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::getValidParameters(){
  14         try {
  15                 string Array[] =  {"label","sorted","outputdir","inputdir"};
  16                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  17                 return myArray;
  18         }
  19         catch(exception& e) {
  20                 m->errorOut(e, "GetRAbundCommand", "getValidParameters");
  21                 exit(1);
  22         }
  23 }
  24 //**********************************************************************************************************************
  25 GetRAbundCommand::GetRAbundCommand(){
  26         try {
  27                 abort = true;
  28                 //initialize outputTypes
  29                 vector<string> tempOutNames;
  30                 outputTypes["rabund"] = tempOutNames;
  31         }
  32         catch(exception& e) {
  33                 m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 vector<string> GetRAbundCommand::getRequiredParameters(){
  39         try {
  40                 vector<string> myArray;
  41                 return myArray;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "GetRAbundCommand", "getRequiredParameters");
  45                 exit(1);
  46         }
  47 }
  48 //**********************************************************************************************************************
  49 vector<string> GetRAbundCommand::getRequiredFiles(){
  50         try {
  51                 string Array[] =  {"list"};
  52                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  53
  54                 return myArray;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "GetRAbundCommand", "getRequiredFiles");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 GetRAbundCommand::GetRAbundCommand(string option)  {
  63         try {
  64                 globaldata = GlobalData::getInstance();
  65                 abort = false;
  66                 allLines = 1;
  67                 labels.clear();
  68
  69                 //allow user to run help
  70                 if(option == "help") { help(); abort = true; }
  71
  72                 else {
  73                         //valid paramters for this command
  74                         string Array[] =  {"label","sorted","outputdir","inputdir"};
  75                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  76
  77                         OptionParser parser(option);
  78                         map<string,string> parameters = parser.getParameters();
  79
  80                         ValidParameters validParameter;
  81
  82                         //check to make sure all parameters are valid for command
  83                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  84                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  85                         }
  86
  87                         //if the user changes the output directory command factory will send this info to us in the output parameter
  88                         string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found"){
  89                                 outputDir = "";
  90                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
  91                         }
  92
  93                         //initialize outputTypes
  94                         vector<string> tempOutNames;
  95                         outputTypes["rabund"] = tempOutNames;
  96
  97                         //make sure the user has already run the read.otu command
  98                         if (globaldata->getListFile() == "") { m->mothurOut("You must read a listfile before you can use the get.rabund command."); m->mothurOutEndLine(); abort = true; }
  99
 100                         //check for optional parameter and set defaults
 101                         // ...at some point should added some additional type checking...
 102
 103                         string temp;
 104                         temp = validParameter.validFile(parameters, "sorted", false);                   if (temp == "not found") { temp = "T"; }
 105                         sorted = m->isTrue(temp);
 106
 107                         label = validParameter.validFile(parameters, "label", false);
 108                         if (label == "not found") { label = ""; }
 109                         else {
 110                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 111                                 else { allLines = 1;  }
 112                         }
 113
 114                         //if the user has not specified any labels use the ones from read.otu
 115                         if(label == "") {
 116                                 allLines = globaldata->allLines;
 117                                 labels = globaldata->labels;
 118                         }
 119
 120                         if (abort == false) {
 121                                 filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "rabund";
 122                                 m->openOutputFile(filename, out);
 123                         }
 124                 }
 125
 126         }
 127         catch(exception& e) {
 128                 m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
 129                 exit(1);
 130         }
 131 }
 132 //**********************************************************************************************************************
 133
 134 void GetRAbundCommand::help(){
 135         try {
 136                 m->mothurOut("The get.rabund command can only be executed after a successful read.otu of a listfile.\n");
 137                 m->mothurOut("The get.rabund command parameters are label and sorted.  No parameters are required.\n");
 138                 m->mothurOut("The label parameter allows you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n");
 139                 m->mothurOut("The sorted parameters allows you to print the rabund results sorted by abundance or not.  The default is sorted.\n");
 140                 m->mothurOut("The get.rabund command should be in the following format: get.rabund(label=yourLabels, sorted=yourSorted).\n");
 141                 m->mothurOut("Example get.rabund(sorted=F).\n");
 142                 m->mothurOut("The default value for label is all labels in your inputfile.\n");
 143                 m->mothurOut("The get.rabund command outputs a .rabund file containing the lines you selected.\n");
 144                 m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
 145         }
 146         catch(exception& e) {
 147                 m->errorOut(e, "GetRAbundCommand", "help");
 148                 exit(1);
 149         }
 150 }
 151
 152 //**********************************************************************************************************************
 153
 154 GetRAbundCommand::~GetRAbundCommand(){}
 155
 156 //**********************************************************************************************************************
 157
 158 int GetRAbundCommand::execute(){
 159         try {
 160
 161                 if (abort == true) { return 0; }
 162
 163                 //read first line
 164                 read = new ReadOTUFile(globaldata->inputFileName);
 165                 read->read(&*globaldata);
 166
 167                 input = globaldata->ginput;
 168                 list = globaldata->gListVector;
 169                 string lastLabel = list->getLabel();
 170
 171                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 172                 set<string> processedLabels;
 173                 set<string> userLabels = labels;
 174
 175                 if (m->control_pressed) {  outputTypes.clear();  out.close(); remove(filename.c_str());  delete list; globaldata->gListVector = NULL;  return 0; }
 176
 177                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 178
 179                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
 180                                         m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 181                                         rabund = new RAbundVector();
 182                                         *rabund = (list->getRAbundVector());
 183
 184                                         if (m->control_pressed) {   outputTypes.clear(); out.close(); remove(filename.c_str());  delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
 185
 186
 187                                         if(sorted)      {   rabund->print(out);                         }
 188                                         else            {       rabund->nonSortedPrint(out);    }
 189
 190                                         delete rabund;
 191
 192                                         processedLabels.insert(list->getLabel());
 193                                         userLabels.erase(list->getLabel());
 194                         }
 195
 196                         if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 197                                         string saveLabel = list->getLabel();
 198
 199                                         delete list;
 200                                         list = input->getListVector(lastLabel);
 201
 202                                         m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 203                                         rabund = new RAbundVector();
 204                                         *rabund = (list->getRAbundVector());
 205
 206                                         if (m->control_pressed) {   outputTypes.clear(); out.close(); remove(filename.c_str());  delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
 207
 208                                         if(sorted)      {   rabund->print(out);                         }
 209                                         else            {       rabund->nonSortedPrint(out);    }
 210
 211                                         delete rabund;
 212
 213                                         processedLabels.insert(list->getLabel());
 214                                         userLabels.erase(list->getLabel());
 215
 216                                         //restore real lastlabel to save below
 217                                         list->setLabel(saveLabel);
 218                         }
 219
 220                         lastLabel = list->getLabel();
 221
 222                         delete list;
 223                         list = input->getListVector();
 224                 }
 225
 226                 //output error messages about any remaining user labels
 227                 set<string>::iterator it;
 228                 bool needToRun = false;
 229                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 230                         m->mothurOut("Your file does not include the label " + *it);
 231                         if (processedLabels.count(lastLabel) != 1) {
 232                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 233                                 needToRun = true;
 234                         }else {
 235                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 236                         }
 237                 }
 238
 239                 //run last label if you need to
 240                 if (needToRun == true)  {
 241                         if (list != NULL) {     delete list;    }
 242                         list = input->getListVector(lastLabel);
 243
 244                         m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 245                         rabund = new RAbundVector();
 246                         *rabund = (list->getRAbundVector());
 247
 248                         if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
 249
 250                         if(sorted)      {   rabund->print(out);                         }
 251                         else            {       rabund->nonSortedPrint(out);    }
 252
 253                         delete rabund;
 254                         delete list;
 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                 globaldata->gListVector = NULL;
 265
 266                 return 0;
 267         }
 268
 269         catch(exception& e) {
 270                 m->errorOut(e, "GetRAbundCommand", "execute");
 271                 exit(1);
 272         }
 273 }
 274
 275 //**********************************************************************************************************************
 276
 277