removeotulabelscommand.cpp

   1 //
   2 //  removeotulabels.cpp
   3 //  Mothur
   4 //
   5 //  Created by Sarah Westcott on 5/21/12.
   6 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
   7 //
   8
   9 #include "removeotulabelscommand.h"
  10
  11 //**********************************************************************************************************************
  12 vector<string> RemoveOtuLabelsCommand::setParameters(){
  13         try {
  14         CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos);
  15         CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pconstaxonomy);
  16                 CommandParameter potucorr("otucorr", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(potucorr);
  17         CommandParameter pcorraxes("corraxes", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pcorraxes);
  18         CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  19                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  20
  21                 vector<string> myArray;
  22                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  23                 return myArray;
  24         }
  25         catch(exception& e) {
  26                 m->errorOut(e, "RemoveOtuLabelsCommand", "setParameters");
  27                 exit(1);
  28         }
  29 }
  30 //**********************************************************************************************************************
  31 string RemoveOtuLabelsCommand::getHelpString(){
  32         try {
  33                 string helpString = "";
  34                 helpString += "The remove.otulabels command can be used to remove specific otus with the output from classify.otu, otu.association, or corr.axes.\n";
  35                 helpString += "The remove.otulabels parameters are: constaxonomy, otucorr, corraxes, and accnos.\n";
  36                 helpString += "The constaxonomy parameter is input the results of the classify.otu command.\n";
  37         helpString += "The otucorr parameter is input the results of the otu.association command.\n";
  38         helpString += "The corraxes parameter is input the results of the corr.axes command.\n";
  39                 helpString += "The remove.otulabels commmand should be in the following format: \n";
  40                 helpString += "remove.otulabels(accnos=yourListOfOTULabels, corraxes=yourCorrAxesFile)\n";
  41                 return helpString;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "RemoveOtuLabelsCommand", "getHelpString");
  45                 exit(1);
  46         }
  47 }
  48 //**********************************************************************************************************************
  49 RemoveOtuLabelsCommand::RemoveOtuLabelsCommand(){
  50         try {
  51                 abort = true; calledHelp = true;
  52                 setParameters();
  53         vector<string> tempOutNames;
  54                 outputTypes["contaxonomy"] = tempOutNames;
  55         outputTypes["otu.corr"] = tempOutNames;
  56         outputTypes["corr.axes"] = tempOutNames;
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "RemoveOtuLabelsCommand", "RemoveOtuLabelsCommand");
  60                 exit(1);
  61         }
  62 }
  63 //**********************************************************************************************************************
  64 RemoveOtuLabelsCommand::RemoveOtuLabelsCommand(string option)  {
  65         try {
  66                 abort = false; calledHelp = false;
  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("constaxonomy");
  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["constaxonomy"] = inputDir + it->second;             }
 101                                 }
 102
 103                 it = parameters.find("accnos");
 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["accnos"] = inputDir + it->second;           }
 109                                 }
 110
 111                 it = parameters.find("corraxes");
 112                                 //user has given a template file
 113                                 if(it != parameters.end()){
 114                                         path = m->hasPath(it->second);
 115                                         //if the user has not given a path then, add inputdir. else leave path alone.
 116                                         if (path == "") {       parameters["corraxes"] = inputDir + it->second;         }
 117                                 }
 118
 119                 it = parameters.find("otucorr");
 120                                 //user has given a template file
 121                                 if(it != parameters.end()){
 122                                         path = m->hasPath(it->second);
 123                                         //if the user has not given a path then, add inputdir. else leave path alone.
 124                                         if (path == "") {       parameters["otucorr"] = inputDir + it->second;          }
 125                                 }
 126             }
 127
 128             vector<string> tempOutNames;
 129             outputTypes["contaxonomy"] = tempOutNames;
 130             outputTypes["otu.corr"] = tempOutNames;
 131             outputTypes["corr.axes"] = tempOutNames;
 132
 133                         //check for parameters
 134             accnosfile = validParameter.validFile(parameters, "accnos", true);
 135                         if (accnosfile == "not open") { abort = true; }
 136                         else if (accnosfile == "not found") {
 137                                 accnosfile = m->getAccnosFile();
 138                                 if (accnosfile != "") {  m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); }
 139                                 else {
 140                                         m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine();
 141                                         abort = true;
 142                                 }
 143                         }else { m->setAccnosFile(accnosfile); }
 144
 145                         constaxonomyfile = validParameter.validFile(parameters, "constaxonomy", true);
 146                         if (constaxonomyfile == "not open") { constaxonomyfile = ""; abort = true; }
 147                         else if (constaxonomyfile == "not found") {  constaxonomyfile = "";  }
 148
 149             corraxesfile = validParameter.validFile(parameters, "corraxes", true);
 150                         if (corraxesfile == "not open") { corraxesfile = ""; abort = true; }
 151                         else if (corraxesfile == "not found") {  corraxesfile = "";  }
 152
 153             otucorrfile = validParameter.validFile(parameters, "otucorr", true);
 154                         if (otucorrfile == "not open") { otucorrfile = ""; abort = true; }
 155                         else if (otucorrfile == "not found") {  otucorrfile = "";  }
 156
 157
 158             //if the user changes the output directory command factory will send this info to us in the output parameter
 159                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){   outputDir = "";        }
 160
 161             if ((constaxonomyfile == "") && (corraxesfile == "") && (otucorrfile == ""))  { m->mothurOut("You must provide one of the following: constaxonomy, corraxes or otucorr."); m->mothurOutEndLine(); abort = true; }
 162                 }
 163
 164         }
 165         catch(exception& e) {
 166                 m->errorOut(e, "RemoveOtuLabelsCommand", "RemoveOtuLabelsCommand");
 167                 exit(1);
 168         }
 169 }
 170 //**********************************************************************************************************************
 171
 172 int RemoveOtuLabelsCommand::execute(){
 173         try {
 174
 175                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 176
 177         //get labels you want to keep
 178                 readAccnos();
 179
 180                 if (m->control_pressed) { return 0; }
 181
 182                 //read through the correct file and output lines you want to keep
 183                 if (constaxonomyfile != "")     {               readClassifyOtu();      }
 184                 if (corraxesfile != "")         {               readCorrAxes();         }
 185                 if (otucorrfile != "")          {               readOtuAssociation();   }
 186
 187         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }  return 0; }
 188
 189         //output files created by command
 190                 m->mothurOutEndLine();
 191                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 192                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 193                 m->mothurOutEndLine();
 194
 195         return 0;
 196     }
 197         catch(exception& e) {
 198                 m->errorOut(e, "GetOtuLabelsCommand", "execute");
 199                 exit(1);
 200         }
 201 }
 202 //**********************************************************************************************************************
 203 int RemoveOtuLabelsCommand::readClassifyOtu(){
 204         try {
 205                 string thisOutputDir = outputDir;
 206                 if (outputDir == "") {  thisOutputDir += m->hasPath(constaxonomyfile);  }
 207                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(constaxonomyfile)) + "pick.taxonomy";
 208                 ofstream out;
 209                 m->openOutputFile(outputFileName, out);
 210
 211                 ifstream in;
 212                 m->openInputFile(constaxonomyfile, in);
 213
 214                 bool wroteSomething = false;
 215                 int removedCount = 0;
 216
 217         //read headers
 218         string headers = m->getline(in);
 219         out << headers << endl;
 220
 221         while (!in.eof()) {
 222
 223             if (m->control_pressed) { break; }
 224
 225             string otu = ""; string tax = "unknown";
 226             int size = 0;
 227
 228             in >> otu >> size >> tax; m->gobble(in);
 229
 230             if (labels.count(otu) == 0) {
 231                                 wroteSomething = true;
 232                 out << otu << '\t' << size << '\t' << tax << endl;
 233             }else {  removedCount++;  }
 234         }
 235         in.close();
 236         out.close();
 237
 238                 if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine();  }
 239                 outputNames.push_back(outputFileName);  outputTypes["constaxonomy"].push_back(outputFileName);
 240
 241                 m->mothurOut("Removed " + toString(removedCount) + " otus from your constaxonomy file."); m->mothurOutEndLine();
 242
 243                 return 0;
 244
 245         }
 246         catch(exception& e) {
 247                 m->errorOut(e, "RemoveOtuLabelsCommand", "readClassifyOtu");
 248                 exit(1);
 249         }
 250 }
 251 //**********************************************************************************************************************
 252 int RemoveOtuLabelsCommand::readOtuAssociation(){
 253         try {
 254                 string thisOutputDir = outputDir;
 255                 if (outputDir == "") {  thisOutputDir += m->hasPath(otucorrfile);  }
 256                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(otucorrfile)) + "pick.corr";
 257                 ofstream out;
 258                 m->openOutputFile(outputFileName, out);
 259
 260                 ifstream in;
 261                 m->openInputFile(otucorrfile, in);
 262
 263                 bool wroteSomething = false;
 264                 int removedCount = 0;
 265
 266         //read headers
 267         string headers = m->getline(in);
 268         out << headers << endl;
 269
 270         while (!in.eof()) {
 271
 272             if (m->control_pressed) { break; }
 273
 274             string otu1 = "";
 275             string otu2 = "";
 276             in >> otu1 >> otu2;
 277             string line = m->getline(in); m->gobble(in);
 278
 279             if ((labels.count(otu1) == 0) && (labels.count(otu2) == 0)){
 280                                 wroteSomething = true;
 281
 282                 out << otu1 << '\t' << otu2 << '\t' << line << endl;
 283             }else { removedCount++; }
 284         }
 285         in.close();
 286         out.close();
 287
 288                 if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine();  }
 289                 outputNames.push_back(outputFileName);  outputTypes["otu.corr"].push_back(outputFileName);
 290
 291                 m->mothurOut("Removed " + toString(removedCount) + " lines from your otu.corr file."); m->mothurOutEndLine();
 292
 293                 return 0;
 294
 295         }
 296         catch(exception& e) {
 297                 m->errorOut(e, "RemoveOtuLabelsCommand", "readOtuAssociation");
 298                 exit(1);
 299         }
 300 }
 301 //**********************************************************************************************************************
 302 int RemoveOtuLabelsCommand::readCorrAxes(){
 303         try {
 304                 string thisOutputDir = outputDir;
 305                 if (outputDir == "") {  thisOutputDir += m->hasPath(corraxesfile);  }
 306                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(corraxesfile)) + "pick.axes";
 307                 ofstream out;
 308                 m->openOutputFile(outputFileName, out);
 309
 310
 311                 ifstream in;
 312                 m->openInputFile(corraxesfile, in);
 313
 314                 bool wroteSomething = false;
 315                 int removedCount = 0;
 316
 317         //read headers
 318         string headers = m->getline(in);
 319         out << headers << endl;
 320
 321         while (!in.eof()) {
 322
 323             if (m->control_pressed) { break; }
 324
 325             string otu = "";
 326             in >> otu;
 327             string line = m->getline(in); m->gobble(in);
 328
 329             if (labels.count(otu) == 0) {
 330                                 wroteSomething = true;
 331
 332                 out << otu << '\t' << line << endl;
 333             }else { removedCount++; }
 334         }
 335         in.close();
 336         out.close();
 337
 338                 if (wroteSomething == false) { m->mothurOut("Your file only contains labels from the .accnos file."); m->mothurOutEndLine();  }
 339                 outputNames.push_back(outputFileName);  outputTypes["corr.axes"].push_back(outputFileName);
 340
 341                 m->mothurOut("Removed " + toString(removedCount) + " lines from your corr.axes file."); m->mothurOutEndLine();
 342
 343                 return 0;
 344
 345         }
 346         catch(exception& e) {
 347                 m->errorOut(e, "RemoveOtuLabelsCommand", "readCorrAxes");
 348                 exit(1);
 349         }
 350 }
 351
 352 //**********************************************************************************************************************
 353 int RemoveOtuLabelsCommand::readAccnos(){
 354         try {
 355
 356                 ifstream in;
 357                 m->openInputFile(accnosfile, in);
 358                 string name;
 359
 360                 while(!in.eof()){
 361                         in >> name;
 362
 363                         labels.insert(name);
 364
 365                         m->gobble(in);
 366                 }
 367                 in.close();
 368
 369                 return 0;
 370
 371         }
 372         catch(exception& e) {
 373                 m->errorOut(e, "RemoveOtuLabelsCommand", "readAccnos");
 374                 exit(1);
 375         }
 376 }
 377 //**********************************************************************************************************************
 378
 379
 380