catchallcommand.cpp

   1 /*
   2  *  catchallcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 5/11/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "catchallcommand.h"
  11 #include "globaldata.hpp"
  12
  13 //**********************************************************************************************************************
  14 vector<string> CatchAllCommand::getValidParameters(){
  15         try {
  16                 string AlignArray[] =  {"sabund","label","inputdir","outputdir"};
  17                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "CatchAllCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 CatchAllCommand::CatchAllCommand(){
  27         try {
  28                 //initialize outputTypes
  29                 vector<string> tempOutNames;
  30                 outputTypes["csv"] = tempOutNames;
  31                 outputTypes["summary"] = tempOutNames;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
  35                 exit(1);
  36         }
  37 }
  38 //**********************************************************************************************************************
  39 vector<string> CatchAllCommand::getRequiredParameters(){
  40         try {
  41                 string AlignArray[] =  {"sabund"};
  42                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  43                 return myArray;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "CatchAllCommand", "getRequiredParameters");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 vector<string> CatchAllCommand::getRequiredFiles(){
  52         try {
  53                 vector<string> myArray;
  54                 return myArray;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "CatchAllCommand", "getRequiredFiles");
  58                 exit(1);
  59         }
  60 }
  61 /**************************************************************************************/
  62 CatchAllCommand::CatchAllCommand(string option)  {
  63         try {
  64                 globaldata = GlobalData::getInstance();
  65                 abort = false;
  66                 allLines = 1;
  67
  68                 //allow user to run help
  69                 if(option == "help") { help(); abort = true; }
  70
  71                 else {
  72                         //valid paramters for this command
  73                         string Array[] =  {"sabund","label","inputdir","outputdir"};
  74                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  75
  76                         OptionParser parser(option);
  77                         map<string,string> parameters = parser.getParameters();
  78
  79                         ValidParameters validParameter;
  80                         map<string, string>::iterator it;
  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["csv"] = tempOutNames;
  90                         outputTypes["summary"] = tempOutNames;
  91
  92                         //if the user changes the input directory command factory will send this info to us in the output parameter
  93                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  94                         if (inputDir == "not found"){   inputDir = "";          }
  95                         else {
  96                                 string path;
  97                                 it = parameters.find("sabund");
  98                                 //user has given a template file
  99                                 if(it != parameters.end()){
 100                                         path = m->hasPath(it->second);
 101                                         //if the user has not given a path then, add inputdir. else leave path alone.
 102                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 103                                 }
 104                         }
 105
 106                         //check for required parameters
 107                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 108                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 109                         else if (sabundfile == "not found") { sabundfile = "";  m->mothurOut("You must provide a sabund file for the catchall command."); m->mothurOutEndLine(); abort=true; }
 110                         else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
 111
 112                         string label = validParameter.validFile(parameters, "label", false);
 113                         if (label == "not found") { label = ""; }
 114                         else {
 115                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 116                                 else { allLines = 1;  }
 117                         }
 118
 119
 120                         //if the user changes the output directory command factory will send this info to us in the output parameter
 121                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(sabundfile);     }
 122                 }
 123
 124         }
 125         catch(exception& e) {
 126                 m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
 127                 exit(1);
 128         }
 129 }
 130 //**********************************************************************************************************************
 131
 132 void CatchAllCommand::help(){
 133         try {
 134                 m->mothurOut("The catchall command interfaces mothur with the catchall program written by Linda Woodard, Sean Connolly and John Bunge.\n");
 135                 m->mothurOut("For more information about catchall refer to http://www.northeastern.edu/catchall/index.html \n");
 136                 m->mothurOut("The catchall executable must be in a folder called catchall in the same folder as your mothur executable, similar to mothur's requirements for using blast. \n");
 137                 m->mothurOut("If you are a MAC or Linux user you must also have installed mono, a link to mono is on the webpage. \n");
 138                 m->mothurOut("The catchall command parameters are sabund and label, sabund is required. \n");
 139                 m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
 140                 m->mothurOut("The catchall command should be in the following format: \n");
 141                 m->mothurOut("catchall(sabund=yourSabundFile) \n");
 142                 m->mothurOut("Example: catchall(sabund=abrecovery.fn.sabund) \n");
 143         }
 144         catch(exception& e) {
 145                 m->errorOut(e, "CatchAllCommand", "help");
 146                 exit(1);
 147         }
 148 }
 149
 150 /**************************************************************************************/
 151 int CatchAllCommand::execute() {
 152         try {
 153
 154                 if (abort == true) { return 0; }
 155
 156                 //prepare full output directory
 157                 outputDir = m->getFullPathName(outputDir);
 158
 159                 //get location of catchall
 160                 GlobalData* globaldata = GlobalData::getInstance();
 161                 path = globaldata->argv;
 162                 path = path.substr(0, (path.find_last_of('m')));
 163                 path = m->getFullPathName(path);
 164
 165                 string catchAllCommandExe = "";
 166                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 167                         catchAllCommandExe += "mono " + path + "catchall/CatchAllcmdL.exe ";
 168                 #else
 169                         catchAllCommandExe += path + "catchall/CatchAllcmdW.exe ";
 170                 #endif
 171
 172                 read = new ReadOTUFile(sabundfile);
 173                 read->read(&*globaldata);
 174
 175                 SAbundVector* sabund = globaldata->sabund;
 176                 string lastLabel = sabund->getLabel();
 177                 input = globaldata->ginput;
 178
 179                 set<string> processedLabels;
 180                 set<string> userLabels = labels;
 181
 182                 //for each label the user selected
 183                 while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 184
 185
 186                         if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 187                                         m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 188
 189                                         //create catchall input file from mothur's inputfile
 190                                         string filename = process(sabund);
 191                                         string outputPath = m->getPathName(filename);
 192
 193                                         //create system command
 194                                         string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
 195
 196                                         //run catchall
 197                                         system(catchAllCommand.c_str());
 198
 199                                         remove(filename.c_str());
 200
 201                                         filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 202
 203                                         outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 204                                         outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
 205                                         outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
 206                                         outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
 207
 208                                         createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel());
 209
 210                                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete read;  delete input; globaldata->ginput = NULL; delete sabund;  return 0; }
 211
 212                                         processedLabels.insert(sabund->getLabel());
 213                                         userLabels.erase(sabund->getLabel());
 214                         }
 215
 216                         if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 217                                         string saveLabel = sabund->getLabel();
 218
 219                                         delete sabund;
 220                                         sabund = (input->getSAbundVector(lastLabel));
 221
 222                                         m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 223
 224
 225                                         //create catchall input file from mothur's inputfile
 226                                         string filename = process(sabund);
 227                                         string outputPath = m->getPathName(filename);
 228
 229                                         //create system command
 230                                         string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
 231
 232                                         //run catchall
 233                                         system(catchAllCommand.c_str());
 234
 235                                         remove(filename.c_str());
 236
 237                                         filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 238
 239                                         outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 240                                         outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
 241                                         outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
 242                                         outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
 243
 244                                         createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel());
 245
 246                                         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete read;  delete input; globaldata->ginput = NULL; delete sabund;  return 0; }
 247
 248                                         processedLabels.insert(sabund->getLabel());
 249                                         userLabels.erase(sabund->getLabel());
 250
 251                                         //restore real lastlabel to save below
 252                                         sabund->setLabel(saveLabel);
 253                         }
 254
 255
 256                         lastLabel = sabund->getLabel();
 257
 258                         delete sabund;
 259                         sabund = (input->getSAbundVector());
 260                 }
 261
 262                 //output error messages about any remaining user labels
 263                 set<string>::iterator it;
 264                 bool needToRun = false;
 265                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 266                         m->mothurOut("Your file does not include the label " + *it);
 267                         if (processedLabels.count(lastLabel) != 1) {
 268                                 m->mothurOut(". I will use " + lastLabel + ".");  m->mothurOutEndLine();
 269                                 needToRun = true;
 270                         }else {
 271                                 m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
 272                         }
 273                 }
 274
 275                 //run last label if you need to
 276                 if (needToRun == true)  {
 277                         if (sabund != NULL) {   delete sabund;  }
 278                         sabund = (input->getSAbundVector(lastLabel));
 279
 280                         m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 281
 282                         //create catchall input file from mothur's inputfile
 283                         string filename = process(sabund);
 284                         string outputPath = m->getPathName(filename);
 285
 286                         //create system command
 287                         string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
 288
 289                         //run catchall
 290                         system(catchAllCommand.c_str());
 291
 292                         remove(filename.c_str());
 293
 294                         filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 295
 296                         outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
 297                         outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
 298                         outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
 299                         outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
 300
 301                         createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel());
 302
 303                         delete sabund;
 304                 }
 305
 306                 delete read;
 307                 delete input; globaldata->ginput = NULL;
 308
 309                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } return 0; }
 310
 311                 m->mothurOutEndLine();
 312                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 313                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 314                 m->mothurOutEndLine();
 315
 316
 317                 return 0;
 318         }
 319         catch(exception& e) {
 320                 m->errorOut(e, "CatchAllCommand", "execute");
 321                 exit(1);
 322         }
 323 }
 324 //**********************************************************************************************************************
 325 string CatchAllCommand::process(SAbundVector* sabund) {
 326         try {
 327                 string filename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + sabund->getLabel() + ".csv";
 328                 filename = m->getFullPathName(filename);
 329
 330                 ofstream out;
 331                 m->openOutputFile(filename, out);
 332
 333                 for (int i = 1; i <= sabund->getMaxRank(); i++) {
 334                         int temp = sabund->get(i);
 335
 336                         if (temp != 0) {
 337                                 out << i << "," << temp << endl;
 338                         }
 339                 }
 340                 out.close();
 341
 342                 return filename;
 343
 344         }
 345         catch(exception& e) {
 346                 m->errorOut(e, "CatchAllCommand", "process");
 347                 exit(1);
 348         }
 349 }
 350 //**********************************************************************************************************************
 351 string CatchAllCommand::createSummaryFile(string file1, string label) {
 352         try {
 353                 string filename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + label + ".catchall.summary";
 354                 filename = m->getFullPathName(filename);
 355                 outputNames.push_back(filename); outputTypes["summary"].push_back(filename);
 356
 357                 ofstream out;
 358                 m->openOutputFile(filename, out);
 359
 360                 out << "group\tmodel\testimate\tlci\tuci" << endl;
 361
 362                 ifstream in;
 363                 m->openInputFile(file1, in);
 364
 365                 if (!in.eof()) {
 366
 367                         string header = m->getline(in); m->gobble(in);
 368
 369                         int pos = header.find("Total Number of Observed Species =");
 370                         cout << pos << '\t' << header.length() << endl; exit(1);
 371                         if (pos == string::npos) { m->mothurOut("[ERROR]: cannot parse " + file1); m->mothurOutEndLine(); }
 372                         else {
 373                                 //pos will be the position of the T in total, so we want to count to the position of =
 374                                 pos += 34;
 375                                 char c=header[pos];
 376                                 string numString = "";
 377                                 while (c != ','){
 378                                         if (c != ' ') {
 379                                                 numString += c;
 380                                         }
 381                                 }
 382
 383                                 int numOtus; convert(numString, numOtus);
 384                                 cout << numOtus << endl;
 385                         }
 386                 }
 387
 388                 in.close();
 389                 out.close();
 390
 391                 return filename;
 392
 393         }
 394         catch(exception& e) {
 395                 m->errorOut(e, "CatchAllCommand", "createSummaryFile");
 396                 exit(1);
 397         }
 398 }
 399 /**************************************************************************************/
 400
 401
 402