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