clusterdoturcommand.cpp

   1 /*
   2  *  clusterdoturcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 10/27/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "clusterdoturcommand.h"
  11 #include "clusterclassic.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> ClusterDoturCommand::setParameters(){
  15         try {
  16                 CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
  17                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  18                 CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
  19                 CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
  20                 CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
  21                 CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
  22                 CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim);
  23                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  24                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  25
  26                 vector<string> myArray;
  27                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  28                 return myArray;
  29         }
  30         catch(exception& e) {
  31                 m->errorOut(e, "ClusterDoturCommand", "setParameters");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 string ClusterDoturCommand::getHelpString(){
  37         try {
  38                 string helpString = "";
  39                 helpString += "The cluster.classic command clusters using the algorithm from dotur. \n";
  40                 helpString += "The cluster.classic command parameter options are phylip, name, method, cuttoff, hard, sim, precision. Phylip is required, unless you have a valid current file.\n";
  41                 helpString += "The cluster.classic command should be in the following format: \n";
  42                 helpString += "cluster.classic(phylip=yourDistanceMatrix, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
  43                 helpString += "The acceptable cluster methods are furthest, nearest, weighted and average.  If no method is provided then average is assumed.\n";
  44                 return helpString;
  45         }
  46         catch(exception& e) {
  47                 m->errorOut(e, "ClusterDoturCommand", "getHelpString");
  48                 exit(1);
  49         }
  50 }
  51 //**********************************************************************************************************************
  52 ClusterDoturCommand::ClusterDoturCommand(){
  53         try {
  54                 abort = true; calledHelp = true;
  55                 setParameters();
  56                 vector<string> tempOutNames;
  57                 outputTypes["list"] = tempOutNames;
  58                 outputTypes["rabund"] = tempOutNames;
  59                 outputTypes["sabund"] = tempOutNames;
  60         }
  61         catch(exception& e) {
  62                 m->errorOut(e, "ClusterDoturCommand", "ClusterCommand");
  63                 exit(1);
  64         }
  65 }
  66 //**********************************************************************************************************************
  67 //This function checks to make sure the cluster command has no errors and then clusters based on the method chosen.
  68 ClusterDoturCommand::ClusterDoturCommand(string option)  {
  69         try{
  70
  71                 abort = false; calledHelp = false;
  72
  73                 //allow user to run help
  74                 if(option == "help") { help(); abort = true; calledHelp = true; }
  75
  76                 else {
  77                         vector<string> myArray = setParameters();
  78
  79                         OptionParser parser(option);
  80                         map<string,string> parameters = parser.getParameters();
  81
  82                         ValidParameters validParameter;
  83
  84                         //check to make sure all parameters are valid for command
  85                         map<string,string>::iterator it;
  86                         for (it = parameters.begin(); it != parameters.end(); it++) {
  87                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {
  88                                         abort = true;
  89                                 }
  90                         }
  91
  92                         //if the user changes the input directory command factory will send this info to us in the output parameter
  93                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  94                         if (inputDir == "not found"){   inputDir = "";          }
  95                         else {
  96                                 string path;
  97                                 it = parameters.find("phylip");
  98                                 //user has given a template file
  99                                 if(it != parameters.end()){
 100                                         path = m->hasPath(it->second);
 101                                         //if the user has not given a path then, add inputdir. else leave path alone.
 102                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 103                                 }
 104
 105                                 it = parameters.find("name");
 106                                 //user has given a template file
 107                                 if(it != parameters.end()){
 108                                         path = m->hasPath(it->second);
 109                                         //if the user has not given a path then, add inputdir. else leave path alone.
 110                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 111                                 }
 112
 113                         }
 114
 115                         //initialize outputTypes
 116                         vector<string> tempOutNames;
 117                         outputTypes["list"] = tempOutNames;
 118                         outputTypes["rabund"] = tempOutNames;
 119                         outputTypes["sabund"] = tempOutNames;
 120
 121                         //if the user changes the output directory command factory will send this info to us in the output parameter
 122                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 123
 124                         //check for required parameters
 125                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 126                         if (phylipfile == "not open") { abort = true; }
 127                         else if (phylipfile == "not found") {
 128                                 phylipfile = m->getPhylipFile();
 129                                 if (phylipfile != "") {  m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 130                                 else {
 131                                         m->mothurOut("You need to provide a phylip file with the cluster.classic command."); m->mothurOutEndLine();
 132                                         abort = true;
 133                                 }
 134                         }
 135
 136
 137                         //check for optional parameter and set defaults
 138                         namefile = validParameter.validFile(parameters, "name", true);
 139                         if (namefile == "not open") { abort = true; }
 140                         else if (namefile == "not found") { namefile = ""; }
 141
 142                         string temp;
 143                         temp = validParameter.validFile(parameters, "precision", false);
 144                         if (temp == "not found") { temp = "100"; }
 145                         //saves precision legnth for formatting below
 146                         length = temp.length();
 147                         convert(temp, precision);
 148
 149                         temp = validParameter.validFile(parameters, "cutoff", false);
 150                         if (temp == "not found") { temp = "10"; }
 151                         convert(temp, cutoff);
 152                         cutoff += (5 / (precision * 10.0));
 153
 154                         temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "T"; }
 155                         hard = m->isTrue(temp);
 156
 157                         temp = validParameter.validFile(parameters, "sim", false);                              if (temp == "not found") { temp = "F"; }
 158                         sim = m->isTrue(temp);
 159
 160                         method = validParameter.validFile(parameters, "method", false);
 161                         if (method == "not found") { method = "average"; }
 162
 163                         if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) {
 164                                 if (method == "furthest") { tag = "fn"; }
 165                                 else if (method == "nearest") { tag = "nn"; }
 166                                 else if (method == "average") { tag = "an"; }
 167                                 else if (method == "weighted") { tag = "wn"; }
 168                         }else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest, average, weighted."); m->mothurOutEndLine(); abort = true; }
 169                 }
 170         }
 171         catch(exception& e) {
 172                 m->errorOut(e, "ClusterDoturCommand", "ClusterCommand");
 173                 exit(1);
 174         }
 175 }
 176 //**********************************************************************************************************************
 177
 178 int ClusterDoturCommand::execute(){
 179         try {
 180
 181                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 182
 183                 if(namefile != ""){
 184                         nameMap = new NameAssignment(namefile);
 185                         nameMap->readMap();
 186                 }else{
 187                         nameMap = NULL;
 188                 }
 189
 190                 //reads phylip file storing data in 2D vector, also fills list and rabund
 191                 ClusterClassic* cluster = new ClusterClassic(cutoff, method, sim);
 192                 cluster->readPhylipFile(phylipfile, nameMap);
 193
 194                 if (m->control_pressed) { delete cluster; delete list; delete rabund; return 0; }
 195
 196                 list = cluster->getListVector();
 197                 rabund = cluster->getRAbundVector();
 198
 199                 if (outputDir == "") { outputDir += m->hasPath(phylipfile); }
 200                 fileroot = outputDir + m->getRootName(m->getSimpleName(phylipfile));
 201
 202                 m->openOutputFile(fileroot+ tag + ".sabund",    sabundFile);
 203                 m->openOutputFile(fileroot+ tag + ".rabund",    rabundFile);
 204                 m->openOutputFile(fileroot+ tag + ".list",              listFile);
 205
 206                 outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
 207                 outputNames.push_back(fileroot+ tag + ".rabund"); outputTypes["rabund"].push_back(fileroot+ tag + ".rabund");
 208                 outputNames.push_back(fileroot+ tag + ".list"); outputTypes["list"].push_back(fileroot+ tag + ".list");
 209
 210                 float previousDist = 0.00000;
 211                 float rndPreviousDist = 0.00000;
 212                 oldRAbund = *rabund;
 213                 oldList = *list;
 214
 215                 //double saveCutoff = cutoff;
 216
 217                 int estart = time(NULL);
 218
 219                 while ((cluster->getSmallDist() < cutoff) && (cluster->getNSeqs() > 1)){
 220                         if (m->control_pressed) { delete cluster; delete list; delete rabund; sabundFile.close();rabundFile.close();listFile.close();  for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str());         } outputTypes.clear();  return 0;  }
 221
 222                         cluster->update(cutoff);
 223
 224                         float dist = cluster->getSmallDist();
 225                         float rndDist;
 226                         if (hard) {
 227                                 rndDist = m->ceilDist(dist, precision);
 228                         }else{
 229                                 rndDist = m->roundDist(dist, precision);
 230                         }
 231
 232                         if(previousDist <= 0.0000 && dist != previousDist){
 233                                 printData("unique");
 234                         }
 235                         else if(rndDist != rndPreviousDist){
 236                                 printData(toString(rndPreviousDist,  length-1));
 237                         }
 238
 239                         previousDist = dist;
 240                         rndPreviousDist = rndDist;
 241                         oldRAbund = *rabund;
 242                         oldList = *list;
 243                 }
 244
 245                 if(previousDist <= 0.0000){
 246                         printData("unique");
 247                 }
 248                 else if(rndPreviousDist<cutoff){
 249                         printData(toString(rndPreviousDist, length-1));
 250                 }
 251
 252                 sabundFile.close();
 253                 rabundFile.close();
 254                 listFile.close();
 255
 256                 delete cluster; delete nameMap; delete list; delete rabund;
 257
 258                 //if (saveCutoff != cutoff) {
 259                 //      if (hard)       {  saveCutoff = m->ceilDist(saveCutoff, precision);     }
 260                 //      else            {       saveCutoff = m->roundDist(saveCutoff, precision);  }
 261                 //      m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine();
 262                 //}
 263
 264                 //set list file as new current listfile
 265                 string current = "";
 266                 itTypes = outputTypes.find("list");
 267                 if (itTypes != outputTypes.end()) {
 268                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 269                 }
 270
 271                 //set rabund file as new current rabundfile
 272                 itTypes = outputTypes.find("rabund");
 273                 if (itTypes != outputTypes.end()) {
 274                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 275                 }
 276
 277                 //set sabund file as new current sabundfile
 278                 itTypes = outputTypes.find("sabund");
 279                 if (itTypes != outputTypes.end()) {
 280                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
 281                 }
 282
 283                 m->mothurOutEndLine();
 284                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 285                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 286                 m->mothurOutEndLine();
 287
 288                 m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster"); m->mothurOutEndLine();
 289
 290                 return 0;
 291         }
 292         catch(exception& e) {
 293                 m->errorOut(e, "ClusterDoturCommand", "execute");
 294                 exit(1);
 295         }
 296 }
 297
 298 //**********************************************************************************************************************
 299
 300 void ClusterDoturCommand::printData(string label){
 301         try {
 302
 303                 oldRAbund.setLabel(label);
 304                 oldRAbund.print(rabundFile);
 305                 oldRAbund.getSAbundVector().print(sabundFile);
 306
 307                 oldRAbund.getSAbundVector().print(cout);
 308
 309                 oldList.setLabel(label);
 310                 oldList.print(listFile);
 311         }
 312         catch(exception& e) {
 313                 m->errorOut(e, "ClusterDoturCommand", "printData");
 314                 exit(1);
 315         }
 316 }
 317 //**********************************************************************************************************************