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",false,false); parameters.push_back(plist);
  16                 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); 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::getOutputFileNameTag(string type, string inputName=""){
  52         try {
  53         string outputFileName = "";
  54                 map<string, vector<string> >::iterator it;
  55
  56         //is this a type this command creates
  57         it = outputTypes.find(type);
  58         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  59         else {
  60             if (type == "rabund")            {   outputFileName = "rabund";  }
  61             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  62         }
  63         return outputFileName;
  64         }
  65         catch(exception& e) {
  66                 m->errorOut(e, "GetRAbundCommand", "getOutputFileNameTag");
  67                 exit(1);
  68         }
  69 }
  70 //**********************************************************************************************************************
  71 GetRAbundCommand::GetRAbundCommand(){
  72         try {
  73                 abort = true; calledHelp = true;
  74                 setParameters();
  75                 vector<string> tempOutNames;
  76                 outputTypes["rabund"] = tempOutNames;
  77         }
  78         catch(exception& e) {
  79                 m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
  80                 exit(1);
  81         }
  82 }
  83 //**********************************************************************************************************************
  84 GetRAbundCommand::GetRAbundCommand(string option)  {
  85         try {
  86                 abort = false; calledHelp = false;
  87                 allLines = 1;
  88
  89                 //allow user to run help
  90                 if(option == "help") { help(); abort = true; calledHelp = true; }
  91                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  92
  93                 else {
  94                         vector<string> myArray = setParameters();
  95
  96                         OptionParser parser(option);
  97                         map<string,string> parameters = parser.getParameters();
  98                         map<string,string>::iterator it;
  99
 100                         ValidParameters validParameter;
 101
 102                         //check to make sure all parameters are valid for command
 103                         for (it = parameters.begin(); it != parameters.end(); it++) {
 104                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 105                         }
 106
 107                         //initialize outputTypes
 108                         vector<string> tempOutNames;
 109                         outputTypes["rabund"] = tempOutNames;
 110
 111                         //if the user changes the input directory command factory will send this info to us in the output parameter
 112                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 113                         if (inputDir == "not found"){   inputDir = "";          }
 114                         else {
 115                                 string path;
 116                                 it = parameters.find("list");
 117                                 //user has given a template file
 118                                 if(it != parameters.end()){
 119                                         path = m->hasPath(it->second);
 120                                         //if the user has not given a path then, add inputdir. else leave path alone.
 121                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 122                                 }
 123
 124                                 it = parameters.find("sabund");
 125                                 //user has given a template file
 126                                 if(it != parameters.end()){
 127                                         path = m->hasPath(it->second);
 128                                         //if the user has not given a path then, add inputdir. else leave path alone.
 129                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 130                                 }
 131                         }
 132
 133
 134                         //check for required parameters
 135                         listfile = validParameter.validFile(parameters, "list", true);
 136                         if (listfile == "not open") { listfile = ""; abort = true; }
 137                         else if (listfile == "not found") { listfile = ""; }
 138                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 139
 140                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 141                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 142                         else if (sabundfile == "not found") { sabundfile = ""; }
 143                         else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
 144
 145
 146                         //check for optional parameter and set defaults
 147                         // ...at some point should added some additional type checking...
 148                         string temp;
 149                         temp = validParameter.validFile(parameters, "sorted", false);                   if (temp == "not found") { temp = "T"; }
 150                         sorted = m->isTrue(temp);
 151
 152                         label = validParameter.validFile(parameters, "label", false);
 153                         if (label == "not found") { label = ""; }
 154                         else {
 155                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 156                                 else { allLines = 1;  }
 157                         }
 158
 159                         if ((listfile == "") && (sabundfile == "")) {
 160                                 //is there are current file available for any of these?
 161                                 //give priority to shared, then list, then rabund, then sabund
 162                                 //if there is a current shared file, use it
 163                                 listfile = m->getListFile();
 164                                 if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 165                                 else {
 166                                         sabundfile = m->getSabundFile();
 167                                         if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 168                                         else {
 169                                                 m->mothurOut("No valid current files. You must provide a list or sabund file."); m->mothurOutEndLine();
 170                                                 abort = true;
 171                                         }
 172                                 }
 173                         }
 174
 175
 176                         //if the user changes the output directory command factory will send this info to us in the output parameter
 177                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);      }
 178
 179                 }
 180
 181
 182         }
 183         catch(exception& e) {
 184                 m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
 185                 exit(1);
 186         }
 187 }
 188 //**********************************************************************************************************************
 189
 190 int GetRAbundCommand::execute(){
 191         try {
 192
 193                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 194
 195                 filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + getOutputFileNameTag("rabund");
 196                 m->openOutputFile(filename, out);
 197
 198                 input = new InputData(inputfile, format);
 199                 rabund = input->getRAbundVector();
 200                 string lastLabel = rabund->getLabel();
 201
 202                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 203                 set<string> processedLabels;
 204                 set<string> userLabels = labels;
 205
 206                 if (m->control_pressed) {  outputTypes.clear();  out.close(); m->mothurRemove(filename); delete rabund; delete input; return 0; }
 207
 208                 while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 209
 210                         if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
 211                                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 212
 213                                         if (m->control_pressed) {   outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0;  }
 214
 215                                         if(sorted)      {   rabund->print(out);                         }
 216                                         else            {       rabund->nonSortedPrint(out);    }
 217
 218                                         processedLabels.insert(rabund->getLabel());
 219                                         userLabels.erase(rabund->getLabel());
 220                         }
 221
 222                         if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 223                                         string saveLabel = rabund->getLabel();
 224
 225                                         delete rabund;
 226                                         rabund = input->getRAbundVector(lastLabel);
 227
 228                                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 229
 230                                         if (m->control_pressed) {   outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0;  }
 231
 232                                         if(sorted)      {   rabund->print(out);                         }
 233                                         else            {       rabund->nonSortedPrint(out);    }
 234
 235                                         processedLabels.insert(rabund->getLabel());
 236                                         userLabels.erase(rabund->getLabel());
 237
 238                                         //restore real lastlabel to save below
 239                                         rabund->setLabel(saveLabel);
 240                         }
 241
 242                         lastLabel = rabund->getLabel();
 243
 244                         delete rabund;
 245                         rabund = input->getRAbundVector();
 246                 }
 247
 248                 //output error messages about any remaining user labels
 249                 set<string>::iterator it;
 250                 bool needToRun = false;
 251                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 252                         m->mothurOut("Your file does not include the label " + *it);
 253                         if (processedLabels.count(lastLabel) != 1) {
 254                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 255                                 needToRun = true;
 256                         }else {
 257                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 258                         }
 259                 }
 260
 261                 //run last label if you need to
 262                 if (needToRun == true)  {
 263                         if (rabund != NULL) {   delete rabund;  }
 264                         rabund = input->getRAbundVector(lastLabel);
 265
 266                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 267
 268                         if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0; }
 269
 270                         if(sorted)      {   rabund->print(out);                         }
 271                         else            {       rabund->nonSortedPrint(out);    }
 272
 273                         delete rabund;
 274                 }
 275
 276                 m->mothurOutEndLine();
 277                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 278                 m->mothurOut(filename); m->mothurOutEndLine();  outputNames.push_back(filename); outputTypes["rabund"].push_back(filename);
 279                 m->mothurOutEndLine();
 280
 281                 out.close();
 282
 283                 //set rabund file as new current rabundfile
 284                 string current = "";
 285                 itTypes = outputTypes.find("rabund");
 286                 if (itTypes != outputTypes.end()) {
 287                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 288                 }
 289
 290                 return 0;
 291         }
 292
 293         catch(exception& e) {
 294                 m->errorOut(e, "GetRAbundCommand", "execute");
 295                 exit(1);
 296         }
 297 }
 298
 299 //**********************************************************************************************************************
 300
 301