                                 else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
 113                         }
 114
 115
 116                         //if the user changes the output directory command factory will send this info to us in the output parameter
 117                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(sharedfile);             }
 118
 119                         //check for optional parameter and set defaults
 120                         // ...at some point should added some additional type checking...
 121                         label = validParameter.validFile(parameters, "label", false);
 122                         if (label == "not found") { label = ""; }
 123                         else {
 124                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 125                                 else { allLines = 1;  }
 126                         }
 127
 128                         groups = validParameter.validFile(parameters, "groups", false);
 129                         if (groups == "not found") { groups = ""; pickedGroups = false; }
 130                         else {
 131                                 pickedGroups = true;
 132                                 m->splitAtDash(groups, Groups);
 133                                 m->Groups = Groups;
 134                         }
 135
 136                         scale = validParameter.validFile(parameters, "scale", false);                           if (scale == "not found") { scale = "totalgroup"; }
 137
 138                         if ((scale != "totalgroup") && (scale != "totalotu") && (scale != "averagegroup") && (scale != "averageotu")) {
 139                                 m->mothurOut(scale + " is not a valid scaling option for the get.relabund command. Choices are totalgroup, totalotu, averagegroup, averageotu."); m->mothurOutEndLine(); abort = true;
 140                         }
 141                 }
 142
 143         }
 144         catch(exception& e) {
 145                 m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
 146                 exit(1);
 147         }
 148 }
 149 //**********************************************************************************************************************
 150
 151 int GetRelAbundCommand::execute(){
 152         try {
 153
 154                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 155
 156                 string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "relabund";
 157                 ofstream out;
 158                 m->openOutputFile(outputFileName, out);
 159                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 160
 161                 input = new InputData(sharedfile, "sharedfile");
 162                 lookup = input->getSharedRAbundVectors();
 163                 string lastLabel = lookup[0]->getLabel();
 164
 165                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 166                 set<string> processedLabels;
 167                 set<string> userLabels = labels;
 168
 169                 //as long as you are not at the end of the file or done wih the lines you want
 170                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 171
 172                         if (m->control_pressed) {  outputTypes.clear();  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear(); delete input;  out.close(); remove(outputFileName.c_str()); return 0; }
 173
 174                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 175
 176                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 177                                 getRelAbundance(lookup, out);
 178
 179                                 processedLabels.insert(lookup[0]->getLabel());
 180                                 userLabels.erase(lookup[0]->getLabel());
 181                         }
 182
 183                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 184                                 string saveLabel = lookup[0]->getLabel();
 185
 186                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 187                                 lookup = input->getSharedRAbundVectors(lastLabel);
 188                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 189
 190                                 getRelAbundance(lookup, out);
 191
 192                                 processedLabels.insert(lookup[0]->getLabel());
 193                                 userLabels.erase(lookup[0]->getLabel());
 194
 195                                 //restore real lastlabel to save below
 196                                 lookup[0]->setLabel(saveLabel);
 197                         }
 198
 199                         lastLabel = lookup[0]->getLabel();
 200                         //prevent memory leak
 201                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 202
 203                         if (m->control_pressed) {  outputTypes.clear();  m->Groups.clear(); delete input;  out.close(); remove(outputFileName.c_str()); return 0; }
 204
 205                         //get next line to process
 206                         lookup = input->getSharedRAbundVectors();
 207                 }
 208
 209                 if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); delete input;  out.close(); remove(outputFileName.c_str());  return 0; }
 210
 211                 //output error messages about any remaining user labels
 212                 set<string>::iterator it;
 213                 bool needToRun = false;
 214                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 215                         m->mothurOut("Your file does not include the label " + *it);
 216                         if (processedLabels.count(lastLabel) != 1) {
 217                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 218                                 needToRun = true;
 219                         }else {
 220                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 221                         }
 222                 }
 223
 224                 //run last label if you need to
 225                 if (needToRun == true)  {
 226                         for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 227                         lookup = input->getSharedRAbundVectors(lastLabel);
 228
 229                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 230
 231                         getRelAbundance(lookup, out);
 232
 233                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 234                 }
 235
 236                 //reset groups parameter
 237                 m->Groups.clear();
 238                 delete input;
 239                 out.close();
 240
 241                 if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0;}
 242
 243                 m->mothurOutEndLine();
 244                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 245                 m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["relabund"].push_back(outputFileName);
 246                 m->mothurOutEndLine();
 247
 248                 //set relabund file as new current relabundfile
 249                 string current = "";
 250                 itTypes = outputTypes.find("relabund");
 251                 if (itTypes != outputTypes.end()) {
 252                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRelAbundFile(current); }
 253                 }
 254
 255                 return 0;
 256         }
 257         catch(exception& e) {
 258                 m->errorOut(e, "GetRelAbundCommand", "execute");
 259                 exit(1);
 260         }
 261 }
 262 //**********************************************************************************************************************
 263
 264 int GetRelAbundCommand::getRelAbundance(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
 265         try {
 266
 267                  for (int i = 0; i < thisLookUp.size(); i++) {
 268                         out << thisLookUp[i]->getLabel() << '\t' << thisLookUp[i]->getGroup() << '\t' << thisLookUp[i]->getNumBins() << '\t';
 269
 270                         for (int j = 0; j < thisLookUp[i]->getNumBins(); j++) {
 271
 272                                 if (m->control_pressed) { return 0; }
 273
 274                                 int abund = thisLookUp[i]->getAbundance(j);
 275
 276                                 float relabund = 0.0;
 277
 278                                 if (scale == "totalgroup") {
 279                                         relabund = abund / (float) thisLookUp[i]->getNumSeqs();
 280                                 }else if (scale == "totalotu") {
 281                                         //calc the total in this otu
 282                                         int totalOtu = 0;
 283                                         for (int l = 0; l < thisLookUp.size(); l++) {  totalOtu += thisLookUp[l]->getAbundance(j); }
 284                                         relabund = abund / (float) totalOtu;
 285                                 }else if (scale == "averagegroup") {
 286                                         relabund = abund / (float) (thisLookUp[i]->getNumSeqs() / (float) thisLookUp[i]->getNumBins());
 287                                 }else if (scale == "averageotu") {
 288                                         //calc the total in this otu
 289                                         int totalOtu = 0;
 290                                         for (int l = 0; l < thisLookUp.size(); l++) {  totalOtu += thisLookUp[l]->getAbundance(j); }
 291                                         float averageOtu = totalOtu / (float) thisLookUp.size();
 292
 293                                         relabund = abund / (float) averageOtu;
 294                                 }else{ m->mothurOut(scale + " is not a valid scaling option."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
 295
 296                                 out << relabund << '\t';
 297                         }
 298                         out << endl;
 299                  }
 300
 301                  return 0;
 302         }
 303         catch(exception& e) {
 304                 m->errorOut(e, "GetRelAbundCommand", "getRelAbundance");
 305                 exit(1);
 306         }
 307 }
 308 //**********************************************************************************************************************
 309
 310