unifracunweightedcommand.cpp

   1 /*
   2  *  unifracunweightedcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 2/9/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "unifracunweightedcommand.h"
  11
  12 /***********************************************************/
  13 UnifracUnweightedCommand::UnifracUnweightedCommand(string option) {
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16                 abort = false;
  17                 Groups.clear();
  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[] =  {"groups","iters","distance","random"};
  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
  32                         //check to make sure all parameters are valid for command
  33                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  34                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  35                         }
  36
  37                         if (globaldata->gTree.size() == 0) {//no trees were read
  38                                 mothurOut("You must execute the read.tree command, before you may execute the unifrac.unweighted command."); mothurOutEndLine(); abort = true;  }
  39
  40                         //check for optional parameter and set defaults
  41                         // ...at some point should added some additional type checking...
  42                         groups = validParameter.validFile(parameters, "groups", false);
  43                         if (groups == "not found") { groups = ""; }
  44                         else {
  45                                 splitAtDash(groups, Groups);
  46                                 globaldata->Groups = Groups;
  47                         }
  48
  49                         itersString = validParameter.validFile(parameters, "iters", false);                             if (itersString == "not found") { itersString = "1000"; }
  50                         convert(itersString, iters);
  51
  52                         string temp = validParameter.validFile(parameters, "distance", false);                  if (temp == "not found") { temp = "false"; }
  53                         phylip = isTrue(temp);
  54
  55                         temp = validParameter.validFile(parameters, "random", false);                                   if (temp == "not found") { temp = "true"; }
  56                         random = isTrue(temp);
  57
  58                         if (!random) {  iters = 0;  } //turn off random calcs
  59
  60                         //if user selects distance = true and no groups it won't calc the pairwise
  61                         if ((phylip) && (Groups.size() == 0)) {
  62                                 groups = "all";
  63                                 splitAtDash(groups, Groups);
  64                                 globaldata->Groups = Groups;
  65                         }
  66
  67                         if (abort == false) {
  68                                 T = globaldata->gTree;
  69                                 tmap = globaldata->gTreemap;
  70                                 sumFile = globaldata->getTreeFile() + ".uwsummary";
  71                                 openOutputFile(sumFile, outSum);
  72
  73                                 util = new SharedUtil();
  74                                 util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "unweighted");   //sets the groups the user wants to analyze
  75                                 util->getCombos(groupComb, globaldata->Groups, numComp);
  76
  77                                 if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
  78
  79                                 unweighted = new Unweighted(tmap);
  80
  81                         }
  82
  83                 }
  84
  85         }
  86         catch(exception& e) {
  87                 errorOut(e, "UnifracUnweightedCommand", "UnifracUnweightedCommand");
  88                 exit(1);
  89         }
  90 }
  91
  92 //**********************************************************************************************************************
  93
  94 void UnifracUnweightedCommand::help(){
  95         try {
  96                 mothurOut("The unifrac.unweighted command can only be executed after a successful read.tree command.\n");
  97                 mothurOut("The unifrac.unweighted command parameters are groups, iters, distance and random.  No parameters are required.\n");
  98                 mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 1 valid group.\n");
  99                 mothurOut("The group names are separated by dashes.  The iters parameter allows you to specify how many random trees you would like compared to your tree.\n");
 100                 mothurOut("The distance parameter allows you to create a distance file from the results. The default is false.\n");
 101                 mothurOut("The random parameter allows you to shut off the comparison to random trees. The default is true, meaning compare your trees with randomly generated trees.\n");
 102                 mothurOut("The unifrac.unweighted command should be in the following format: unifrac.unweighted(groups=yourGroups, iters=yourIters).\n");
 103                 mothurOut("Example unifrac.unweighted(groups=A-B-C, iters=500).\n");
 104                 mothurOut("The default value for groups is all the groups in your groupfile, and iters is 1000.\n");
 105                 mothurOut("The unifrac.unweighted command output two files: .unweighted and .uwsummary their descriptions are in the manual.\n");
 106                 mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 107         }
 108         catch(exception& e) {
 109                 errorOut(e, "UnifracUnweightedCommand", "help");
 110                 exit(1);
 111         }
 112 }
 113
 114
 115 /***********************************************************/
 116 int UnifracUnweightedCommand::execute() {
 117         try {
 118
 119                 if (abort == true) { return 0; }
 120
 121                 userData.resize(numComp,0);  //data[0] = unweightedscore
 122                 randomData.resize(numComp,0); //data[0] = unweightedscore
 123                 //create new tree with same num nodes and leaves as users
 124
 125                 outSum << "Tree#" << '\t' << "Groups" << '\t'  <<  "UWScore" <<'\t' << "UWSig" <<  endl;
 126                 mothurOut("Tree#\tGroups\tUWScore\tUWSig"); mothurOutEndLine();
 127
 128                 //get pscores for users trees
 129                 for (int i = 0; i < T.size(); i++) {
 130                         counter = 0;
 131
 132                         if (random)  {  output = new ColumnFile(globaldata->getTreeFile()  + toString(i+1) + ".unweighted", itersString);  }
 133
 134                         //get unweighted for users tree
 135                         rscoreFreq.resize(numComp);
 136                         rCumul.resize(numComp);
 137                         utreeScores.resize(numComp);
 138                         UWScoreSig.resize(numComp);
 139
 140                         userData = unweighted->getValues(T[i]);  //userData[0] = unweightedscore
 141
 142                         //output scores for each combination
 143                         for(int k = 0; k < numComp; k++) {
 144                                 //saves users score
 145                                 utreeScores[k].push_back(userData[k]);
 146
 147                                 //add users score to validscores
 148                                 validScores[userData[k]] = userData[k];
 149                         }
 150
 151                         //get unweighted scores for random trees
 152                         for (int j = 0; j < iters; j++) {
 153                                 //we need a different getValues because when we swap the labels we only want to swap those in each pairwise comparison
 154                                 randomData = unweighted->getValues(T[i], "", "");
 155
 156                                 for(int k = 0; k < numComp; k++) {
 157                                         //add trees unweighted score to map of scores
 158                                         map<float,float>::iterator it = rscoreFreq[k].find(randomData[k]);
 159                                         if (it != rscoreFreq[k].end()) {//already have that score
 160                                                 rscoreFreq[k][randomData[k]]++;
 161                                         }else{//first time we have seen this score
 162                                                 rscoreFreq[k][randomData[k]] = 1;
 163                                         }
 164
 165                                         //add randoms score to validscores
 166                                         validScores[randomData[k]] = randomData[k];
 167                                 }
 168                         }
 169
 170                         for(int a = 0; a < numComp; a++) {
 171                                 float rcumul = 1.0000;
 172                                 //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
 173                                 for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
 174                                         //make rscoreFreq map and rCumul
 175                                         map<float,float>::iterator it2 = rscoreFreq[a].find(it->first);
 176                                         rCumul[a][it->first] = rcumul;
 177                                         //get percentage of random trees with that info
 178                                         if (it2 != rscoreFreq[a].end()) {  rscoreFreq[a][it->first] /= iters; rcumul-= it2->second;  }
 179                                         else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
 180                                 }
 181
 182                                 if (random) {   UWScoreSig[a].push_back(rCumul[a][userData[a]]);        }
 183                                 else            {       UWScoreSig[a].push_back(0.0);                                           }
 184                         }
 185
 186                         //print output files
 187                         printUWSummaryFile(i);
 188                         if (random)  {  printUnweightedFile();  delete output;  }
 189                         if (phylip) {   createPhylipFile(i);            }
 190
 191                         rscoreFreq.clear();
 192                         rCumul.clear();
 193                         validScores.clear();
 194                         utreeScores.clear();
 195                         UWScoreSig.clear();
 196                 }
 197
 198                 //reset groups parameter
 199                 globaldata->Groups.clear();
 200                 outSum.close();
 201
 202                 return 0;
 203
 204         }
 205         catch(exception& e) {
 206                 errorOut(e, "UnifracUnweightedCommand", "execute");
 207                 exit(1);
 208         }
 209 }
 210 /***********************************************************/
 211 void UnifracUnweightedCommand::printUnweightedFile() {
 212         try {
 213                 vector<double> data;
 214                 vector<string> tags;
 215
 216                 tags.push_back("Score");
 217                 tags.push_back("RandFreq"); tags.push_back("RandCumul");
 218
 219                 for(int a = 0; a < numComp; a++) {
 220                         output->initFile(groupComb[a], tags);
 221                         //print each line
 222                         for (map<float,float>::iterator it = validScores.begin(); it != validScores.end(); it++) {
 223                                 data.push_back(it->first);  data.push_back(rscoreFreq[a][it->first]); data.push_back(rCumul[a][it->first]);
 224                                 output->output(data);
 225                                 data.clear();
 226                         }
 227                         output->resetFile();
 228                 }
 229         }
 230         catch(exception& e) {
 231                 errorOut(e, "UnifracUnweightedCommand", "printUnweightedFile");
 232                 exit(1);
 233         }
 234 }
 235
 236 /***********************************************************/
 237 void UnifracUnweightedCommand::printUWSummaryFile(int i) {
 238         try {
 239
 240                 //format output
 241                 outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
 242
 243                 //print each line
 244
 245                 for(int a = 0; a < numComp; a++) {
 246                         outSum << i+1 << '\t';
 247                         mothurOut(toString(i+1) + "\t");
 248
 249                         if (random) {
 250                                 if (UWScoreSig[a][0] > (1/(float)iters)) {
 251                                         outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
 252                                         cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << UWScoreSig[a][0] << endl;
 253                                         mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t" + toString(UWScoreSig[a][0])); mothurOutEndLine();
 254                                 }else {
 255                                         outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
 256                                         cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(itersString.length()) << "<" << (1/float(iters)) << endl;
 257                                         mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t<" + toString((1/float(iters)))); mothurOutEndLine();
 258                                 }
 259                         }else{
 260                                 outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl;
 261                                 cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << "0.00" << endl;
 262                                 mothurOutJustToLog(groupComb[a]  + "\t" + toString(utreeScores[a][0])  + "\t0.00"); mothurOutEndLine();
 263                         }
 264                 }
 265
 266         }
 267         catch(exception& e) {
 268                 errorOut(e, "UnifracUnweightedCommand", "printUWSummaryFile");
 269                 exit(1);
 270         }
 271 }
 272 /***********************************************************/
 273 void UnifracUnweightedCommand::createPhylipFile(int i) {
 274         try {
 275                 string phylipFileName = globaldata->getTreeFile()  + toString(i+1) + ".unweighted.dist";
 276                 ofstream out;
 277                 openOutputFile(phylipFileName, out);
 278
 279                 //output numSeqs
 280                 out << globaldata->Groups.size() << endl;
 281
 282                 //make matrix with scores in it
 283                 vector< vector<float> > dists;  dists.resize(globaldata->Groups.size());
 284                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 285                         dists[i].resize(globaldata->Groups.size(), 0.0);
 286                 }
 287
 288                 //flip it so you can print it
 289                 int count = 0;
 290                 for (int r=0; r<globaldata->Groups.size(); r++) {
 291                         for (int l = r+1; l < globaldata->Groups.size(); l++) {
 292                                 dists[r][l] = (1.0 - utreeScores[count][0]);
 293                                 dists[l][r] = (1.0 - utreeScores[count][0]);
 294                                 count++;
 295                         }
 296                 }
 297
 298                 //output to file
 299                 for (int r=0; r<globaldata->Groups.size(); r++) {
 300                         //output name
 301                         out << globaldata->Groups[r] << '\t';
 302
 303                         //output distances
 304                         for (int l = 0; l < r; l++) {   out  << dists[r][l] << '\t';  }
 305                         out << endl;
 306                 }
 307                 out.close();
 308         }
 309         catch(exception& e) {
 310                 errorOut(e, "UnifracUnweightedCommand", "createPhylipFile");
 311                 exit(1);
 312         }
 313 }
 314 /***********************************************************/
 315
 316
 317