catchallcommand.cpp

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