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