listotulabelscommand.cpp

   1 //
   2 //  listotucommand.cpp
   3 //  Mothur
   4 //
   5 //  Created by Sarah Westcott on 5/15/12.
   6 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
   7 //
   8
   9 #include "listotulabelscommand.h"
  10 #include "inputdata.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> ListOtuLabelsCommand::setParameters(){
  14         try {
  15         CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(pshared);
  16                 CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(prelabund);
  17         CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  18                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  19         //every command must have inputdir and outputdir.  This allows mothur users to redirect input and output files.
  20                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  21                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  22
  23                 vector<string> myArray;
  24                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  25                 return myArray;
  26         }
  27         catch(exception& e) {
  28                 m->errorOut(e, "ListOtuLabelsCommand", "setParameters");
  29                 exit(1);
  30         }
  31 }
  32 //**********************************************************************************************************************
  33 string ListOtuLabelsCommand::getHelpString(){
  34         try {
  35                 string helpString = "";
  36                 helpString += "The list.otulabels lists otu labels from shared or relabund file. The results can be used by the get.otulabels to select specific otus with the output from classify.otu, otu.association, or corr.axes.\n";
  37                 helpString += "The list.otulabels parameters are: shared, relabund, label and groups.\n";
  38                 helpString += "The label parameter is used to analyze specific labels in your input.\n";
  39                 helpString += "The groups parameter allows you to specify which of the groups you would like analyzed.\n";
  40                 helpString += "The list.otulabels commmand should be in the following format: \n";
  41                 helpString += "list.otulabels(shared=yourSharedFile, groups=yourGroup1-yourGroup2)\n";
  42                 return helpString;
  43         }
  44         catch(exception& e) {
  45                 m->errorOut(e, "ListOtuLabelsCommand", "getHelpString");
  46                 exit(1);
  47         }
  48 }
  49 //**********************************************************************************************************************
  50 ListOtuLabelsCommand::ListOtuLabelsCommand(){
  51         try {
  52                 abort = true; calledHelp = true;
  53                 setParameters();
  54         vector<string> tempOutNames;
  55                 outputTypes["otulabels"] = tempOutNames;
  56         }
  57         catch(exception& e) {
  58                 m->errorOut(e, "ListOtuLabelsCommand", "ListOtuLabelsCommand");
  59                 exit(1);
  60         }
  61 }
  62 //**********************************************************************************************************************
  63 ListOtuLabelsCommand::ListOtuLabelsCommand(string option)  {
  64         try {
  65                 abort = false; calledHelp = false;
  66                 allLines = 1;
  67
  68                 //allow user to run help
  69                 if(option == "help") { help(); abort = true; calledHelp = true; }
  70                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  71
  72                 else {
  73                         //valid paramters for this command
  74                         vector<string> myArray = setParameters();
  75
  76                         OptionParser parser(option);
  77                         map<string,string> parameters = parser.getParameters();
  78
  79                         ValidParameters validParameter;
  80                         map<string,string>::iterator it;
  81                         //check to make sure all parameters are valid for command
  82                         for (it = parameters.begin(); it != parameters.end(); it++) {
  83                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  84                         }
  85
  86
  87                         //if the user changes the input directory command factory will send this info to us in the output parameter
  88                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  89                         if (inputDir == "not found"){   inputDir = "";          }
  90                         else {
  91
  92                 //edit file types below to include only the types you added as parameters
  93
  94                                 string path;
  95                 it = parameters.find("relabund");
  96                                 //user has given a template file
  97                                 if(it != parameters.end()){
  98                                         path = m->hasPath(it->second);
  99                                         //if the user has not given a path then, add inputdir. else leave path alone.
 100                                         if (path == "") {       parameters["relabund"] = inputDir + it->second;         }
 101                                 }
 102
 103                 it = parameters.find("shared");
 104                                 //user has given a template file
 105                                 if(it != parameters.end()){
 106                                         path = m->hasPath(it->second);
 107                                         //if the user has not given a path then, add inputdir. else leave path alone.
 108                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 109                                 }
 110             }
 111
 112             vector<string> tempOutNames;
 113             outputTypes["otulabels"] = tempOutNames;
 114
 115                         //check for parameters
 116             sharedfile = validParameter.validFile(parameters, "shared", true);
 117                         if (sharedfile == "not open") { abort = true; }
 118                         else if (sharedfile == "not found") { sharedfile = ""; }
 119                         else { inputFileName = sharedfile; format = "sharedfile"; m->setSharedFile(sharedfile); }
 120
 121                         relabundfile = validParameter.validFile(parameters, "relabund", true);
 122                         if (relabundfile == "not open") { abort = true; }
 123                         else if (relabundfile == "not found") { relabundfile = ""; }
 124                         else { inputFileName = relabundfile; format = "relabund"; m->setRelAbundFile(relabundfile); }
 125
 126             if ((relabundfile == "") && (sharedfile == "")) {
 127                                 //is there are current file available for either of these?
 128                                 //give priority to shared, then relabund
 129                                 sharedfile = m->getSharedFile();
 130                                 if (sharedfile != "") {  inputFileName = sharedfile; format="sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 131                                 else {
 132                                         relabundfile = m->getRelAbundFile();
 133                                         if (relabundfile != "") {  inputFileName = relabundfile; format="relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
 134                                         else {
 135                                                 m->mothurOut("No valid current files. You must provide a shared or relabund."); m->mothurOutEndLine();
 136                                                 abort = true;
 137                                         }
 138                                 }
 139                         }
 140
 141             //if the user changes the output directory command factory will send this info to us in the output parameter
 142                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 143                                 outputDir = m->hasPath(inputFileName); //if user entered a file with a path then preserve it
 144                         }
 145
 146             string groups = validParameter.validFile(parameters, "groups", false);
 147                         if (groups == "not found") { groups = ""; }
 148                         else { m->splitAtDash(groups, Groups); }
 149                         m->setGroups(Groups);
 150
 151             string label = validParameter.validFile(parameters, "label", false);
 152                         if (label == "not found") { label = ""; }
 153                         else {
 154                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 155                                 else { allLines = 1;  }
 156                         }
 157                 }
 158
 159         }
 160         catch(exception& e) {
 161                 m->errorOut(e, "ListOtuLabelsCommand", "ListOtuLabelsCommand");
 162                 exit(1);
 163         }
 164 }
 165 //**********************************************************************************************************************
 166
 167 int ListOtuLabelsCommand::execute(){
 168         try {
 169
 170                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 171
 172         InputData input(inputFileName, format);
 173
 174         if (format == "relabund") {
 175             vector<SharedRAbundFloatVector*> lookup = input.getSharedRAbundFloatVectors();
 176             string lastLabel = lookup[0]->getLabel();
 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 (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
 186
 187                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 188
 189                     m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 190
 191                     createList(lookup);
 192
 193                     processedLabels.insert(lookup[0]->getLabel());
 194                     userLabels.erase(lookup[0]->getLabel());
 195                 }
 196
 197                 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 198                     string saveLabel = lookup[0]->getLabel();
 199
 200                     for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 201                     lookup = input.getSharedRAbundFloatVectors(lastLabel);
 202                     m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 203
 204                     createList(lookup);
 205
 206                     processedLabels.insert(lookup[0]->getLabel());
 207                     userLabels.erase(lookup[0]->getLabel());
 208
 209                     //restore real lastlabel to save below
 210                     lookup[0]->setLabel(saveLabel);
 211                 }
 212
 213                 lastLabel = lookup[0]->getLabel();
 214                 //prevent memory leak
 215                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 216
 217                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }  return 0; }
 218
 219                 //get next line to process
 220                 lookup = input.getSharedRAbundFloatVectors();
 221             }
 222
 223             if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }  return 0; }
 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                 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 241                 lookup = input.getSharedRAbundFloatVectors(lastLabel);
 242
 243                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 244
 245                 createList(lookup);
 246
 247                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 248             }
 249         }else {
 250
 251             vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 252             string lastLabel = lookup[0]->getLabel();
 253
 254             //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 255             set<string> processedLabels;
 256             set<string> userLabels = labels;
 257
 258             //as long as you are not at the end of the file or done wih the lines you want
 259             while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 260
 261                 if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }  for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
 262
 263                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 264
 265                     m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 266
 267                     createList(lookup);
 268
 269                     processedLabels.insert(lookup[0]->getLabel());
 270                     userLabels.erase(lookup[0]->getLabel());
 271                 }
 272
 273                 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 274                     string saveLabel = lookup[0]->getLabel();
 275
 276                     for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 277                     lookup = input.getSharedRAbundVectors(lastLabel);
 278                     m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 279
 280                     createList(lookup);
 281
 282                     processedLabels.insert(lookup[0]->getLabel());
 283                     userLabels.erase(lookup[0]->getLabel());
 284
 285                     //restore real lastlabel to save below
 286                     lookup[0]->setLabel(saveLabel);
 287                 }
 288
 289                 lastLabel = lookup[0]->getLabel();
 290                 //prevent memory leak
 291                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 292
 293                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }  return 0; }
 294
 295                 //get next line to process
 296                 lookup = input.getSharedRAbundVectors();
 297             }
 298
 299             if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }  return 0; }
 300
 301             //output error messages about any remaining user labels
 302             set<string>::iterator it;
 303             bool needToRun = false;
 304             for (it = userLabels.begin(); it != userLabels.end(); it++) {
 305                 m->mothurOut("Your file does not include the label " + *it);
 306                 if (processedLabels.count(lastLabel) != 1) {
 307                     m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 308                     needToRun = true;
 309                 }else {
 310                     m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 311                 }
 312             }
 313
 314             //run last label if you need to
 315             if (needToRun == true)  {
 316                 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 317                 lookup = input.getSharedRAbundVectors(lastLabel);
 318
 319                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 320
 321                 createList(lookup);
 322
 323                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 324             }
 325         }
 326
 327         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }  return 0; }
 328
 329         //output files created by command
 330                 m->mothurOutEndLine();
 331                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 332                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 333                 m->mothurOutEndLine();
 334         return 0;
 335
 336     }
 337         catch(exception& e) {
 338                 m->errorOut(e, "ListOtuLabelsCommand", "execute");
 339                 exit(1);
 340         }
 341 }
 342 //**********************************************************************************************************************
 343
 344 int ListOtuLabelsCommand::createList(vector<SharedRAbundVector*>& lookup){
 345         try {
 346
 347         string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".otu.labels";
 348         outputNames.push_back(outputFileName);  outputTypes["otulabels"].push_back(outputFileName);
 349                 ofstream out;
 350                 m->openOutputFile(outputFileName, out);
 351
 352         for (int i = 0; i < m->currentBinLabels.size(); i++) {  out << m->currentBinLabels[i] << endl;  }
 353
 354         out.close();
 355
 356         return 0;
 357     }
 358         catch(exception& e) {
 359                 m->errorOut(e, "ListOtuLabelsCommand", "createTable");
 360                 exit(1);
 361         }
 362 }
 363
 364 //**********************************************************************************************************************
 365
 366 int ListOtuLabelsCommand::createList(vector<SharedRAbundFloatVector*>& lookup){
 367         try {
 368
 369         string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".otu.labels";
 370         outputNames.push_back(outputFileName);  outputTypes["accnos"].push_back(outputFileName);
 371                 ofstream out;
 372                 m->openOutputFile(outputFileName, out);
 373
 374         for (int i = 0; i < m->currentBinLabels.size(); i++) {  out << m->currentBinLabels[i] << endl;  }
 375
 376         out.close();
 377
 378         return 0;
 379     }
 380         catch(exception& e) {
 381                 m->errorOut(e, "ListOtuLabelsCommand", "createTable");
 382                 exit(1);
 383         }
 384 }
 385
 386 //**********************************************************************************************************************
 387