getsabundcommand.cpp

   1 /*
   2  *  getsabundcommand.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 "getsabundcommand.h"
  11
  12 //**********************************************************************************************************************
  13
  14 GetSAbundCommand::GetSAbundCommand(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","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 += m->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() == "") && (globaldata->getRabundFile() == "")) { m->mothurOut("You must read a list or rabund before you can use the get.sabund 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                         label = validParameter.validFile(parameters, "label", false);
  51                         if (label == "not found") { label = ""; }
  52                         else {
  53                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
  54                                 else { allLines = 1;  }
  55                         }
  56
  57                         //if the user has not specified any labels use the ones from read.otu
  58                         if(label == "") {
  59                                 allLines = globaldata->allLines;
  60                                 labels = globaldata->labels;
  61                         }
  62
  63                         if (abort == false) {
  64                                 filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "sabund";
  65                                 m->openOutputFile(filename, out);
  66                         }
  67                 }
  68
  69         }
  70         catch(exception& e) {
  71                 m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
  72                 exit(1);
  73         }
  74 }
  75 //**********************************************************************************************************************
  76
  77 void GetSAbundCommand::help(){
  78         try {
  79                 m->mothurOut("The get.sabund command can only be executed after a successful read.otu of a listfile or rabundfile.\n");
  80                 m->mothurOut("The get.sabund command parameters is label.  No parameters are required.\n");
  81                 m->mothurOut("The label parameter allows you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n");
  82                 m->mothurOut("The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n");
  83                 m->mothurOut("Example get.sabund().\n");
  84                 m->mothurOut("The default value for label is all labels in your inputfile.\n");
  85                 m->mothurOut("The get.sabund command outputs a .sabund file containing the labels you selected.\n");
  86                 m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
  87         }
  88         catch(exception& e) {
  89                 m->errorOut(e, "GetSAbundCommand", "help");
  90                 exit(1);
  91         }
  92 }
  93
  94 //**********************************************************************************************************************
  95
  96 GetSAbundCommand::~GetSAbundCommand(){
  97 }
  98
  99 //**********************************************************************************************************************
 100
 101 int GetSAbundCommand::execute(){
 102         try {
 103
 104                 if (abort == true) { return 0; }
 105
 106                 //using order vector so you don't have to distinguish between the list and rabund files
 107                 read = new ReadOTUFile(globaldata->inputFileName);
 108                 read->read(&*globaldata);
 109
 110                 order = globaldata->gorder;
 111                 string lastLabel = order->getLabel();
 112                 input = globaldata->ginput;
 113
 114                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 115                 set<string> processedLabels;
 116                 set<string> userLabels = labels;
 117
 118                 if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 119
 120
 121                 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 122
 123                         if(allLines == 1 || labels.count(order->getLabel()) == 1){
 124                                         m->mothurOut(order->getLabel());  m->mothurOutEndLine();
 125                                         sabund = new SAbundVector();
 126                                         *sabund = (order->getSAbundVector());
 127                                         sabund->print(out);
 128                                         delete sabund;
 129
 130                                         if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 131
 132                                         processedLabels.insert(order->getLabel());
 133                                         userLabels.erase(order->getLabel());
 134                         }
 135
 136                         if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 137                                         string saveLabel = order->getLabel();
 138
 139                                         delete order;
 140                                         order = (input->getOrderVector(lastLabel));
 141
 142                                         m->mothurOut(order->getLabel());  m->mothurOutEndLine();
 143                                         sabund = new SAbundVector();
 144                                         *sabund = (order->getSAbundVector());
 145                                         sabund->print(out);
 146                                         delete sabund;
 147
 148                                         if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 149
 150                                         processedLabels.insert(order->getLabel());
 151                                         userLabels.erase(order->getLabel());
 152
 153                                         //restore real lastlabel to save below
 154                                         order->setLabel(saveLabel);
 155                         }
 156
 157
 158                         lastLabel = order->getLabel();
 159
 160                         delete order;
 161                         order = (input->getOrderVector());
 162                 }
 163
 164                 //output error messages about any remaining user labels
 165                 set<string>::iterator it;
 166                 bool needToRun = false;
 167                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 168                         m->mothurOut("Your file does not include the label " + *it);
 169                         if (processedLabels.count(lastLabel) != 1) {
 170                                 m->mothurOut(". I will use " + lastLabel + ".");  m->mothurOutEndLine();
 171                                 needToRun = true;
 172                         }else {
 173                                 m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
 174                         }
 175                 }
 176
 177                 //run last label if you need to
 178                 if (needToRun == true)  {
 179                         if (order != NULL) {    delete order;   }
 180                         order = (input->getOrderVector(lastLabel));
 181
 182                         m->mothurOut(order->getLabel());  m->mothurOutEndLine();
 183                         sabund = new SAbundVector();
 184                         *sabund = (order->getSAbundVector());
 185                         sabund->print(out);
 186                         delete sabund;
 187
 188                         if (m->control_pressed) {  out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 189
 190                         delete order;
 191                 }
 192                 globaldata->gorder = NULL;
 193
 194                 out.close();
 195
 196                 m->mothurOutEndLine();
 197                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 198                 m->mothurOut(filename); m->mothurOutEndLine();
 199                 m->mothurOutEndLine();
 200
 201                 return 0;
 202         }
 203
 204         catch(exception& e) {
 205                 m->errorOut(e, "GetSAbundCommand", "execute");
 206                 exit(1);
 207         }
 208 }
 209
 210 //**********************************************************************************************************************
 211
 212