hclustercommand.cpp

   1 /*
   2  *  hclustercommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 10/13/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "hclustercommand.h"
  11
  12 //**********************************************************************************************************************
  13 //This function checks to make sure the cluster command has no errors and then clusters based on the method chosen.
  14 HClusterCommand::HClusterCommand(string option)  {
  15         try{
  16                 globaldata = GlobalData::getInstance();
  17                 abort = false;
  18
  19                 //allow user to run help
  20                 if(option == "help") { help(); abort = true; }
  21
  22                 else {
  23                         //valid paramters for this command
  24                         string Array[] =  {"cutoff","hard","precision","method","phylip","column","name","sorted","showabund","timing","outputdir","inputdir"};
  25                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  26
  27                         OptionParser parser(option);
  28                         map<string,string> parameters = parser.getParameters();
  29
  30                         ValidParameters validParameter;
  31                         map<string,string>::iterator it;
  32
  33                         //check to make sure all parameters are valid for command
  34                         for (it = parameters.begin(); it != parameters.end(); it++) {
  35                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {
  36                                         abort = true;
  37                                 }
  38                         }
  39
  40                         globaldata->newRead();
  41
  42                         //if the user changes the input directory command factory will send this info to us in the output parameter
  43                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  44                         if (inputDir == "not found"){   inputDir = "";          }
  45                         else {
  46                                 string path;
  47                                 it = parameters.find("phylip");
  48                                 //user has given a template file
  49                                 if(it != parameters.end()){
  50                                         path = m->hasPath(it->second);
  51                                         //if the user has not given a path then, add inputdir. else leave path alone.
  52                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
  53                                 }
  54
  55                                 it = parameters.find("column");
  56                                 //user has given a template file
  57                                 if(it != parameters.end()){
  58                                         path = m->hasPath(it->second);
  59                                         //if the user has not given a path then, add inputdir. else leave path alone.
  60                                         if (path == "") {       parameters["column"] = inputDir + it->second;           }
  61                                 }
  62
  63                                 it = parameters.find("name");
  64                                 //user has given a template file
  65                                 if(it != parameters.end()){
  66                                         path = m->hasPath(it->second);
  67                                         //if the user has not given a path then, add inputdir. else leave path alone.
  68                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
  69                                 }
  70                         }
  71
  72                         //if the user changes the output directory command factory will send this info to us in the output parameter
  73                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
  74
  75                         //check for required parameters
  76                         phylipfile = validParameter.validFile(parameters, "phylip", true);
  77                         if (phylipfile == "not open") { abort = true; }
  78                         else if (phylipfile == "not found") { phylipfile = ""; }
  79                         else {  distfile = phylipfile;  format = "phylip";      }
  80
  81                         columnfile = validParameter.validFile(parameters, "column", true);
  82                         if (columnfile == "not open") { abort = true; }
  83                         else if (columnfile == "not found") { columnfile = ""; }
  84                         else {  distfile = columnfile; format = "column";       }
  85
  86                         namefile = validParameter.validFile(parameters, "name", true);
  87                         if (namefile == "not open") { abort = true; }
  88                         else if (namefile == "not found") { namefile = ""; }
  89
  90                         if ((phylipfile == "") && (columnfile == "")) { m->mothurOut("When executing a hcluster command you must enter a phylip or a column."); m->mothurOutEndLine(); abort = true; }
  91                         else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a hcluster command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; }
  92
  93                         if (columnfile != "") {
  94                                 if (namefile == "") {  cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }
  95                         }
  96
  97                         //check for optional parameter and set defaults
  98                         // ...at some point should added some additional type checking...
  99                         //get user cutoff and precision or use defaults
 100                         string temp;
 101                         temp = validParameter.validFile(parameters, "precision", false);
 102                         if (temp == "not found") { temp = "100"; }
 103                         //saves precision legnth for formatting below
 104                         length = temp.length();
 105                         convert(temp, precision);
 106
 107                         temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
 108                         hard = m->isTrue(temp);
 109
 110                         temp = validParameter.validFile(parameters, "cutoff", false);
 111                         if (temp == "not found") { temp = "10"; }
 112                         convert(temp, cutoff);
 113                         cutoff += (5 / (precision * 10.0));
 114
 115                         method = validParameter.validFile(parameters, "method", false);
 116                         if (method == "not found") { method = "furthest"; }
 117
 118                         if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
 119                         else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
 120
 121                         showabund = validParameter.validFile(parameters, "showabund", false);
 122                         if (showabund == "not found") { showabund = "T"; }
 123
 124                         sort = validParameter.validFile(parameters, "sorted", false);
 125                         if (sort == "not found") { sort = "F"; }
 126                         sorted = m->isTrue(sort);
 127
 128                         timing = validParameter.validFile(parameters, "timing", false);
 129                         if (timing == "not found") { timing = "F"; }
 130
 131
 132                         if (abort == false) {
 133
 134                                 if (outputDir == "") {  outputDir += m->hasPath(distfile); }
 135                                 fileroot = outputDir + m->getRootName(m->getSimpleName(distfile));
 136
 137                                 if (method == "furthest")               { tag = "fn";  }
 138                                 else if (method == "nearest")   { tag = "nn";  }
 139                                 else                                                    { tag = "an";  }
 140
 141                                 m->openOutputFile(fileroot+ tag + ".sabund",    sabundFile);
 142                                 m->openOutputFile(fileroot+ tag + ".rabund",    rabundFile);
 143                                 m->openOutputFile(fileroot+ tag + ".list",              listFile);
 144
 145                                 outputNames.push_back(fileroot+ tag + ".sabund");
 146                                 outputNames.push_back(fileroot+ tag + ".rabund");
 147                                 outputNames.push_back(fileroot+ tag + ".list");
 148                         }
 149                 }
 150         }
 151         catch(exception& e) {
 152                 m->errorOut(e, "HClusterCommand", "HClusterCommand");
 153                 exit(1);
 154         }
 155 }
 156
 157 //**********************************************************************************************************************
 158
 159 void HClusterCommand::help(){
 160         try {
 161                 m->mothurOut("The hcluster command parameter options are cutoff, precision, method, phylip, column, name, showabund, timing and sorted. Phylip or column and name are required.\n");
 162                 m->mothurOut("The phylip and column parameter allow you to enter your distance file, and sorted indicates whether your column distance file is already sorted. \n");
 163                 m->mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n");
 164                 m->mothurOut("The hcluster command should be in the following format: \n");
 165                 m->mothurOut("hcluster(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
 166                 m->mothurOut("The acceptable hcluster methods are furthest, nearest and average.\n\n");
 167         }
 168         catch(exception& e) {
 169                 m->errorOut(e, "HClusterCommand", "help");
 170                 exit(1);
 171         }
 172 }
 173
 174 //**********************************************************************************************************************
 175
 176 HClusterCommand::~HClusterCommand(){}
 177
 178 //**********************************************************************************************************************
 179
 180 int HClusterCommand::execute(){
 181         try {
 182
 183                 if (abort == true) {    return 0;       }
 184
 185                 if(namefile != ""){
 186                         globaldata->nameMap = new NameAssignment(namefile);
 187                         globaldata->nameMap->readMap();
 188                 }else{
 189                         globaldata->nameMap = NULL;
 190                 }
 191
 192                 time_t estart = time(NULL);
 193
 194                 if (!sorted) {
 195                         read = new ReadCluster(distfile, cutoff, outputDir, true);
 196                         read->setFormat(format);
 197                         read->read(globaldata->nameMap);
 198
 199                         if (m->control_pressed) {
 200                                 delete read;
 201                                 sabundFile.close();
 202                                 rabundFile.close();
 203                                 listFile.close();
 204                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 205                                 return 0;
 206                         }
 207
 208                         distfile = read->getOutputFile();
 209
 210                         list = read->getListVector();
 211                         delete read;
 212                 }else {
 213                         list = new ListVector(globaldata->nameMap->getListVector());
 214                 }
 215
 216                 if (m->control_pressed) {
 217                         sabundFile.close();
 218                         rabundFile.close();
 219                         listFile.close();
 220                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 221                         return 0;
 222                 }
 223
 224                 m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to sort. "); m->mothurOutEndLine();
 225                 estart = time(NULL);
 226
 227                 //list vector made by read contains all sequence names
 228                 if(list != NULL){
 229                         rabund = new RAbundVector(list->getRAbundVector());
 230                 }else{
 231                         m->mothurOut("Error: no list vector!"); m->mothurOutEndLine(); return 0;
 232                 }
 233
 234                 float previousDist = 0.00000;
 235                 float rndPreviousDist = 0.00000;
 236                 oldRAbund = *rabund;
 237                 oldList = *list;
 238
 239                 print_start = true;
 240                 start = time(NULL);
 241
 242                 cluster = new HCluster(rabund, list, method, distfile, globaldata->nameMap, cutoff);
 243                 vector<seqDist> seqs; seqs.resize(1); // to start loop
 244
 245                 if (m->control_pressed) {
 246                                 delete cluster;
 247                                 sabundFile.close();
 248                                 rabundFile.close();
 249                                 listFile.close();
 250                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 251                                 return 0;
 252                 }
 253
 254
 255                 while (seqs.size() != 0){
 256
 257                         seqs = cluster->getSeqs();
 258
 259                         if (m->control_pressed) {
 260                                 delete cluster;
 261                                 sabundFile.close();
 262                                 rabundFile.close();
 263                                 listFile.close();
 264                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 265                                 return 0;
 266                         }
 267
 268                         for (int i = 0; i < seqs.size(); i++) {  //-1 means skip me
 269
 270                                 if (seqs[i].seq1 != seqs[i].seq2) {
 271                                         cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
 272
 273                                         if (m->control_pressed) {
 274                                                 delete cluster;
 275                                                 sabundFile.close();
 276                                                 rabundFile.close();
 277                                                 listFile.close();
 278                                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 279                                                 return 0;
 280                                         }
 281
 282
 283                                         float rndDist;
 284                                         if (hard) {
 285                                                 rndDist = m->ceilDist(seqs[i].dist, precision);
 286                                         }else{
 287                                                 rndDist = m->roundDist(seqs[i].dist, precision);
 288                                         }
 289
 290
 291                                         if((previousDist <= 0.0000) && (seqs[i].dist != previousDist)){
 292                                                 printData("unique");
 293                                         }
 294                                         else if((rndDist != rndPreviousDist)){
 295                                                 printData(toString(rndPreviousDist,  length-1));
 296                                         }
 297
 298                                         previousDist = seqs[i].dist;
 299                                         rndPreviousDist = rndDist;
 300                                         oldRAbund = *rabund;
 301                                         oldList = *list;
 302                                 }
 303                         }
 304                 }
 305
 306                 if (m->control_pressed) {
 307                         delete cluster;
 308                         sabundFile.close();
 309                         rabundFile.close();
 310                         listFile.close();
 311                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 312                         return 0;
 313                 }
 314
 315                 if(previousDist <= 0.0000){
 316                         printData("unique");
 317                 }
 318                 else if(rndPreviousDist<cutoff){
 319                         printData(toString(rndPreviousDist, length-1));
 320                 }
 321
 322                 //delete globaldata's copy of the sparsematrix and listvector to free up memory
 323                 delete globaldata->gListVector;  globaldata->gListVector = NULL;
 324
 325                 //saves .list file so you can do the collect, rarefaction and summary commands without doing a read.list
 326                 if (globaldata->getFormat() == "phylip") { globaldata->setPhylipFile(""); }
 327                 else if (globaldata->getFormat() == "column") { globaldata->setColumnFile(""); }
 328
 329                 globaldata->setListFile(fileroot+ tag + ".list");
 330                 globaldata->setNameFile("");
 331                 globaldata->setFormat("list");
 332
 333                 sabundFile.close();
 334                 rabundFile.close();
 335                 listFile.close();
 336                 delete cluster;
 337
 338                 if (m->control_pressed) {
 339                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 340                         return 0;
 341                 }
 342
 343
 344                 m->mothurOutEndLine();
 345                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 346                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 347                 m->mothurOutEndLine();
 348
 349                 m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster. "); m->mothurOutEndLine();
 350
 351                 return 0;
 352         }
 353         catch(exception& e) {
 354                 m->errorOut(e, "HClusterCommand", "execute");
 355                 exit(1);
 356         }
 357 }
 358
 359 //**********************************************************************************************************************
 360
 361 void HClusterCommand::printData(string label){
 362         try {
 363                 if (m->isTrue(timing)) {
 364                         m->mothurOut("\tTime: " + toString(time(NULL) - start) + "\tsecs for " + toString(oldRAbund.getNumBins())
 365                      + "\tclusters. Updates: " + toString(loops)); m->mothurOutEndLine();
 366                 }
 367                 print_start = true;
 368                 loops = 0;
 369                 start = time(NULL);
 370
 371                 oldRAbund.setLabel(label);
 372                 if (m->isTrue(showabund)) {
 373                         oldRAbund.getSAbundVector().print(cout);
 374                 }
 375                 oldRAbund.print(rabundFile);
 376                 oldRAbund.getSAbundVector().print(sabundFile);
 377
 378                 oldList.setLabel(label);
 379                 oldList.print(listFile);
 380         }
 381         catch(exception& e) {
 382                 m->errorOut(e, "HClusterCommand", "printData");
 383                 exit(1);
 384         }
 385
 386
 387 }
 388 //**********************************************************************************************************************
 389