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                         parser = new OptionParser();
  39                         parser->parse(option, parameters);  delete parser;
  40
  41                         ValidParameters* validParameter = new ValidParameters();
  42
  43                         //check to make sure all parameters are valid for command
  44                         for (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                                  cout << "You must read a list, or a list and a group, or a shared before you can use the venn command." << endl; 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 != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; 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                         delete validParameter;
 104
 105                         if (abort == false) {
 106                                 validCalculator = new ValidCalculators();
 107
 108                                 int i;
 109
 110                                 if (format == "list") {
 111                                         for (i=0; i<Estimators.size(); i++) {
 112                                                 if (validCalculator->isValidCalculator("vennsingle", Estimators[i]) == true) {
 113                                                         if (Estimators[i] == "sobs") {
 114                                                                 vennCalculators.push_back(new Sobs());
 115                                                         }else if (Estimators[i] == "chao") {
 116                                                                 vennCalculators.push_back(new Chao1());
 117                                                         }else if (Estimators[i] == "ace") {
 118                                                                 if(abund < 5)
 119                                                                         abund = 10;
 120                                                                 vennCalculators.push_back(new Ace(abund));
 121                                                         }
 122                                                 }
 123                                         }
 124                                 }else {
 125                                         for (i=0; i<Estimators.size(); i++) {
 126                                                 if (validCalculator->isValidCalculator("vennshared", Estimators[i]) == true) {
 127                                                         if (Estimators[i] == "sharedsobs") {
 128                                                                 vennCalculators.push_back(new SharedSobsCS());
 129                                                         }else if (Estimators[i] == "sharedchao") {
 130                                                                 vennCalculators.push_back(new SharedChao1());
 131                                                         }else if (Estimators[i] == "sharedace") {
 132                                                                 vennCalculators.push_back(new SharedAce());
 133                                                         }
 134                                                 }
 135                                         }
 136                                 }
 137
 138                                 venn = new Venn();
 139                         }
 140                 }
 141
 142
 143
 144         }
 145         catch(exception& e) {
 146                 cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 147                 exit(1);
 148         }
 149         catch(...) {
 150                 cout << "An unknown error has occurred in the VennCommand class function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 151                 exit(1);
 152         }
 153 }
 154
 155 //**********************************************************************************************************************
 156
 157 void VennCommand::help(){
 158         try {
 159                 cout << "The venn command can only be executed after a successful read.otu command." << "\n";
 160                 cout << "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";
 161                 cout << "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";
 162                 cout << "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";
 163                 cout << "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, abund=yourAbund)." << "\n";
 164                 cout << "Example venn(groups=A-B-C, line=1-3-5, calc=sharedsobs-sharedchao, abund=20)." << "\n";
 165                 cout << "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";
 166                 cout << "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";
 167                 cout << "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";
 168                 cout << "The only estmiator available four 4 groups is sharedsobs." << "\n";
 169                 cout << "The venn command outputs a .svg file for each calculator you specify at each distance you choose." << "\n";
 170                 cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
 171         }
 172         catch(exception& e) {
 173                 cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 174                 exit(1);
 175         }
 176         catch(...) {
 177                 cout << "An unknown error has occurred in the VennCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 178                 exit(1);
 179         }
 180 }
 181
 182
 183 //**********************************************************************************************************************
 184
 185 VennCommand::~VennCommand(){
 186         delete input;
 187         delete read;
 188         delete venn;
 189         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 190 }
 191
 192 //**********************************************************************************************************************
 193
 194 int VennCommand::execute(){
 195         try {
 196
 197                 if (abort == true) { return 0; }
 198
 199                 int count = 1;
 200                 SAbundVector* lastSAbund;
 201                 vector<SharedRAbundVector*> lastLookup;
 202
 203                 //if the users entered no valid calculators don't execute command
 204                 if (vennCalculators.size() == 0) { return 0; }
 205
 206                 if (format == "sharedfile") {
 207                         //you have groups
 208                         read = new ReadOTUFile(globaldata->inputFileName);
 209                         read->read(&*globaldata);
 210
 211                         input = globaldata->ginput;
 212                         lookup = input->getSharedRAbundVectors();
 213                         lastLookup = lookup;
 214                 }else if (format == "list") {
 215                         //you are using just a list file and have only one group
 216                         read = new ReadOTUFile(globaldata->inputFileName);
 217                         read->read(&*globaldata);
 218
 219                         sabund = globaldata->sabund;
 220                         lastSAbund = globaldata->sabund;
 221                         input = globaldata->ginput;
 222                 }
 223
 224                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 225                 set<string> processedLabels;
 226                 set<string> userLabels = labels;
 227                 set<int> userLines = lines;
 228
 229                 if (format != "list") {
 230
 231                         //as long as you are not at the end of the file or done wih the lines you want
 232                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 233
 234                                 if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
 235                                         cout << lookup[0]->getLabel() << '\t' << count << endl;
 236                                         processedLabels.insert(lookup[0]->getLabel());
 237                                         userLabels.erase(lookup[0]->getLabel());
 238                                         userLines.erase(count);
 239
 240                                         if (lookup.size() > 4) {
 241                                                 cout << "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." << endl;
 242                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 243                                         }
 244                                         venn->getPic(lookup, vennCalculators);
 245                                 }
 246
 247                                 if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
 248                                         cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 249                                         processedLabels.insert(lastLookup[0]->getLabel());
 250                                         userLabels.erase(lastLookup[0]->getLabel());
 251
 252                                         if (lastLookup.size() > 4) {
 253                                                 cout << "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." << endl;
 254                                                 for (int i = lastLookup.size(); i > 4; i--) { lastLookup.pop_back(); } //no memmory leak because pop_back calls destructor
 255                                         }
 256                                         venn->getPic(lastLookup, vennCalculators);
 257                                 }
 258
 259                                 //prevent memory leak
 260                                 if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
 261                                 lastLookup = lookup;
 262
 263                                 //get next line to process
 264                                 lookup = input->getSharedRAbundVectors();
 265                                 count++;
 266                         }
 267
 268                         //output error messages about any remaining user labels
 269                         set<string>::iterator it;
 270                         bool needToRun = false;
 271                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 272                                 cout << "Your file does not include the label "<< *it;
 273                                 if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
 274                                         cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
 275                                         needToRun = true;
 276                                 }else {
 277                                         cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
 278                                 }
 279                         }
 280
 281                         //run last line if you need to
 282                         if (needToRun == true)  {
 283                                 cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 284                                 if (lastLookup.size() > 4) {
 285                                         cout << "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." << endl;
 286                                         for (int i = lastLookup.size(); i > 3; i--) { delete lastLookup[i]; lastLookup.pop_back(); }
 287                                 }
 288                                 venn->getPic(lastLookup, vennCalculators);
 289                         }
 290
 291                         for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  }
 292
 293                         //reset groups parameter
 294                         globaldata->Groups.clear();
 295
 296                 }else{
 297
 298                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 299
 300                                 if(allLines == 1 || lines.count(count) == 1 || labels.count(sabund->getLabel()) == 1){
 301
 302                                         cout << sabund->getLabel() << '\t' << count << endl;
 303                                         venn->getPic(sabund, vennCalculators);
 304
 305                                         processedLabels.insert(sabund->getLabel());
 306                                         userLabels.erase(sabund->getLabel());
 307                                         userLines.erase(count);
 308                                 }
 309
 310                                 if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastSAbund->getLabel()) != 1)) {
 311
 312                                         cout << lastSAbund->getLabel() << '\t' << count << endl;
 313                                         venn->getPic(lastSAbund, vennCalculators);
 314
 315                                         processedLabels.insert(lastSAbund->getLabel());
 316                                         userLabels.erase(lastSAbund->getLabel());
 317                                 }
 318
 319                                 if (count != 1) { delete lastSAbund; }
 320                                 lastSAbund = sabund;
 321
 322                                 sabund = input->getSAbundVector();
 323                                 count++;
 324                         }
 325
 326                         //output error messages about any remaining user labels
 327                         set<string>::iterator it;
 328                         bool needToRun = false;
 329                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 330                                 cout << "Your file does not include the label "<< *it;
 331                                 if (processedLabels.count(lastSAbund->getLabel()) != 1) {
 332                                         cout << ". I will use " << lastSAbund->getLabel() << "." << endl;
 333                                         needToRun = true;
 334                                 }else {
 335                                         cout << ". Please refer to " << lastSAbund->getLabel() << "." << endl;
 336                                 }
 337                         }
 338
 339                         //run last line if you need to
 340                         if (needToRun == true)  {
 341                                 cout << lastSAbund->getLabel() << '\t' << count << endl;
 342                                 venn->getPic(lastSAbund, vennCalculators);
 343                         }
 344                         delete lastSAbund;
 345                 }
 346
 347                 return 0;
 348         }
 349         catch(exception& e) {
 350                 cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 351                 exit(1);
 352         }
 353         catch(...) {
 354                 cout << "An unknown error has occurred in the VennCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 355                 exit(1);
 356         }
 357 }
 358
 359 //**********************************************************************************************************************