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 CatchAllCommand::CatchAllCommand(string option)  {
  15         try {
  16                 globaldata = GlobalData::getInstance();
  17                 abort = false;
  18                 allLines = 0;
  19
  20                 //allow user to run help
  21                 if(option == "help") { help(); abort = true; }
  22
  23                 else {
  24                         //valid paramters for this command
  25                         string Array[] =  {"sabund","label","inputdir","outputdir"};
  26                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  27
  28                         OptionParser parser(option);
  29                         map<string,string> parameters = parser.getParameters();
  30
  31                         ValidParameters validParameter;
  32                         map<string, string>::iterator it;
  33
  34                         //check to make sure all parameters are valid for command
  35                         for (it = parameters.begin(); it != parameters.end(); it++) {
  36                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  37                         }
  38
  39                         //if the user changes the input directory command factory will send this info to us in the output parameter
  40                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  41                         if (inputDir == "not found"){   inputDir = "";          }
  42                         else {
  43                                 string path;
  44                                 it = parameters.find("sabund");
  45                                 //user has given a template file
  46                                 if(it != parameters.end()){
  47                                         path = m->hasPath(it->second);
  48                                         //if the user has not given a path then, add inputdir. else leave path alone.
  49                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
  50                                 }
  51                         }
  52
  53                         //check for required parameters
  54                         sabundfile = validParameter.validFile(parameters, "sabund", true);
  55                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
  56                         else if (sabundfile == "not found") { sabundfile = "";  m->mothurOut("You must provide either a sabund file for the catchall command."); m->mothurOutEndLine(); abort=true; }
  57                         else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
  58
  59                         string label = validParameter.validFile(parameters, "label", false);
  60                         if (label == "not found") { label = ""; }
  61                         else {
  62                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
  63                                 else { allLines = 1;  }
  64                         }
  65
  66
  67                         //if the user changes the output directory command factory will send this info to us in the output parameter
  68                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "./";       }
  69                 }
  70
  71         }
  72         catch(exception& e) {
  73                 m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
  74                 exit(1);
  75         }
  76 }
  77 //**********************************************************************************************************************
  78
  79 void CatchAllCommand::help(){
  80         try {
  81                 m->mothurOut("The catchall command interfaces mothur with the catchall program written by ...citation goes here...\n");
  82                 m->mothurOut("For more information about clearcut refer to http://catchall.cac.cornell.edu/ \n");
  83                 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");
  84                 m->mothurOut("The catchall command parameters are sabund and label, sabund is required. \n");
  85                 m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
  86                 m->mothurOut("The catchall command should be in the following format: \n");
  87                 m->mothurOut("catchall(sabund=yourSabundFile) \n");
  88                 m->mothurOut("Example: catchall(sabund=abrecovery.fn.sabund) \n");
  89         }
  90         catch(exception& e) {
  91                 m->errorOut(e, "CatchAllCommand", "help");
  92                 exit(1);
  93         }
  94 }
  95
  96 /**************************************************************************************/
  97 int CatchAllCommand::execute() {
  98         try {
  99
 100                 if (abort == true) { return 0; }
 101
 102                 vector<string> outputNames;
 103
 104                 //prepare full output directory
 105                 outputDir = m->getFullPathName(outputDir);
 106
 107                 //get location of catchall
 108                 GlobalData* globaldata = GlobalData::getInstance();
 109                 string path = globaldata->argv;
 110                 path = path.substr(0, (path.find_last_of('m')));
 111                 path = m->getFullPathName(path);
 112
 113                 string catchAllCommandExe = "";
 114                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 115                         catchAllCommandExe += "mono " + path + "catchall/CatchAllcmdL.exe ";
 116                 #else
 117                         catchAllCommandExe += path + "catchall/CatchAllcmdW.exe ";
 118                 #endif
 119
 120                 read = new ReadOTUFile(sabundfile);
 121                 read->read(&*globaldata);
 122
 123                 SAbundVector* sabund = globaldata->sabund;
 124                 string lastLabel = sabund->getLabel();
 125                 input = globaldata->ginput;
 126
 127                 set<string> processedLabels;
 128                 set<string> userLabels = labels;
 129
 130                 //for each label the user selected
 131                 while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 132
 133
 134                         if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 135                                         m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 136
 137                                         //create list of output files catchall will make
 138                                         //datasetname_Analysis.csv
 139                                         //datasetname_BestModelsAnalysis.csv
 140                                         //datasetname_BestModelsFits.csv
 141                                         //datasetname_BubblePlot.csv
 142                                         //datasetname_Poisson_fits.csv
 143                                         //datasetname_SingleExp_fits.csv
 144                                         //datasetname_ThreeMixedExp_fits.csv
 145                                         //datasetname_TwoMixedExp_fits.csv
 146
 147                                         //create catchall input file from mothur's inputfile
 148                                         string filename = process(sabund);
 149         sabund->print(cout);
 150                                         //create system command
 151                                         string catchAllCommand = catchAllCommandExe + filename + " " + path;
 152 cout << catchAllCommand << endl;
 153                                         //run catchall
 154                                         system(catchAllCommand.c_str());
 155
 156                                         if (m->control_pressed) { delete read;  delete input; globaldata->ginput = NULL; delete sabund;  return 0; }
 157
 158                                         processedLabels.insert(sabund->getLabel());
 159                                         userLabels.erase(sabund->getLabel());
 160                         }
 161
 162                         if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 163                                         string saveLabel = sabund->getLabel();
 164
 165                                         delete sabund;
 166                                         sabund = (input->getSAbundVector(lastLabel));
 167
 168                                         m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 169
 170                                         //create list of output files catchall will make
 171                                         //datasetname_Analysis.csv
 172                                         //datasetname_BestModelsAnalysis.csv
 173                                         //datasetname_BestModelsFits.csv
 174                                         //datasetname_BubblePlot.csv
 175                                         //datasetname_Poisson_fits.csv
 176                                         //datasetname_SingleExp_fits.csv
 177                                         //datasetname_ThreeMixedExp_fits.csv
 178                                         //datasetname_TwoMixedExp_fits.csv
 179
 180
 181                                         //create catchall input file from mothur's inputfile
 182                                         string filename = process(sabund);
 183
 184                                         //create system command
 185                                         string catchAllCommand = catchAllCommandExe + filename + " " + path;
 186 cout << catchAllCommand << endl;
 187                                         //run catchall
 188                                         system(catchAllCommand.c_str());
 189
 190                                         if (m->control_pressed) { delete read;  delete input; globaldata->ginput = NULL; delete sabund;  return 0; }
 191
 192                                         processedLabels.insert(sabund->getLabel());
 193                                         userLabels.erase(sabund->getLabel());
 194
 195                                         //restore real lastlabel to save below
 196                                         sabund->setLabel(saveLabel);
 197                         }
 198
 199
 200                         lastLabel = sabund->getLabel();
 201
 202                         delete sabund;
 203                         sabund = (input->getSAbundVector());
 204                 }
 205
 206                 //output error messages about any remaining user labels
 207                 set<string>::iterator it;
 208                 bool needToRun = false;
 209                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 210                         m->mothurOut("Your file does not include the label " + *it);
 211                         if (processedLabels.count(lastLabel) != 1) {
 212                                 m->mothurOut(". I will use " + lastLabel + ".");  m->mothurOutEndLine();
 213                                 needToRun = true;
 214                         }else {
 215                                 m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
 216                         }
 217                 }
 218
 219                 //run last label if you need to
 220                 if (needToRun == true)  {
 221                         if (sabund != NULL) {   delete sabund;  }
 222                         sabund = (input->getSAbundVector(lastLabel));
 223
 224                         m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 225                         //create list of output files catchall will make
 226                         //datasetname_Analysis.csv
 227                         //datasetname_BestModelsAnalysis.csv
 228                         //datasetname_BestModelsFits.csv
 229                         //datasetname_BubblePlot.csv
 230                         //datasetname_Poisson_fits.csv
 231                         //datasetname_SingleExp_fits.csv
 232                         //datasetname_ThreeMixedExp_fits.csv
 233                         //datasetname_TwoMixedExp_fits.csv
 234
 235                         //create catchall input file from mothur's inputfile
 236                         string filename = process(sabund);
 237
 238                         //create system command
 239                         string catchAllCommand = catchAllCommandExe + filename + " " + path;
 240 cout << catchAllCommand << endl;
 241                         //run catchall
 242                         system(catchAllCommand.c_str());
 243
 244
 245                         delete sabund;
 246                 }
 247
 248                 delete read;
 249                 delete input; globaldata->ginput = NULL;
 250
 251                 m->mothurOutEndLine();
 252                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 253                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 254                 m->mothurOutEndLine();
 255
 256
 257                 return 0;
 258         }
 259         catch(exception& e) {
 260                 m->errorOut(e, "CatchAllCommand", "execute");
 261                 exit(1);
 262         }
 263 }
 264 //**********************************************************************************************************************
 265 string CatchAllCommand::process(SAbundVector* sabund) {
 266         try {
 267                 string filename = outputDir + m->getRootName(m->getSimpleName(sabundfile)) + sabund->getLabel() + ".catchall";
 268                 filename = m->getFullPathName(filename);
 269
 270                 ofstream out;
 271                 m->openOutputFile(filename, out);
 272
 273                 for (int i = 1; i <= sabund->getMaxRank(); i++) {
 274                         int temp = sabund->get(i);
 275
 276                         if (temp != 0) {
 277                                 out << i << "," << temp << endl;
 278                         }
 279                 }
 280                 out.close();
 281
 282                 return filename;
 283
 284         }
 285         catch(exception& e) {
 286                 m->errorOut(e, "CatchAllCommand", "process");
 287                 exit(1);
 288         }
 289 }
 290 /**************************************************************************************/
 291
 292
 293