getrelabundcommand.cpp

   1 /*
   2  *  getrelabundcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 6/21/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "getrelabundcommand.h"
  11
  12 //**********************************************************************************************************************
  13
  14 GetRelAbundCommand::GetRelAbundCommand(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 AlignArray[] =  {"groups","label","scale","outputdir","inputdir"};
  27                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/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                         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->getSharedFile() == "")) {
  47                                  m->mothurOut("You must read a list and a group, or a shared file before you can use the get.relabund command."); m->mothurOutEndLine(); abort = true;
  48                         }
  49
  50                         //check for optional parameter and set defaults
  51                         // ...at some point should added some additional type checking...
  52                         label = validParameter.validFile(parameters, "label", false);
  53                         if (label == "not found") { label = ""; }
  54                         else {
  55                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  56                                 else { allLines = 1;  }
  57                         }
  58
  59                         //if the user has not specified any labels use the ones from read.otu
  60                         if (label == "") {
  61                                 allLines = globaldata->allLines;
  62                                 labels = globaldata->labels;
  63                         }
  64
  65                         groups = validParameter.validFile(parameters, "groups", false);
  66                         if (groups == "not found") { groups = ""; }
  67                         else {
  68                                 splitAtDash(groups, Groups);
  69                                 globaldata->Groups = Groups;
  70                         }
  71
  72                         scale = validParameter.validFile(parameters, "scale", false);                           if (scale == "not found") { scale = "totalgroup"; }
  73
  74                         if ((scale != "totalgroup") && (scale != "totalgroup") && (scale != "totalgroup") && (scale != "totalgroup")) {
  75                                 m->mothurOut(scale + " is not a valid scaling option for the get.relabund command. Choices are totalgroup, totalotu, averagegroup, averageotu."); m->mothurOutEndLine(); abort = true;
  76                         }
  77                 }
  78
  79         }
  80         catch(exception& e) {
  81                 m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
  82                 exit(1);
  83         }
  84 }
  85
  86 //**********************************************************************************************************************
  87
  88 void GetRelAbundCommand::help(){
  89         try {
  90                 m->mothurOut("The get.relabund command can only be executed after a successful read.otu command of a list and group or shared file.\n");
  91                 m->mothurOut("The get.relabund command parameters are groups, scale and label.  No parameters are required.\n");
  92                 m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n");
  93                 m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");
  94                 m->mothurOut("The scale parameter allows you to select what scale you would like to use. Choices are totalgroup, totalotu, averagegroup, averageotu, default is totalgroup.\n");
  95                 m->mothurOut("The get.relabund command should be in the following format: get.relabund(groups=yourGroups, label=yourLabels).\n");
  96                 m->mothurOut("Example get.relabund(groups=A-B-C, scale=log10).\n");
  97                 m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
  98                 m->mothurOut("The get.relabund command outputs a .relabund file.\n");
  99                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 100
 101         }
 102         catch(exception& e) {
 103                 m->errorOut(e, "GetRelAbundCommand", "help");
 104                 exit(1);
 105         }
 106 }
 107
 108 //**********************************************************************************************************************
 109
 110 GetRelAbundCommand::~GetRelAbundCommand(){
 111 }
 112
 113 //**********************************************************************************************************************
 114
 115 int GetRelAbundCommand::execute(){
 116         try {
 117
 118                 if (abort == true) { return 0; }
 119
 120                 string outputFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "relabund";
 121                 ofstream out;
 122                 openOutputFile(outputFileName, out);
 123
 124                 read = new ReadOTUFile(globaldata->inputFileName);
 125                 read->read(&*globaldata);
 126                 input = globaldata->ginput;
 127                 lookup = input->getSharedRAbundVectors();
 128                 string lastLabel = lookup[0]->getLabel();
 129
 130                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 131                 set<string> processedLabels;
 132                 set<string> userLabels = labels;
 133
 134                 //as long as you are not at the end of the file or done wih the lines you want
 135                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 136
 137                         if (m->control_pressed) {  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str()); return 0; }
 138
 139                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 140
 141                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 142                                 getRelAbundance(lookup, out);
 143
 144                                 processedLabels.insert(lookup[0]->getLabel());
 145                                 userLabels.erase(lookup[0]->getLabel());
 146                         }
 147
 148                         if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 149                                 string saveLabel = lookup[0]->getLabel();
 150
 151                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 152                                 lookup = input->getSharedRAbundVectors(lastLabel);
 153                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 154
 155                                 getRelAbundance(lookup, out);
 156
 157                                 processedLabels.insert(lookup[0]->getLabel());
 158                                 userLabels.erase(lookup[0]->getLabel());
 159
 160                                 //restore real lastlabel to save below
 161                                 lookup[0]->setLabel(saveLabel);
 162                         }
 163
 164                         lastLabel = lookup[0]->getLabel();
 165                         //prevent memory leak
 166                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 167
 168                         //get next line to process
 169                         lookup = input->getSharedRAbundVectors();
 170                 }
 171
 172                 if (m->control_pressed) { globaldata->Groups.clear(); delete read;  out.close(); remove(outputFileName.c_str());  return 0; }
 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                         for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 190                         lookup = input->getSharedRAbundVectors(lastLabel);
 191
 192                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 193
 194                         getRelAbundance(lookup, out);
 195
 196                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 197                 }
 198
 199                 //reset groups parameter
 200                 globaldata->Groups.clear();
 201                 delete input; globaldata->ginput = NULL;
 202                 delete read;
 203                 out.close();
 204
 205                 if (m->control_pressed) { remove(outputFileName.c_str()); return 0;}
 206
 207                 m->mothurOutEndLine();
 208                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 209                 m->mothurOut(outputFileName); m->mothurOutEndLine();
 210                 m->mothurOutEndLine();
 211
 212                 return 0;
 213         }
 214         catch(exception& e) {
 215                 m->errorOut(e, "GetRelAbundCommand", "execute");
 216                 exit(1);
 217         }
 218 }
 219 //**********************************************************************************************************************
 220
 221 int GetRelAbundCommand::getRelAbundance(vector<SharedRAbundVector*> thisLookUp, ofstream& out){
 222         try {
 223
 224
 225         }
 226         catch(exception& e) {
 227                 m->errorOut(e, "GetRelAbundCommand", "getRelAbundance");
 228                 exit(1);
 229         }
 230 }
 231 //**********************************************************************************************************************
 232
 233