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                 lines.clear();
  28                 labels.clear();
  29
  30                 //allow user to run help
  31                 if(option == "help") { help(); abort = true; }
  32
  33                 else {
  34                         //valid paramters for this command
  35                         string AlignArray[] =  {"groups","line","label","calc", "abund"};
  36                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  37
  38                         OptionParser parser(option);
  39                         map<string,string> parameters = parser.getParameters();
  40
  41                         ValidParameters validParameter;
  42
  43                         //check to make sure all parameters are valid for command
  44                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  45                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  46                         }
  47
  48                         //make sure the user has already run the read.otu command
  49                         if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
  50                                 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;
  51                         }
  52
  53                         //check for optional parameter and set defaults
  54                         // ...at some point should added some additional type checking...
  55                         line = validParameter.validFile(parameters, "line", false);
  56                         if (line == "not found") { line = "";  }
  57                         else {
  58                                 if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
  59                                 else { allLines = 1;  }
  60                         }
  61
  62                         label = validParameter.validFile(parameters, "label", false);
  63                         if (label == "not found") { label = ""; }
  64                         else {
  65                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  66                                 else { allLines = 1;  }
  67                         }
  68
  69                         //make sure user did not use both the line and label parameters
  70                         if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
  71                         //if the user has not specified any line or labels use the ones from read.otu
  72                         else if ((line == "") && (label == "")) {
  73                                 allLines = globaldata->allLines;
  74                                 labels = globaldata->labels;
  75                                 lines = globaldata->lines;
  76                         }
  77
  78                         groups = validParameter.validFile(parameters, "groups", false);
  79                         if (groups == "not found") { groups = ""; }
  80                         else {
  81                                 splitAtDash(groups, Groups);
  82                                 globaldata->Groups = Groups;
  83                         }
  84
  85                         format = globaldata->getFormat();
  86                         calc = validParameter.validFile(parameters, "calc", false);
  87                         if (calc == "not found") {
  88                                 if(format == "list") { calc = "sobs"; }
  89                                 else { calc = "sharedsobs"; }
  90                         }
  91                         else {
  92                                  if (calc == "default")  {
  93                                         if(format == "list") { calc = "sobs"; }
  94                                         else { calc = "sharedsobs"; }
  95                                 }
  96                         }
  97                         splitAtDash(calc, Estimators);
  98
  99                         string temp;
 100                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
 101                         convert(temp, abund);
 102
 103                         if (abort == false) {
 104                                 validCalculator = new ValidCalculators();
 105
 106                                 int i;
 107
 108                                 if (format == "list") {
 109                                         for (i=0; i<Estimators.size(); i++) {
 110                                                 if (validCalculator->isValidCalculator("vennsingle", Estimators[i]) == true) {
 111                                                         if (Estimators[i] == "sobs") {
 112                                                                 vennCalculators.push_back(new Sobs());
 113                                                         }else if (Estimators[i] == "chao") {
 114                                                                 vennCalculators.push_back(new Chao1());
 115                                                         }else if (Estimators[i] == "ace") {
 116                                                                 if(abund < 5)
 117                                                                         abund = 10;
 118                                                                 vennCalculators.push_back(new Ace(abund));
 119                                                         }
 120                                                 }
 121                                         }
 122                                 }else {
 123                                         for (i=0; i<Estimators.size(); i++) {
 124                                                 if (validCalculator->isValidCalculator("vennshared", Estimators[i]) == true) {
 125                                                         if (Estimators[i] == "sharedsobs") {
 126                                                                 vennCalculators.push_back(new SharedSobsCS());
 127                                                         }else if (Estimators[i] == "sharedchao") {
 128                                                                 vennCalculators.push_back(new SharedChao1());
 129                                                         }else if (Estimators[i] == "sharedace") {
 130                                                                 vennCalculators.push_back(new SharedAce());
 131                                                         }
 132                                                 }
 133                                         }
 134                                 }
 135
 136                                 venn = new Venn();
 137                         }
 138                 }
 139
 140
 141
 142         }
 143         catch(exception& e) {
 144                 errorOut(e, "VennCommand", "VennCommand");
 145                 exit(1);
 146         }
 147 }
 148
 149 //**********************************************************************************************************************
 150
 151 void VennCommand::help(){
 152         try {
 153                 mothurOut("The venn command can only be executed after a successful read.otu command.\n");
 154                 mothurOut("The venn command parameters are groups, calc, abund, line and label.  No parameters are required, but you may not use line and label at the same time.\n");
 155                 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");
 156                 mothurOut("The group names are separated by dashes. The line and label allow you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n");
 157                 mothurOut("The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, abund=yourAbund).\n");
 158                 mothurOut("Example venn(groups=A-B-C, line=1-3-5, calc=sharedsobs-sharedchao, abund=20).\n");
 159                 mothurOut("The default value for groups is all the groups in your groupfile up to 4, and all lines in your inputfile will be used.\n");
 160                 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");
 161                 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");
 162                 mothurOut("The only estmiator available four 4 groups is sharedsobs.\n");
 163                 mothurOut("The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n");
 164                 mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 165         }
 166         catch(exception& e) {
 167                 errorOut(e, "VennCommand", "help");
 168                 exit(1);
 169         }
 170 }
 171
 172
 173 //**********************************************************************************************************************
 174
 175 VennCommand::~VennCommand(){
 176         if (abort == false) {
 177                 delete input; globaldata->ginput = NULL;
 178                 delete read;
 179                 delete venn;
 180                 globaldata->sabund = NULL;
 181         }
 182
 183 }
 184
 185 //**********************************************************************************************************************
 186
 187 int VennCommand::execute(){
 188         try {
 189
 190                 if (abort == true) { return 0; }
 191
 192                 int count = 1;
 193                 string lastLabel;
 194
 195                 //if the users entered no valid calculators don't execute command
 196                 if (vennCalculators.size() == 0) { return 0; }
 197
 198                 if (format == "sharedfile") {
 199                         //you have groups
 200                         read = new ReadOTUFile(globaldata->inputFileName);
 201                         read->read(&*globaldata);
 202
 203                         input = globaldata->ginput;
 204                         lookup = input->getSharedRAbundVectors();
 205                         lastLabel = lookup[0]->getLabel();
 206                 }else if (format == "list") {
 207                         //you are using just a list file and have only one group
 208                         read = new ReadOTUFile(globaldata->inputFileName);
 209                         read->read(&*globaldata);
 210
 211                         sabund = globaldata->sabund;
 212                         lastLabel = sabund->getLabel();
 213                         input = globaldata->ginput;
 214                 }
 215
 216                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 217                 set<string> processedLabels;
 218                 set<string> userLabels = labels;
 219                 set<int> userLines = lines;
 220
 221                 if (format != "list") {
 222
 223                         //as long as you are not at the end of the file or done wih the lines you want
 224                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 225
 226                                 if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
 227                                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 228                                         processedLabels.insert(lookup[0]->getLabel());
 229                                         userLabels.erase(lookup[0]->getLabel());
 230                                         userLines.erase(count);
 231
 232                                         if (lookup.size() > 4) {
 233                                                 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();
 234                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 235                                         }
 236                                         venn->getPic(lookup, vennCalculators);
 237                                 }
 238
 239                                 if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 240                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 241                                         lookup = input->getSharedRAbundVectors(lastLabel);
 242
 243                                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 244                                         processedLabels.insert(lookup[0]->getLabel());
 245                                         userLabels.erase(lookup[0]->getLabel());
 246
 247                                         if (lookup.size() > 4) {
 248                                                 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();
 249                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 250                                         }
 251                                         venn->getPic(lookup, vennCalculators);
 252                                 }
 253
 254
 255                                 lastLabel = lookup[0]->getLabel();
 256
 257                                 //get next line to process
 258                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 259                                 lookup = input->getSharedRAbundVectors();
 260                                 count++;
 261                         }
 262
 263                         //output error messages about any remaining user labels
 264                         set<string>::iterator it;
 265                         bool needToRun = false;
 266                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 267                                 mothurOut("Your file does not include the label " + *it);
 268                                 if (processedLabels.count(lastLabel) != 1) {
 269                                         mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
 270                                         needToRun = true;
 271                                 }else {
 272                                         mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
 273                                 }
 274                         }
 275
 276                         //run last line if you need to
 277                         if (needToRun == true)  {
 278                                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i]; }  }
 279                                         lookup = input->getSharedRAbundVectors(lastLabel);
 280
 281                                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 282                                         processedLabels.insert(lookup[0]->getLabel());
 283                                         userLabels.erase(lookup[0]->getLabel());
 284
 285                                         if (lookup.size() > 4) {
 286                                                 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();
 287                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 288                                         }
 289                                         venn->getPic(lookup, vennCalculators);
 290                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 291                         }
 292
 293
 294                         //reset groups parameter
 295                         globaldata->Groups.clear();
 296
 297                 }else{
 298
 299                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 300
 301                                 if(allLines == 1 || lines.count(count) == 1 || labels.count(sabund->getLabel()) == 1){
 302
 303                                         mothurOut(sabund->getLabel()); mothurOutEndLine();
 304                                         venn->getPic(sabund, vennCalculators);
 305
 306                                         processedLabels.insert(sabund->getLabel());
 307                                         userLabels.erase(sabund->getLabel());
 308                                         userLines.erase(count);
 309                                 }
 310
 311                                 if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 312                                         delete sabund;
 313                                         sabund = input->getSAbundVector(lastLabel);
 314
 315                                         mothurOut(sabund->getLabel()); mothurOutEndLine();
 316                                         venn->getPic(sabund, vennCalculators);
 317
 318                                         processedLabels.insert(sabund->getLabel());
 319                                         userLabels.erase(sabund->getLabel());
 320                                 }
 321
 322                                 lastLabel = sabund->getLabel();
 323
 324                                 delete sabund;
 325                                 sabund = input->getSAbundVector();
 326                                 count++;
 327                         }
 328
 329                         //output error messages about any remaining user labels
 330                         set<string>::iterator it;
 331                         bool needToRun = false;
 332                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 333                                 mothurOut("Your file does not include the label " + *it);
 334                                 if (processedLabels.count(lastLabel) != 1) {
 335                                         mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
 336                                         needToRun = true;
 337                                 }else {
 338                                         mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
 339                                 }
 340                         }
 341
 342                         //run last line if you need to
 343                         if (needToRun == true)  {
 344                                 if (sabund != NULL) {   delete sabund;  }
 345                                 sabund = input->getSAbundVector(lastLabel);
 346
 347                                 mothurOut(sabund->getLabel()); mothurOutEndLine();
 348                                 venn->getPic(sabund, vennCalculators);
 349                                 delete sabund;
 350
 351                         }
 352
 353                 }
 354
 355                 for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 356                 return 0;
 357         }
 358         catch(exception& e) {
 359                 errorOut(e, "VennCommand", "execute");
 360                 exit(1);
 361         }
 362 }
 363
 364 //**********************************************************************************************************************