getrabundcommand.cpp

   1 /*
   2  *  getrabundcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 6/2/09.
   6  *  Copyright 2009 Schloss Lab Umass Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "getrabundcommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> GetRAbundCommand::setParameters(){
  14         try {
  15                 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","rabund",false,false, true); parameters.push_back(plist);
  16                 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","rabund",false,false, true); parameters.push_back(psabund);
  17                 CommandParameter psorted("sorted", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(psorted);
  18                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  19                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  20                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  21
  22                 vector<string> myArray;
  23                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  24                 return myArray;
  25         }
  26         catch(exception& e) {
  27                 m->errorOut(e, "GetRAbundCommand", "setParameters");
  28                 exit(1);
  29         }
  30 }
  31 //**********************************************************************************************************************
  32 string GetRAbundCommand::getHelpString(){
  33         try {
  34                 string helpString = "";
  35                 helpString += "The get.rabund command parameters are list, sabund, label and sorted.  list or sabund parameters are required, unless you have valid current files.\n";
  36                 helpString += "The label parameter allows you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n";
  37                 helpString += "The sorted parameters allows you to print the rabund results sorted by abundance or not.  The default is sorted.\n";
  38                 helpString += "The get.rabund command should be in the following format: get.rabund(label=yourLabels, sorted=yourSorted).\n";
  39                 helpString += "Example get.rabund(sorted=F).\n";
  40                 helpString += "The default value for label is all labels in your inputfile.\n";
  41                 helpString += "The get.rabund command outputs a .rabund file containing the lines you selected.\n";
  42                 helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n";
  43                 return helpString;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "GetRAbundCommand", "getHelpString");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 string GetRAbundCommand::getOutputPattern(string type) {
  52     try {
  53         string pattern = "";
  54
  55         if (type == "rabund")      {   pattern = "[filename],rabund";    }
  56         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  57
  58         return pattern;
  59     }
  60     catch(exception& e) {
  61         m->errorOut(e, "GetRAbundCommand", "getOutputPattern");
  62         exit(1);
  63     }
  64 }
  65
  66 //**********************************************************************************************************************
  67 GetRAbundCommand::GetRAbundCommand(){
  68         try {
  69                 abort = true; calledHelp = true;
  70                 setParameters();
  71                 vector<string> tempOutNames;
  72                 outputTypes["rabund"] = tempOutNames;
  73         }
  74         catch(exception& e) {
  75                 m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
  76                 exit(1);
  77         }
  78 }
  79 //**********************************************************************************************************************
  80 GetRAbundCommand::GetRAbundCommand(string option)  {
  81         try {
  82                 abort = false; calledHelp = false;
  83                 allLines = 1;
  84
  85                 //allow user to run help
  86                 if(option == "help") { help(); abort = true; calledHelp = true; }
  87                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  88
  89                 else {
  90                         vector<string> myArray = setParameters();
  91
  92                         OptionParser parser(option);
  93                         map<string,string> parameters = parser.getParameters();
  94                         map<string,string>::iterator it;
  95
  96                         ValidParameters validParameter;
  97
  98                         //check to make sure all parameters are valid for command
  99                         for (it = parameters.begin(); it != parameters.end(); it++) {
 100                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 101                         }
 102
 103                         //initialize outputTypes
 104                         vector<string> tempOutNames;
 105                         outputTypes["rabund"] = tempOutNames;
 106
 107                         //if the user changes the input directory command factory will send this info to us in the output parameter
 108                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 109                         if (inputDir == "not found"){   inputDir = "";          }
 110                         else {
 111                                 string path;
 112                                 it = parameters.find("list");
 113                                 //user has given a template file
 114                                 if(it != parameters.end()){
 115                                         path = m->hasPath(it->second);
 116                                         //if the user has not given a path then, add inputdir. else leave path alone.
 117                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 118                                 }
 119
 120                                 it = parameters.find("sabund");
 121                                 //user has given a template file
 122                                 if(it != parameters.end()){
 123                                         path = m->hasPath(it->second);
 124                                         //if the user has not given a path then, add inputdir. else leave path alone.
 125                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 126                                 }
 127                         }
 128
 129
 130                         //check for required parameters
 131                         listfile = validParameter.validFile(parameters, "list", true);
 132                         if (listfile == "not open") { listfile = ""; abort = true; }
 133                         else if (listfile == "not found") { listfile = ""; }
 134                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 135
 136                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 137                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 138                         else if (sabundfile == "not found") { sabundfile = ""; }
 139                         else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
 140
 141
 142                         //check for optional parameter and set defaults
 143                         // ...at some point should added some additional type checking...
 144                         string temp;
 145                         temp = validParameter.validFile(parameters, "sorted", false);                   if (temp == "not found") { temp = "T"; }
 146                         sorted = m->isTrue(temp);
 147
 148                         label = validParameter.validFile(parameters, "label", false);
 149                         if (label == "not found") { label = ""; }
 150                         else {
 151                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 152                                 else { allLines = 1;  }
 153                         }
 154
 155                         if ((listfile == "") && (sabundfile == "")) {
 156                                 //is there are current file available for any of these?
 157                                 //give priority to shared, then list, then rabund, then sabund
 158                                 //if there is a current shared file, use it
 159                                 listfile = m->getListFile();
 160                                 if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 161                                 else {
 162                                         sabundfile = m->getSabundFile();
 163                                         if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 164                                         else {
 165                                                 m->mothurOut("No valid current files. You must provide a list or sabund file."); m->mothurOutEndLine();
 166                                                 abort = true;
 167                                         }
 168                                 }
 169                         }
 170
 171
 172                         //if the user changes the output directory command factory will send this info to us in the output parameter
 173                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);      }
 174
 175                 }
 176
 177
 178         }
 179         catch(exception& e) {
 180                 m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
 181                 exit(1);
 182         }
 183 }
 184 //**********************************************************************************************************************
 185
 186 int GetRAbundCommand::execute(){
 187         try {
 188
 189                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 190
 191         map<string, string> variables;
 192         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
 193                 filename = getOutputFileName("rabund", variables);
 194                 m->openOutputFile(filename, out);
 195
 196                 input = new InputData(inputfile, format);
 197                 rabund = input->getRAbundVector();
 198                 string lastLabel = rabund->getLabel();
 199
 200                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 201                 set<string> processedLabels;
 202                 set<string> userLabels = labels;
 203
 204                 if (m->control_pressed) {  outputTypes.clear();  out.close(); m->mothurRemove(filename); delete rabund; delete input; return 0; }
 205
 206                 while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 207
 208                         if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
 209                                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 210
 211                                         if (m->control_pressed) {   outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0;  }
 212
 213                                         if(sorted)      {   rabund->print(out);                         }
 214                                         else            {       rabund->nonSortedPrint(out);    }
 215
 216                                         processedLabels.insert(rabund->getLabel());
 217                                         userLabels.erase(rabund->getLabel());
 218                         }
 219
 220                         if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 221                                         string saveLabel = rabund->getLabel();
 222
 223                                         delete rabund;
 224                                         rabund = input->getRAbundVector(lastLabel);
 225
 226                                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 227
 228                                         if (m->control_pressed) {   outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0;  }
 229
 230                                         if(sorted)      {   rabund->print(out);                         }
 231                                         else            {       rabund->nonSortedPrint(out);    }
 232
 233                                         processedLabels.insert(rabund->getLabel());
 234                                         userLabels.erase(rabund->getLabel());
 235
 236                                         //restore real lastlabel to save below
 237                                         rabund->setLabel(saveLabel);
 238                         }
 239
 240                         lastLabel = rabund->getLabel();
 241
 242                         delete rabund;
 243                         rabund = input->getRAbundVector();
 244                 }
 245
 246                 //output error messages about any remaining user labels
 247                 set<string>::iterator it;
 248                 bool needToRun = false;
 249                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 250                         m->mothurOut("Your file does not include the label " + *it);
 251                         if (processedLabels.count(lastLabel) != 1) {
 252                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 253                                 needToRun = true;
 254                         }else {
 255                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 256                         }
 257                 }
 258
 259                 //run last label if you need to
 260                 if (needToRun == true)  {
 261                         if (rabund != NULL) {   delete rabund;  }
 262                         rabund = input->getRAbundVector(lastLabel);
 263
 264                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 265
 266                         if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0; }
 267
 268                         if(sorted)      {   rabund->print(out);                         }
 269                         else            {       rabund->nonSortedPrint(out);    }
 270
 271                         delete rabund;
 272                 }
 273
 274                 m->mothurOutEndLine();
 275                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 276                 m->mothurOut(filename); m->mothurOutEndLine();  outputNames.push_back(filename); outputTypes["rabund"].push_back(filename);
 277                 m->mothurOutEndLine();
 278
 279                 out.close();
 280
 281                 //set rabund file as new current rabundfile
 282                 string current = "";
 283                 itTypes = outputTypes.find("rabund");
 284                 if (itTypes != outputTypes.end()) {
 285                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 286                 }
 287
 288                 return 0;
 289         }
 290
 291         catch(exception& e) {
 292                 m->errorOut(e, "GetRAbundCommand", "execute");
 293                 exit(1);
 294         }
 295 }
 296
 297 //**********************************************************************************************************************
 298
 299