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
  30                 //need to determine outputFIles and types
  31         }
  32         catch(exception& e) {
  33                 m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 vector<string> CatchAllCommand::getRequiredParameters(){
  39         try {
  40                 string AlignArray[] =  {"sabund"};
  41                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  42                 return myArray;
  43         }
  44         catch(exception& e) {
  45                 m->errorOut(e, "CatchAllCommand", "getRequiredParameters");
  46                 exit(1);
  47         }
  48 }
  49 //**********************************************************************************************************************
  50 vector<string> CatchAllCommand::getRequiredFiles(){
  51         try {
  52                 vector<string> myArray;
  53                 return myArray;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "CatchAllCommand", "getRequiredFiles");
  57                 exit(1);
  58         }
  59 }
  60 /**************************************************************************************/
  61 CatchAllCommand::CatchAllCommand(string option)  {
  62         try {
  63                 globaldata = GlobalData::getInstance();
  64                 abort = false;
  65                 allLines = 1;
  66
  67                 //allow user to run help
  68                 if(option == "help") { help(); abort = true; }
  69
  70                 else {
  71                         //valid paramters for this command
  72                         string Array[] =  {"sabund","label","inputdir","outputdir"};
  73                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  74
  75                         OptionParser parser(option);
  76                         map<string,string> parameters = parser.getParameters();
  77
  78                         ValidParameters validParameter;
  79                         map<string, string>::iterator it;
  80
  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                         //initialize outputTypes
  88                         //need to determine outputFIles and types
  89
  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("sabund");
  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["sabund"] = inputDir + it->second;           }
 102                                 }
 103                         }
 104
 105                         //check for required parameters
 106                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 107                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 108                         else if (sabundfile == "not found") { sabundfile = "";  m->mothurOut("You must provide a sabund file for the catchall command."); m->mothurOutEndLine(); abort=true; }
 109                         else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
 110
 111                         string label = validParameter.validFile(parameters, "label", false);
 112                         if (label == "not found") { label = ""; }
 113                         else {
 114                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 115                                 else { allLines = 1;  }
 116                         }
 117
 118
 119                         //if the user changes the output directory command factory will send this info to us in the output parameter
 120                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(sabundfile);     }
 121                 }
 122
 123         }
 124         catch(exception& e) {
 125                 m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
 126                 exit(1);
 127         }
 128 }
 129 //**********************************************************************************************************************
 130
 131 void CatchAllCommand::help(){
 132         try {
 133                 m->mothurOut("The catchall command interfaces mothur with the catchall program written by Linda Woodard, Sean Connolly and John Bunge.\n");
 134                 m->mothurOut("For more information about catchall refer to http://www.northeastern.edu/catchall/index.html \n");
 135                 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");
 136                 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");
 137                 m->mothurOut("The catchall command parameters are sabund and label, sabund is required. \n");
 138                 m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
 139                 m->mothurOut("The catchall command should be in the following format: \n");
 140                 m->mothurOut("catchall(sabund=yourSabundFile) \n");
 141                 m->mothurOut("Example: catchall(sabund=abrecovery.fn.sabund) \n");
 142         }
 143         catch(exception& e) {
 144                 m->errorOut(e, "CatchAllCommand", "help");
 145                 exit(1);
 146         }
 147 }
 148
 149 /**************************************************************************************/
 150 int CatchAllCommand::execute() {
 151         try {
 152
 153                 if (abort == true) { return 0; }
 154
 155                 //prepare full output directory
 156                 outputDir = m->getFullPathName(outputDir);
 157
 158                 //get location of catchall
 159                 GlobalData* globaldata = GlobalData::getInstance();
 160                 path = globaldata->argv;
 161                 path = path.substr(0, (path.find_last_of('m')));
 162                 path = m->getFullPathName(path);
 163
 164                 string catchAllCommandExe = "";
 165                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 166                         catchAllCommandExe += "mono " + path + "catchall/CatchAllcmdL.exe ";
 167                 #else
 168                         catchAllCommandExe += path + "catchall/CatchAllcmdW.exe ";
 169                 #endif
 170
 171                 read = new ReadOTUFile(sabundfile);
 172                 read->read(&*globaldata);
 173
 174                 SAbundVector* sabund = globaldata->sabund;
 175                 string lastLabel = sabund->getLabel();
 176                 input = globaldata->ginput;
 177
 178                 set<string> processedLabels;
 179                 set<string> userLabels = labels;
 180
 181                 //for each label the user selected
 182                 while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 183
 184
 185                         if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 186                                         m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 187
 188                                         //create catchall input file from mothur's inputfile
 189                                         string filename = process(sabund);
 190                                         string outputPath = m->getPathName(filename);
 191
 192                                         //create system command
 193                                         string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
 194
 195                                         //run catchall
 196                                         system(catchAllCommand.c_str());
 197
 198                                         remove(filename.c_str());
 199
 200                                         filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 201
 202                                         outputNames.push_back(filename + "_Analysis.csv");
 203                                         outputNames.push_back(filename + "_BestModelsAnalysis.csv");
 204                                         outputNames.push_back(filename + "_BestModelsFits.csv");
 205                                         outputNames.push_back(filename + "_BubblePlot.csv");
 206
 207
 208                                         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; }
 209
 210                                         processedLabels.insert(sabund->getLabel());
 211                                         userLabels.erase(sabund->getLabel());
 212                         }
 213
 214                         if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 215                                         string saveLabel = sabund->getLabel();
 216
 217                                         delete sabund;
 218                                         sabund = (input->getSAbundVector(lastLabel));
 219
 220                                         m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 221
 222
 223                                         //create catchall input file from mothur's inputfile
 224                                         string filename = process(sabund);
 225                                         string outputPath = m->getPathName(filename);
 226
 227                                         //create system command
 228                                         string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
 229
 230                                         //run catchall
 231                                         system(catchAllCommand.c_str());
 232
 233                                         remove(filename.c_str());
 234
 235                                         filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 236
 237                                         outputNames.push_back(filename + "_Analysis.csv");
 238                                         outputNames.push_back(filename + "_BestModelsAnalysis.csv");
 239                                         outputNames.push_back(filename + "_BestModelsFits.csv");
 240                                         outputNames.push_back(filename + "_BubblePlot.csv");
 241
 242                                         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; }
 243
 244                                         processedLabels.insert(sabund->getLabel());
 245                                         userLabels.erase(sabund->getLabel());
 246
 247                                         //restore real lastlabel to save below
 248                                         sabund->setLabel(saveLabel);
 249                         }
 250
 251
 252                         lastLabel = sabund->getLabel();
 253
 254                         delete sabund;
 255                         sabund = (input->getSAbundVector());
 256                 }
 257
 258                 //output error messages about any remaining user labels
 259                 set<string>::iterator it;
 260                 bool needToRun = false;
 261                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 262                         m->mothurOut("Your file does not include the label " + *it);
 263                         if (processedLabels.count(lastLabel) != 1) {
 264                                 m->mothurOut(". I will use " + lastLabel + ".");  m->mothurOutEndLine();
 265                                 needToRun = true;
 266                         }else {
 267                                 m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
 268                         }
 269                 }
 270
 271                 //run last label if you need to
 272                 if (needToRun == true)  {
 273                         if (sabund != NULL) {   delete sabund;  }
 274                         sabund = (input->getSAbundVector(lastLabel));
 275
 276                         m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 277
 278                         //create catchall input file from mothur's inputfile
 279                         string filename = process(sabund);
 280                         string outputPath = m->getPathName(filename);
 281
 282                         //create system command
 283                         string catchAllCommand = catchAllCommandExe + filename + " " + outputPath + " 1";
 284
 285                         //run catchall
 286                         system(catchAllCommand.c_str());
 287
 288                         remove(filename.c_str());
 289
 290                         filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
 291
 292                         outputNames.push_back(filename + "_Analysis.csv");
 293                         outputNames.push_back(filename + "_BestModelsAnalysis.csv");
 294                         outputNames.push_back(filename + "_BestModelsFits.csv");
 295                         outputNames.push_back(filename + "_BubblePlot.csv");
 296
 297
 298                         delete sabund;
 299                 }
 300
 301                 delete read;
 302                 delete input; globaldata->ginput = NULL;
 303
 304                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } return 0; }
 305
 306                 m->mothurOutEndLine();
 307                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 308                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 309                 m->mothurOutEndLine();
 310
 311
 312                 return 0;
 313         }
 314         catch(exception& e) {
 315                 m->errorOut(e, "CatchAllCommand", "execute");
 316                 exit(1);
 317         }
 318 }
 319 //**********************************************************************************************************************
 320 string CatchAllCommand::process(SAbundVector* sabund) {
 321         try {
 322                 string filename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + sabund->getLabel() + ".csv";
 323                 filename = m->getFullPathName(filename);
 324
 325                 ofstream out;
 326                 m->openOutputFile(filename, out);
 327
 328                 for (int i = 1; i <= sabund->getMaxRank(); i++) {
 329                         int temp = sabund->get(i);
 330
 331                         if (temp != 0) {
 332                                 out << i << "," << temp << endl;
 333                         }
 334                 }
 335                 out.close();
 336
 337                 return filename;
 338
 339         }
 340         catch(exception& e) {
 341                 m->errorOut(e, "CatchAllCommand", "process");
 342                 exit(1);
 343         }
 344 }
 345 /**************************************************************************************/
 346
 347
 348