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() == "") { m->mothurOut("You must read a listfile before you can use the get.rabund command."); m->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                 m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
  77                 exit(1);
  78         }
  79 }
  80 //**********************************************************************************************************************
  81
  82 void GetRAbundCommand::help(){
  83         try {
  84                 m->mothurOut("The get.rabund command can only be executed after a successful read.otu of a listfile.\n");
  85                 m->mothurOut("The get.rabund command parameters are label and sorted.  No parameters are required.\n");
  86                 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");
  87                 m->mothurOut("The sorted parameters allows you to print the rabund results sorted by abundance or not.  The default is sorted.\n");
  88                 m->mothurOut("The get.rabund command should be in the following format: get.rabund(label=yourLabels, sorted=yourSorted).\n");
  89                 m->mothurOut("Example get.rabund(sorted=F).\n");
  90                 m->mothurOut("The default value for label is all labels in your inputfile.\n");
  91                 m->mothurOut("The get.rabund command outputs a .rabund file containing the lines you selected.\n");
  92                 m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
  93         }
  94         catch(exception& e) {
  95                 m->errorOut(e, "GetRAbundCommand", "help");
  96                 exit(1);
  97         }
  98 }
  99
 100 //**********************************************************************************************************************
 101
 102 GetRAbundCommand::~GetRAbundCommand(){}
 103
 104 //**********************************************************************************************************************
 105
 106 int GetRAbundCommand::execute(){
 107         try {
 108
 109                 if (abort == true) { return 0; }
 110
 111                 //read first line
 112                 read = new ReadOTUFile(globaldata->inputFileName);
 113                 read->read(&*globaldata);
 114
 115                 input = globaldata->ginput;
 116                 list = globaldata->gListVector;
 117                 string lastLabel = list->getLabel();
 118
 119                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 120                 set<string> processedLabels;
 121                 set<string> userLabels = labels;
 122
 123                 if (m->control_pressed) {  out.close(); remove(filename.c_str()); delete read; delete input; delete list; globaldata->gListVector = NULL;  return 0; }
 124
 125                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 126
 127                         if(allLines == 1 || labels.count(list->getLabel()) == 1){
 128                                         m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 129                                         rabund = new RAbundVector();
 130                                         *rabund = (list->getRAbundVector());
 131
 132                                         if (m->control_pressed) {  out.close(); remove(filename.c_str()); delete read; delete input; delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
 133
 134
 135                                         if(sorted)      {   rabund->print(out);                         }
 136                                         else            {       rabund->nonSortedPrint(out);    }
 137
 138                                         delete rabund;
 139
 140                                         processedLabels.insert(list->getLabel());
 141                                         userLabels.erase(list->getLabel());
 142                         }
 143
 144                         if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 145                                         string saveLabel = list->getLabel();
 146
 147                                         delete list;
 148                                         list = input->getListVector(lastLabel);
 149
 150                                         m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 151                                         rabund = new RAbundVector();
 152                                         *rabund = (list->getRAbundVector());
 153
 154                                         if (m->control_pressed) {  out.close(); remove(filename.c_str()); delete read; delete input; delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
 155
 156                                         if(sorted)      {   rabund->print(out);                         }
 157                                         else            {       rabund->nonSortedPrint(out);    }
 158
 159                                         delete rabund;
 160
 161                                         processedLabels.insert(list->getLabel());
 162                                         userLabels.erase(list->getLabel());
 163
 164                                         //restore real lastlabel to save below
 165                                         list->setLabel(saveLabel);
 166                         }
 167
 168                         lastLabel = list->getLabel();
 169
 170                         delete list;
 171                         list = input->getListVector();
 172                 }
 173
 174                 //output error messages about any remaining user labels
 175                 set<string>::iterator it;
 176                 bool needToRun = false;
 177                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 178                         m->mothurOut("Your file does not include the label " + *it);
 179                         if (processedLabels.count(lastLabel) != 1) {
 180                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 181                                 needToRun = true;
 182                         }else {
 183                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 184                         }
 185                 }
 186
 187                 //run last label if you need to
 188                 if (needToRun == true)  {
 189                         if (list != NULL) {     delete list;    }
 190                         list = input->getListVector(lastLabel);
 191
 192                         m->mothurOut(list->getLabel()); m->mothurOutEndLine();
 193                         rabund = new RAbundVector();
 194                         *rabund = (list->getRAbundVector());
 195
 196                         if (m->control_pressed) {  out.close(); remove(filename.c_str()); delete read; delete input; delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
 197
 198                         if(sorted)      {   rabund->print(out);                         }
 199                         else            {       rabund->nonSortedPrint(out);    }
 200
 201                         delete rabund;
 202                         delete list;
 203                 }
 204
 205                 m->mothurOutEndLine();
 206                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 207                 m->mothurOut(filename); m->mothurOutEndLine();
 208                 m->mothurOutEndLine();
 209
 210
 211                 out.close();
 212                 delete read; delete input;
 213                 globaldata->gListVector = NULL;
 214
 215                 return 0;
 216         }
 217
 218         catch(exception& e) {
 219                 m->errorOut(e, "GetRAbundCommand", "execute");
 220                 exit(1);
 221         }
 222 }
 223
 224 //**********************************************************************************************************************
 225
 226