clustercommand.cpp

   1 /*
   2  *  clustercommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "clustercommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> ClusterCommand::getValidParameters(){
  14         try {
  15                 string AlignArray[] =  {"cutoff","precision","method","showabund","timing","hard","outputdir","inputdir"};
  16                 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  17                 return myArray;
  18         }
  19         catch(exception& e) {
  20                 m->errorOut(e, "ClusterCommand", "getValidParameters");
  21                 exit(1);
  22         }
  23 }
  24 //**********************************************************************************************************************
  25 ClusterCommand::ClusterCommand(){
  26         try {
  27                 abort = true;
  28                 //initialize outputTypes
  29                 vector<string> tempOutNames;
  30                 outputTypes["list"] = tempOutNames;
  31                 outputTypes["rabund"] = tempOutNames;
  32                 outputTypes["sabund"] = tempOutNames;
  33         }
  34         catch(exception& e) {
  35                 m->errorOut(e, "ClusterCommand", "ClusterCommand");
  36                 exit(1);
  37         }
  38 }
  39 //**********************************************************************************************************************
  40 vector<string> ClusterCommand::getRequiredParameters(){
  41         try {
  42                 vector<string> myArray;
  43                 return myArray;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "ClusterCommand", "getRequiredParameters");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 vector<string> ClusterCommand::getRequiredFiles(){
  52         try {
  53                 string Array[] =  {"phylip","column","or"};
  54                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  55                 return myArray;
  56         }
  57         catch(exception& e) {
  58                 m->errorOut(e, "ClusterCommand", "getRequiredFiles");
  59                 exit(1);
  60         }
  61 }
  62 //**********************************************************************************************************************
  63 //This function checks to make sure the cluster command has no errors and then clusters based on the method chosen.
  64 ClusterCommand::ClusterCommand(string option)  {
  65         try{
  66                 globaldata = GlobalData::getInstance();
  67
  68                 abort = false;
  69
  70                 //allow user to run help
  71                 if(option == "help") { help(); abort = true; }
  72
  73                 else {
  74                         //valid paramters for this command
  75                         string Array[] =  {"cutoff","precision","method","showabund","timing","hard","outputdir","inputdir"};
  76                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  77
  78                         OptionParser parser(option);
  79                         map<string,string> parameters = parser.getParameters();
  80
  81                         ValidParameters validParameter;
  82
  83                         //check to make sure all parameters are valid for command
  84                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  85                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {
  86                                         abort = true;
  87                                 }
  88                         }
  89
  90                         //initialize outputTypes
  91                         vector<string> tempOutNames;
  92                         outputTypes["list"] = tempOutNames;
  93                         outputTypes["rabund"] = tempOutNames;
  94                         outputTypes["sabund"] = tempOutNames;
  95
  96                         //if the user changes the output directory command factory will send this info to us in the output parameter
  97                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
  98
  99                         //error checking to make sure they read a distance file
 100                         if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
 101                                 m->mothurOut("Before you use the cluster command, you first need to read in a distance matrix."); m->mothurOutEndLine();
 102                                 abort = true;
 103                         }
 104
 105                         //check for optional parameter and set defaults
 106                         // ...at some point should added some additional type checking...
 107                         //get user cutoff and precision or use defaults
 108                         string temp;
 109                         temp = validParameter.validFile(parameters, "precision", false);
 110                         if (temp == "not found") { temp = "100"; }
 111                         //saves precision legnth for formatting below
 112                         length = temp.length();
 113                         convert(temp, precision);
 114
 115                         temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
 116                         hard = m->isTrue(temp);
 117
 118                         temp = validParameter.validFile(parameters, "cutoff", false);
 119                         if (temp == "not found") { temp = "10"; }
 120                         convert(temp, cutoff);
 121                         cutoff += (5 / (precision * 10.0));
 122
 123                         method = validParameter.validFile(parameters, "method", false);
 124                         if (method == "not found") { method = "furthest"; }
 125
 126                         if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) { }
 127                         else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest, average, and weighted."); m->mothurOutEndLine(); abort = true; }
 128
 129                         showabund = validParameter.validFile(parameters, "showabund", false);
 130                         if (showabund == "not found") { showabund = "T"; }
 131
 132                         timing = validParameter.validFile(parameters, "timing", false);
 133                         if (timing == "not found") { timing = "F"; }
 134
 135                         if (abort == false) {
 136
 137
 138                                                         //get matrix, list and rabund for execute
 139                                 if(globaldata->gSparseMatrix != NULL)   {       matrix = globaldata->gSparseMatrix;             }
 140
 141                                 if(globaldata->gListVector != NULL){
 142                                         list = globaldata->gListVector;
 143                                         rabund = new RAbundVector(list->getRAbundVector());
 144                                 }
 145
 146                                 //create cluster
 147                                 if (method == "furthest")       {       cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method); }
 148                                 else if(method == "nearest"){   cluster = new SingleLinkage(rabund, list, matrix, cutoff, method); }
 149                                 else if(method == "average"){   cluster = new AverageLinkage(rabund, list, matrix, cutoff, method);     }
 150                                 else if(method == "weighted"){  cluster = new WeightedLinkage(rabund, list, matrix, cutoff, method);    }
 151                                 tag = cluster->getTag();
 152
 153                                 if (outputDir == "") { outputDir += m->hasPath(globaldata->inputFileName); }
 154                                 fileroot = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName));
 155
 156                                 m->openOutputFile(fileroot+ tag + ".sabund",    sabundFile);
 157                                 m->openOutputFile(fileroot+ tag + ".rabund",    rabundFile);
 158                                 m->openOutputFile(fileroot+ tag + ".list",              listFile);
 159
 160                                 outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
 161                                 outputNames.push_back(fileroot+ tag + ".rabund"); outputTypes["rabund"].push_back(fileroot+ tag + ".rabund");
 162                                 outputNames.push_back(fileroot+ tag + ".list"); outputTypes["list"].push_back(fileroot+ tag + ".list");
 163                         }
 164                 }
 165         }
 166         catch(exception& e) {
 167                 m->errorOut(e, "ClusterCommand", "ClusterCommand");
 168                 exit(1);
 169         }
 170 }
 171
 172 //**********************************************************************************************************************
 173
 174 void ClusterCommand::help(){
 175         try {
 176                 m->mothurOut("The cluster command can only be executed after a successful read.dist command.\n");
 177                 m->mothurOut("The cluster command parameter options are method, cuttoff, hard, precision, showabund and timing. No parameters are required.\n");
 178                 m->mothurOut("The cluster command should be in the following format: \n");
 179                 m->mothurOut("cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
 180                 m->mothurOut("The acceptable cluster methods are furthest, nearest and average.  If no method is provided then furthest is assumed.\n\n");
 181         }
 182         catch(exception& e) {
 183                 m->errorOut(e, "ClusterCommand", "help");
 184                 exit(1);
 185         }
 186 }
 187
 188 //**********************************************************************************************************************
 189
 190 ClusterCommand::~ClusterCommand(){
 191         if (abort == false) {
 192                 delete cluster;
 193                 delete rabund;
 194         }
 195 }
 196
 197 //**********************************************************************************************************************
 198
 199 int ClusterCommand::execute(){
 200         try {
 201
 202                 if (abort == true) {    return 0;       }
 203
 204                 time_t estart = time(NULL);
 205                 //int ndist = matrix->getNNodes();
 206                 float previousDist = 0.00000;
 207                 float rndPreviousDist = 0.00000;
 208                 oldRAbund = *rabund;
 209                 oldList = *list;
 210
 211                 print_start = true;
 212                 start = time(NULL);
 213                 loops = 0;
 214                 double saveCutoff = cutoff;
 215
 216                 while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){
 217
 218                         if (m->control_pressed) { //clean up
 219                                 delete globaldata->gSparseMatrix;  globaldata->gSparseMatrix = NULL;
 220                                 delete globaldata->gListVector;  globaldata->gListVector = NULL;
 221                                 if (globaldata->getFormat() == "phylip") { globaldata->setPhylipFile(""); }
 222                                 else if (globaldata->getFormat() == "column") { globaldata->setColumnFile(""); }
 223                                 sabundFile.close();rabundFile.close();listFile.close();
 224                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         } outputTypes.clear();
 225                                 return 0;
 226                         }
 227
 228                         if (print_start && m->isTrue(timing)) {
 229                                 m->mothurOut("Clustering (" + tag + ") dist " + toString(matrix->getSmallDist()) + "/"
 230                                         + toString(m->roundDist(matrix->getSmallDist(), precision))
 231                                         + "\t(precision: " + toString(precision) + ", Nodes: " + toString(matrix->getNNodes()) + ")");
 232                                 cout.flush();
 233                                 print_start = false;
 234                         }
 235
 236                         loops++;
 237
 238                         cluster->update(cutoff);
 239
 240                         float dist = matrix->getSmallDist();
 241                         float rndDist;
 242                         if (hard) {
 243                                 rndDist = m->ceilDist(dist, precision);
 244                         }else{
 245                                 rndDist = m->roundDist(dist, precision);
 246                         }
 247
 248                         if(previousDist <= 0.0000 && dist != previousDist){
 249                                 printData("unique");
 250                         }
 251                         else if(rndDist != rndPreviousDist){
 252                                 printData(toString(rndPreviousDist,  length-1));
 253                         }
 254
 255                         previousDist = dist;
 256                         rndPreviousDist = rndDist;
 257                         oldRAbund = *rabund;
 258                         oldList = *list;
 259                 }
 260
 261                 if (print_start && m->isTrue(timing)) {
 262                         m->mothurOut("Clustering (" + tag + ") for distance " + toString(previousDist) + "/" + toString(rndPreviousDist)
 263                                          + "\t(precision: " + toString(precision) + ", Nodes: " + toString(matrix->getNNodes()) + ")");
 264                         cout.flush();
 265                         print_start = false;
 266                 }
 267
 268                 if(previousDist <= 0.0000){
 269                         printData("unique");
 270                 }
 271                 else if(rndPreviousDist<cutoff){
 272                         printData(toString(rndPreviousDist, length-1));
 273                 }
 274
 275                 //delete globaldata's copy of the sparsematrix and listvector to free up memory
 276                 delete globaldata->gSparseMatrix;  globaldata->gSparseMatrix = NULL;
 277                 delete globaldata->gListVector;  globaldata->gListVector = NULL;
 278
 279                 //saves .list file so you can do the collect, rarefaction and summary commands without doing a read.list
 280                 if (globaldata->getFormat() == "phylip") { globaldata->setPhylipFile(""); }
 281                 else if (globaldata->getFormat() == "column") { globaldata->setColumnFile(""); }
 282
 283                 globaldata->setListFile(fileroot+ tag + ".list");
 284                 globaldata->setNameFile("");
 285                 globaldata->setFormat("list");
 286
 287                 sabundFile.close();
 288                 rabundFile.close();
 289                 listFile.close();
 290
 291                 if (saveCutoff != cutoff) {
 292                         if (hard)       {  saveCutoff = m->ceilDist(saveCutoff, precision);     }
 293                         else            {       saveCutoff = m->roundDist(saveCutoff, precision);  }
 294
 295                         m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine();
 296                 }
 297
 298                 m->mothurOutEndLine();
 299                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 300                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 301                 m->mothurOutEndLine();
 302
 303
 304                 //if (m->isTrue(timing)) {
 305                         m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster"); m->mothurOutEndLine();
 306                 //}
 307
 308
 309                 return 0;
 310         }
 311         catch(exception& e) {
 312                 m->errorOut(e, "ClusterCommand", "execute");
 313                 exit(1);
 314         }
 315 }
 316
 317 //**********************************************************************************************************************
 318
 319 void ClusterCommand::printData(string label){
 320         try {
 321                 if (m->isTrue(timing)) {
 322                         m->mothurOut("\tTime: " + toString(time(NULL) - start) + "\tsecs for " + toString(oldRAbund.getNumBins())
 323                      + "\tclusters. Updates: " + toString(loops)); m->mothurOutEndLine();
 324                 }
 325                 print_start = true;
 326                 loops = 0;
 327                 start = time(NULL);
 328
 329                 oldRAbund.setLabel(label);
 330                 if (m->isTrue(showabund)) {
 331                         oldRAbund.getSAbundVector().print(cout);
 332                 }
 333                 oldRAbund.print(rabundFile);
 334                 oldRAbund.getSAbundVector().print(sabundFile);
 335
 336                 oldList.setLabel(label);
 337                 oldList.print(listFile);
 338         }
 339         catch(exception& e) {
 340                 m->errorOut(e, "ClusterCommand", "printData");
 341                 exit(1);
 342         }
 343
 344
 345 }
 346 //**********************************************************************************************************************