venncommand.cpp

   1 /*
   2  *  venncommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/30/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "venncommand.h"
  11 #include "ace.h"
  12 #include "sobs.h"
  13 #include "chao1.h"
  14 //#include "jackknife.h"
  15 #include "sharedsobscollectsummary.h"
  16 #include "sharedchao1.h"
  17 #include "sharedace.h"
  18
  19
  20 //**********************************************************************************************************************
  21
  22 VennCommand::VennCommand(string option){
  23         try {
  24                 globaldata = GlobalData::getInstance();
  25                 abort = false;
  26                 allLines = 1;
  27                 labels.clear();
  28
  29                 //allow user to run help
  30                 if(option == "help") { help(); abort = true; }
  31
  32                 else {
  33                         //valid paramters for this command
  34                         string AlignArray[] =  {"groups","label","calc", "abund"};
  35                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  36
  37                         OptionParser parser(option);
  38                         map<string,string> parameters = parser.getParameters();
  39
  40                         ValidParameters validParameter;
  41
  42                         //check to make sure all parameters are valid for command
  43                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  44                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  45                         }
  46
  47                         //make sure the user has already run the read.otu command
  48                         if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
  49                                 mothurOut("You must read a list, or a list and a group, or a shared before you can use the venn command."); mothurOutEndLine(); abort = true;
  50                         }
  51
  52                         //check for optional parameter and set defaults
  53                         // ...at some point should added some additional type checking...
  54                         label = validParameter.validFile(parameters, "label", false);
  55                         if (label == "not found") { label = ""; }
  56                         else {
  57                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  58                                 else { allLines = 1;  }
  59                         }
  60
  61                         //if the user has not specified any labels use the ones from read.otu
  62                         if (label == "") {
  63                                 allLines = globaldata->allLines;
  64                                 labels = globaldata->labels;
  65                         }
  66
  67                         groups = validParameter.validFile(parameters, "groups", false);
  68                         if (groups == "not found") { groups = ""; }
  69                         else {
  70                                 splitAtDash(groups, Groups);
  71                                 globaldata->Groups = Groups;
  72                         }
  73
  74                         format = globaldata->getFormat();
  75                         calc = validParameter.validFile(parameters, "calc", false);
  76                         if (calc == "not found") {
  77                                 if(format == "list") { calc = "sobs"; }
  78                                 else { calc = "sharedsobs"; }
  79                         }
  80                         else {
  81                                  if (calc == "default")  {
  82                                         if(format == "list") { calc = "sobs"; }
  83                                         else { calc = "sharedsobs"; }
  84                                 }
  85                         }
  86                         splitAtDash(calc, Estimators);
  87
  88                         string temp;
  89                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
  90                         convert(temp, abund);
  91
  92                         if (abort == false) {
  93                                 validCalculator = new ValidCalculators();
  94
  95                                 int i;
  96
  97                                 if (format == "list") {
  98                                         for (i=0; i<Estimators.size(); i++) {
  99                                                 if (validCalculator->isValidCalculator("vennsingle", Estimators[i]) == true) {
 100                                                         if (Estimators[i] == "sobs") {
 101                                                                 vennCalculators.push_back(new Sobs());
 102                                                         }else if (Estimators[i] == "chao") {
 103                                                                 vennCalculators.push_back(new Chao1());
 104                                                         }else if (Estimators[i] == "ace") {
 105                                                                 if(abund < 5)
 106                                                                         abund = 10;
 107                                                                 vennCalculators.push_back(new Ace(abund));
 108                                                         }
 109                                                 }
 110                                         }
 111                                 }else {
 112                                         for (i=0; i<Estimators.size(); i++) {
 113                                                 if (validCalculator->isValidCalculator("vennshared", Estimators[i]) == true) {
 114                                                         if (Estimators[i] == "sharedsobs") {
 115                                                                 vennCalculators.push_back(new SharedSobsCS());
 116                                                         }else if (Estimators[i] == "sharedchao") {
 117                                                                 vennCalculators.push_back(new SharedChao1());
 118                                                         }else if (Estimators[i] == "sharedace") {
 119                                                                 vennCalculators.push_back(new SharedAce());
 120                                                         }
 121                                                 }
 122                                         }
 123                                 }
 124
 125                                 venn = new Venn();
 126                         }
 127                 }
 128
 129
 130
 131         }
 132         catch(exception& e) {
 133                 errorOut(e, "VennCommand", "VennCommand");
 134                 exit(1);
 135         }
 136 }
 137
 138 //**********************************************************************************************************************
 139
 140 void VennCommand::help(){
 141         try {
 142                 mothurOut("The venn command can only be executed after a successful read.otu command.\n");
 143                 mothurOut("The venn command parameters are groups, calc, abund and label.  No parameters are required.\n");
 144                 mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups.\n");
 145                 mothurOut("The group names are separated by dashes. The label allows you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n");
 146                 mothurOut("The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n");
 147                 mothurOut("Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n");
 148                 mothurOut("The default value for groups is all the groups in your groupfile up to 4, and all labels in your inputfile will be used.\n");
 149                 mothurOut("The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups.\n");
 150                 mothurOut("The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a list and group file or a shared file.\n");
 151                 mothurOut("The only estmiator available four 4 groups is sharedsobs.\n");
 152                 mothurOut("The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n");
 153                 mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 154         }
 155         catch(exception& e) {
 156                 errorOut(e, "VennCommand", "help");
 157                 exit(1);
 158         }
 159 }
 160
 161
 162 //**********************************************************************************************************************
 163
 164 VennCommand::~VennCommand(){
 165         if (abort == false) {
 166                 delete input; globaldata->ginput = NULL;
 167                 delete read;
 168                 delete venn;
 169                 globaldata->sabund = NULL;
 170         }
 171
 172 }
 173
 174 //**********************************************************************************************************************
 175
 176 int VennCommand::execute(){
 177         try {
 178
 179                 if (abort == true) { return 0; }
 180
 181                 string lastLabel;
 182
 183                 //if the users entered no valid calculators don't execute command
 184                 if (vennCalculators.size() == 0) { return 0; }
 185
 186                 if (format == "sharedfile") {
 187                         //you have groups
 188                         read = new ReadOTUFile(globaldata->inputFileName);
 189                         read->read(&*globaldata);
 190
 191                         input = globaldata->ginput;
 192                         lookup = input->getSharedRAbundVectors();
 193                         lastLabel = lookup[0]->getLabel();
 194                 }else if (format == "list") {
 195                         //you are using just a list file and have only one group
 196                         read = new ReadOTUFile(globaldata->inputFileName);
 197                         read->read(&*globaldata);
 198
 199                         sabund = globaldata->sabund;
 200                         lastLabel = sabund->getLabel();
 201                         input = globaldata->ginput;
 202                 }
 203
 204                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 205                 set<string> processedLabels;
 206                 set<string> userLabels = labels;
 207
 208                 if (format != "list") {
 209
 210                         //as long as you are not at the end of the file or done wih the lines you want
 211                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 212
 213                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 214                                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 215                                         processedLabels.insert(lookup[0]->getLabel());
 216                                         userLabels.erase(lookup[0]->getLabel());
 217
 218                                         if (lookup.size() > 4) {
 219                                                 mothurOut("Error: Too many groups chosen.  You may use up to 4 groups with the venn command.  I will use the first four groups in your groupfile."); mothurOutEndLine();
 220                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 221                                         }
 222                                         venn->getPic(lookup, vennCalculators);
 223                                 }
 224
 225                                 if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 226                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 227                                         lookup = input->getSharedRAbundVectors(lastLabel);
 228
 229                                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 230                                         processedLabels.insert(lookup[0]->getLabel());
 231                                         userLabels.erase(lookup[0]->getLabel());
 232
 233                                         if (lookup.size() > 4) {
 234                                                 mothurOut("Error: Too many groups chosen.  You may use up to 4 groups with the venn command.  I will use the first four groups in your groupfile."); mothurOutEndLine();
 235                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 236                                         }
 237                                         venn->getPic(lookup, vennCalculators);
 238                                 }
 239
 240
 241                                 lastLabel = lookup[0]->getLabel();
 242
 243                                 //get next line to process
 244                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 245                                 lookup = input->getSharedRAbundVectors();
 246                         }
 247
 248                         //output error messages about any remaining user labels
 249                         set<string>::iterator it;
 250                         bool needToRun = false;
 251                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 252                                 mothurOut("Your file does not include the label " + *it);
 253                                 if (processedLabels.count(lastLabel) != 1) {
 254                                         mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
 255                                         needToRun = true;
 256                                 }else {
 257                                         mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
 258                                 }
 259                         }
 260
 261                         //run last label if you need to
 262                         if (needToRun == true)  {
 263                                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i]; }  }
 264                                         lookup = input->getSharedRAbundVectors(lastLabel);
 265
 266                                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 267                                         processedLabels.insert(lookup[0]->getLabel());
 268                                         userLabels.erase(lookup[0]->getLabel());
 269
 270                                         if (lookup.size() > 4) {
 271                                                 mothurOut("Error: Too many groups chosen.  You may use up to 4 groups with the venn command.  I will use the first four groups in your groupfile."); mothurOutEndLine();
 272                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 273                                         }
 274                                         venn->getPic(lookup, vennCalculators);
 275                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 276                         }
 277
 278
 279                         //reset groups parameter
 280                         globaldata->Groups.clear();
 281
 282                 }else{
 283
 284                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 285
 286                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 287
 288                                         mothurOut(sabund->getLabel()); mothurOutEndLine();
 289                                         venn->getPic(sabund, vennCalculators);
 290
 291                                         processedLabels.insert(sabund->getLabel());
 292                                         userLabels.erase(sabund->getLabel());
 293                                 }
 294
 295                                 if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 296                                         delete sabund;
 297                                         sabund = input->getSAbundVector(lastLabel);
 298
 299                                         mothurOut(sabund->getLabel()); mothurOutEndLine();
 300                                         venn->getPic(sabund, vennCalculators);
 301
 302                                         processedLabels.insert(sabund->getLabel());
 303                                         userLabels.erase(sabund->getLabel());
 304                                 }
 305
 306                                 lastLabel = sabund->getLabel();
 307
 308                                 delete sabund;
 309                                 sabund = input->getSAbundVector();
 310                         }
 311
 312                         //output error messages about any remaining user labels
 313                         set<string>::iterator it;
 314                         bool needToRun = false;
 315                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 316                                 mothurOut("Your file does not include the label " + *it);
 317                                 if (processedLabels.count(lastLabel) != 1) {
 318                                         mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
 319                                         needToRun = true;
 320                                 }else {
 321                                         mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
 322                                 }
 323                         }
 324
 325                         //run last label if you need to
 326                         if (needToRun == true)  {
 327                                 if (sabund != NULL) {   delete sabund;  }
 328                                 sabund = input->getSAbundVector(lastLabel);
 329
 330                                 mothurOut(sabund->getLabel()); mothurOutEndLine();
 331                                 venn->getPic(sabund, vennCalculators);
 332                                 delete sabund;
 333
 334                         }
 335
 336                 }
 337
 338                 for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 339                 return 0;
 340         }
 341         catch(exception& e) {
 342                 errorOut(e, "VennCommand", "execute");
 343                 exit(1);
 344         }
 345 }
 346
 347 //**********************************************************************************************************************