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