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                 lines.clear();
  20                 labels.clear();
  21
  22                 //allow user to run help
  23                 if(option == "help") { help(); abort = true; }
  24
  25                 else {
  26                         //valid paramters for this command
  27                         string Array[] =  {"line","label","sorted"};
  28                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  29
  30                         OptionParser parser(option);
  31                         map<string,string> parameters = parser.getParameters();
  32
  33                         ValidParameters validParameter;
  34
  35                         //check to make sure all parameters are valid for command
  36                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  37                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  38                         }
  39
  40                         //make sure the user has already run the read.otu command
  41                         if (globaldata->getListFile() == "") { mothurOut("You must read a listfile before you can use the get.rabund command."); mothurOutEndLine(); abort = true; }
  42
  43                         //check for optional parameter and set defaults
  44                         // ...at some point should added some additional type checking...
  45
  46                         string temp;
  47                         temp = validParameter.validFile(parameters, "sorted", false);                   if (temp == "not found") { temp = "T"; }
  48                         sorted = isTrue(temp);
  49
  50                         line = validParameter.validFile(parameters, "line", false);
  51                         if (line == "not found") { line = "";  }
  52                         else {
  53                                 if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
  54                                 else { allLines = 1;  }
  55                         }
  56
  57                         label = validParameter.validFile(parameters, "label", false);
  58                         if (label == "not found") { label = ""; }
  59                         else {
  60                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  61                                 else { allLines = 1;  }
  62                         }
  63
  64                         //make sure user did not use both the line and label parameters
  65                         if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
  66                         //if the user has not specified any line or labels use the ones from read.otu
  67                         else if((line == "") && (label == "")) {
  68                                 allLines = globaldata->allLines;
  69                                 labels = globaldata->labels;
  70                                 lines = globaldata->lines;
  71                         }
  72
  73                         if (abort == false) {
  74                                 filename = getRootName(globaldata->inputFileName) + "rabund";
  75                                 openOutputFile(filename, out);
  76                         }
  77                 }
  78
  79         }
  80         catch(exception& e) {
  81                 errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
  82                 exit(1);
  83         }
  84 }
  85 //**********************************************************************************************************************
  86
  87 void GetRAbundCommand::help(){
  88         try {
  89                 mothurOut("The get.rabund command can only be executed after a successful read.otu of a listfile.\n");
  90                 mothurOut("The get.rabund command parameters are line, label and sorted.  No parameters are required, and you may not use line and label at the same time.\n");
  91                 mothurOut("The line and label allow you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n");
  92                 mothurOut("The sorted parameters allows you to print the rabund results sorted by abundance or not.  The default is sorted.\n");
  93                 mothurOut("The get.rabund command should be in the following format: get.rabund(line=yourLines, label=yourLabels, sorted=yourSorted).\n");
  94                 mothurOut("Example get.rabund(line=1-3-5, sorted=F).\n");
  95                 mothurOut("The default value for line and label are all lines in your inputfile.\n");
  96                 mothurOut("The get.rabund command outputs a .rabund file containing the lines you selected.\n");
  97                 mothurOut("Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines).\n\n");
  98         }
  99         catch(exception& e) {
 100                 errorOut(e, "GetRAbundCommand", "help");
 101                 exit(1);
 102         }
 103 }
 104
 105 //**********************************************************************************************************************
 106
 107 GetRAbundCommand::~GetRAbundCommand(){
 108         if (abort == false) {  globaldata->gListVector = NULL; }
 109 }
 110
 111 //**********************************************************************************************************************
 112
 113 int GetRAbundCommand::execute(){
 114         try {
 115
 116                 if (abort == true) { return 0; }
 117
 118                 int count = 1;
 119
 120                 //read first line
 121                 read = new ReadOTUFile(globaldata->inputFileName);
 122                 read->read(&*globaldata);
 123
 124                 input = globaldata->ginput;
 125                 list = globaldata->gListVector;
 126                 string lastLabel = list->getLabel();
 127
 128                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 129                 set<string> processedLabels;
 130                 set<string> userLabels = labels;
 131                 set<int> userLines = lines;
 132
 133
 134                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 135
 136                         if(allLines == 1 || lines.count(count) == 1 || labels.count(list->getLabel()) == 1){
 137                                         mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
 138                                         rabund = new RAbundVector();
 139                                         *rabund = (list->getRAbundVector());
 140
 141                                         if(sorted)      {   rabund->print(out);                         }
 142                                         else            {       rabund->nonSortedPrint(out);    }
 143
 144                                         delete rabund;
 145
 146                                         processedLabels.insert(list->getLabel());
 147                                         userLabels.erase(list->getLabel());
 148                                         userLines.erase(count);
 149                         }
 150
 151                         if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 152                                         delete list;
 153                                         list = input->getListVector(lastLabel);
 154
 155                                         mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
 156                                         rabund = new RAbundVector();
 157                                         *rabund = (list->getRAbundVector());
 158
 159                                         if(sorted)      {   rabund->print(out);                         }
 160                                         else            {       rabund->nonSortedPrint(out);    }
 161
 162                                         delete rabund;
 163
 164                                         processedLabels.insert(list->getLabel());
 165                                         userLabels.erase(list->getLabel());
 166                         }
 167
 168                         lastLabel = list->getLabel();
 169
 170                         delete list;
 171                         list = input->getListVector();
 172                         count++;
 173                 }
 174
 175                 //output error messages about any remaining user labels
 176                 set<string>::iterator it;
 177                 bool needToRun = false;
 178                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 179                         mothurOut("Your file does not include the label " + *it);
 180                         if (processedLabels.count(lastLabel) != 1) {
 181                                 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
 182                                 needToRun = true;
 183                         }else {
 184                                 mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
 185                         }
 186                 }
 187
 188                 //run last line if you need to
 189                 if (needToRun == true)  {
 190                         delete list;
 191                         list = input->getListVector(lastLabel);
 192
 193                         mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
 194                         rabund = new RAbundVector();
 195                         *rabund = (list->getRAbundVector());
 196
 197                         if(sorted)      {   rabund->print(out);                         }
 198                         else            {       rabund->nonSortedPrint(out);    }
 199
 200                         delete rabund;
 201                         delete list;
 202                 }
 203
 204                 out.close();
 205                 return 0;
 206         }
 207
 208         catch(exception& e) {
 209                 errorOut(e, "GetRAbundCommand", "execute");
 210                 exit(1);
 211         }
 212 }
 213
 214 //**********************************************************************************************************************
 215
 216