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","outputdir","inputdir"};
  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                                 m->mothurOut("You must read a list, or a list and a group, or a shared before you can use the venn command."); m->mothurOutEndLine(); abort = true;
  50                         }
  51
  52                         //if the user changes the output directory command factory will send this info to us in the output parameter
  53                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  54                                 outputDir = "";
  55                                 outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
  56                         }
  57
  58                         //check for optional parameter and set defaults
  59                         // ...at some point should added some additional type checking...
  60                         label = validParameter.validFile(parameters, "label", false);
  61                         if (label == "not found") { label = ""; }
  62                         else {
  63                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  64                                 else { allLines = 1;  }
  65                         }
  66
  67                         //if the user has not specified any labels use the ones from read.otu
  68                         if (label == "") {
  69                                 allLines = globaldata->allLines;
  70                                 labels = globaldata->labels;
  71                         }
  72
  73                         groups = validParameter.validFile(parameters, "groups", false);
  74                         if (groups == "not found") { groups = ""; }
  75                         else {
  76                                 splitAtDash(groups, Groups);
  77                                 globaldata->Groups = Groups;
  78                         }
  79
  80                         format = globaldata->getFormat();
  81                         calc = validParameter.validFile(parameters, "calc", false);
  82                         if (calc == "not found") {
  83                                 if(format == "list") { calc = "sobs"; }
  84                                 else { calc = "sharedsobs"; }
  85                         }
  86                         else {
  87                                  if (calc == "default")  {
  88                                         if(format == "list") { calc = "sobs"; }
  89                                         else { calc = "sharedsobs"; }
  90                                 }
  91                         }
  92                         splitAtDash(calc, Estimators);
  93
  94                         string temp;
  95                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
  96                         convert(temp, abund);
  97
  98                         if (abort == false) {
  99                                 validCalculator = new ValidCalculators();
 100
 101                                 int i;
 102
 103                                 if (format == "list") {
 104                                         for (i=0; i<Estimators.size(); i++) {
 105                                                 if (validCalculator->isValidCalculator("vennsingle", Estimators[i]) == true) {
 106                                                         if (Estimators[i] == "sobs") {
 107                                                                 vennCalculators.push_back(new Sobs());
 108                                                         }else if (Estimators[i] == "chao") {
 109                                                                 vennCalculators.push_back(new Chao1());
 110                                                         }else if (Estimators[i] == "ace") {
 111                                                                 if(abund < 5)
 112                                                                         abund = 10;
 113                                                                 vennCalculators.push_back(new Ace(abund));
 114                                                         }
 115                                                 }
 116                                         }
 117                                 }else {
 118                                         for (i=0; i<Estimators.size(); i++) {
 119                                                 if (validCalculator->isValidCalculator("vennshared", Estimators[i]) == true) {
 120                                                         if (Estimators[i] == "sharedsobs") {
 121                                                                 vennCalculators.push_back(new SharedSobsCS());
 122                                                         }else if (Estimators[i] == "sharedchao") {
 123                                                                 vennCalculators.push_back(new SharedChao1());
 124                                                         }else if (Estimators[i] == "sharedace") {
 125                                                                 vennCalculators.push_back(new SharedAce());
 126                                                         }
 127                                                 }
 128                                         }
 129                                 }
 130
 131                                 venn = new Venn(outputDir);
 132                         }
 133                 }
 134
 135
 136
 137         }
 138         catch(exception& e) {
 139                 m->errorOut(e, "VennCommand", "VennCommand");
 140                 exit(1);
 141         }
 142 }
 143
 144 //**********************************************************************************************************************
 145
 146 void VennCommand::help(){
 147         try {
 148                 m->mothurOut("The venn command can only be executed after a successful read.otu command.\n");
 149                 m->mothurOut("The venn command parameters are groups, calc, abund and label.  No parameters are required.\n");
 150                 m->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");
 151                 m->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");
 152                 m->mothurOut("The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n");
 153                 m->mothurOut("Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n");
 154                 m->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");
 155                 m->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");
 156                 m->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");
 157                 m->mothurOut("The only estmiator available four 4 groups is sharedsobs.\n");
 158                 m->mothurOut("The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n");
 159                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 160         }
 161         catch(exception& e) {
 162                 m->errorOut(e, "VennCommand", "help");
 163                 exit(1);
 164         }
 165 }
 166
 167
 168 //**********************************************************************************************************************
 169
 170 VennCommand::~VennCommand(){
 171         if (abort == false) {
 172                 delete input; globaldata->ginput = NULL;
 173                 delete read;
 174                 delete venn;
 175                 globaldata->sabund = NULL;
 176         }
 177
 178 }
 179
 180 //**********************************************************************************************************************
 181
 182 int VennCommand::execute(){
 183         try {
 184
 185                 if (abort == true) { return 0; }
 186
 187                 string lastLabel;
 188                 vector<string> outputNames;
 189
 190                 //if the users entered no valid calculators don't execute command
 191                 if (vennCalculators.size() == 0) { return 0; }
 192
 193                 if (format == "sharedfile") {
 194                         //you have groups
 195                         read = new ReadOTUFile(globaldata->inputFileName);
 196                         read->read(&*globaldata);
 197
 198                         input = globaldata->ginput;
 199                         lookup = input->getSharedRAbundVectors();
 200                         lastLabel = lookup[0]->getLabel();
 201                 }else if (format == "list") {
 202                         //you are using just a list file and have only one group
 203                         read = new ReadOTUFile(globaldata->inputFileName);
 204                         read->read(&*globaldata);
 205
 206                         sabund = globaldata->sabund;
 207                         lastLabel = sabund->getLabel();
 208                         input = globaldata->ginput;
 209                 }
 210
 211                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 212                 set<string> processedLabels;
 213                 set<string> userLabels = labels;
 214
 215                 if (format != "list") {
 216
 217                         //as long as you are not at the end of the file or done wih the lines you want
 218                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 219
 220                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 221                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 222                                         processedLabels.insert(lookup[0]->getLabel());
 223                                         userLabels.erase(lookup[0]->getLabel());
 224
 225                                         if (lookup.size() > 4) {
 226                                                 m->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."); m->mothurOutEndLine();
 227                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 228                                         }
 229
 230                                         vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 231                                         for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); }
 232                                 }
 233
 234                                 if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 235                                         string saveLabel = lookup[0]->getLabel();
 236
 237                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 238                                         lookup = input->getSharedRAbundVectors(lastLabel);
 239
 240                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 241                                         processedLabels.insert(lookup[0]->getLabel());
 242                                         userLabels.erase(lookup[0]->getLabel());
 243
 244                                         if (lookup.size() > 4) {
 245                                                 m->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."); m->mothurOutEndLine();
 246                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 247                                         }
 248                                         vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 249                                         for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); }
 250
 251                                         //restore real lastlabel to save below
 252                                         lookup[0]->setLabel(saveLabel);
 253                                 }
 254
 255
 256                                 lastLabel = lookup[0]->getLabel();
 257
 258                                 //get next line to process
 259                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 260                                 lookup = input->getSharedRAbundVectors();
 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                                 m->mothurOut("Your file does not include the label " + *it);
 268                                 if (processedLabels.count(lastLabel) != 1) {
 269                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 270                                         needToRun = true;
 271                                 }else {
 272                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 273                                 }
 274                         }
 275
 276                         //run last label 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                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 282                                         processedLabels.insert(lookup[0]->getLabel());
 283                                         userLabels.erase(lookup[0]->getLabel());
 284
 285                                         if (lookup.size() > 4) {
 286                                                 m->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."); m->mothurOutEndLine();
 287                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 288                                         }
 289                                         vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 290                                         for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); }
 291
 292                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 293                         }
 294
 295
 296                         //reset groups parameter
 297                         globaldata->Groups.clear();
 298
 299                 }else{
 300
 301                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 302
 303                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 304
 305                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 306                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 307                                         for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); }
 308
 309
 310                                         processedLabels.insert(sabund->getLabel());
 311                                         userLabels.erase(sabund->getLabel());
 312                                 }
 313
 314                                 if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 315                                         string saveLabel = sabund->getLabel();
 316
 317                                         delete sabund;
 318                                         sabund = input->getSAbundVector(lastLabel);
 319
 320                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 321                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 322                                         for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); }
 323
 324
 325                                         processedLabels.insert(sabund->getLabel());
 326                                         userLabels.erase(sabund->getLabel());
 327
 328                                         //restore real lastlabel to save below
 329                                         sabund->setLabel(saveLabel);
 330                                 }
 331
 332                                 lastLabel = sabund->getLabel();
 333
 334                                 delete sabund;
 335                                 sabund = input->getSAbundVector();
 336                         }
 337
 338                         //output error messages about any remaining user labels
 339                         set<string>::iterator it;
 340                         bool needToRun = false;
 341                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 342                                 m->mothurOut("Your file does not include the label " + *it);
 343                                 if (processedLabels.count(lastLabel) != 1) {
 344                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 345                                         needToRun = true;
 346                                 }else {
 347                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 348                                 }
 349                         }
 350
 351                         //run last label if you need to
 352                         if (needToRun == true)  {
 353                                 if (sabund != NULL) {   delete sabund;  }
 354                                 sabund = input->getSAbundVector(lastLabel);
 355
 356                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 357                                 vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 358                                 for(int i = 0; i < outfilenames.size(); i++) { outputNames.push_back(outfilenames[i]); }
 359
 360                                 delete sabund;
 361
 362                         }
 363
 364                 }
 365
 366                 for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 367
 368                 m->mothurOutEndLine();
 369                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 370                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 371                 m->mothurOutEndLine();
 372
 373
 374                 return 0;
 375         }
 376         catch(exception& e) {
 377                 m->errorOut(e, "VennCommand", "execute");
 378                 exit(1);
 379         }
 380 }
 381
 382 //**********************************************************************************************************************