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