pcoacommand.cpp

   1
   2 /*
   3  *  pcacommand.cpp
   4  *  Mothur
   5  *
   6  *  Created by westcott on 1/4/10.
   7  *  Copyright 2010 Schloss Lab. All rights reserved.
   8  *
   9  */
  10
  11 #include "pcoacommand.h"
  12 #include "readphylipvector.h"
  13
  14
  15 //**********************************************************************************************************************
  16 vector<string> PCOACommand::setParameters(){
  17         try {
  18                 CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
  19                 CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmetric);
  20                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  21                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  22
  23                 vector<string> myArray;
  24                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  25                 return myArray;
  26         }
  27         catch(exception& e) {
  28                 m->errorOut(e, "PCOACommand", "setParameters");
  29                 exit(1);
  30         }
  31 }
  32 //**********************************************************************************************************************
  33 string PCOACommand::getHelpString(){
  34         try {
  35                 string helpString = "";
  36                 helpString += "The pcoa command parameters are phylip and metric";
  37                 helpString += "The phylip parameter allows you to enter your distance file.";
  38                 helpString += "The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True";
  39                 helpString += "Example pcoa(phylip=yourDistanceFile).\n";
  40                 helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n";
  41                 return helpString;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "PCOACommand", "getHelpString");
  45                 exit(1);
  46         }
  47 }
  48
  49 //**********************************************************************************************************************
  50 string PCOACommand::getOutputFileNameTag(string type, string inputName=""){
  51         try {
  52         string outputFileName = "";
  53                 map<string, vector<string> >::iterator it;
  54
  55         //is this a type this command creates
  56         it = outputTypes.find(type);
  57         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  58         else {
  59             if (type == "pcoa") {  outputFileName =  "pcoa.axes"; }
  60             else if (type == "loadings") {  outputFileName =  "pcoa.loadings"; }
  61             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  62         }
  63         return outputFileName;
  64         }
  65         catch(exception& e) {
  66                 m->errorOut(e, "PCOACommand", "getOutputFileNameTag");
  67                 exit(1);
  68         }
  69 }
  70
  71 //**********************************************************************************************************************
  72 PCOACommand::PCOACommand(){
  73         try {
  74                 abort = true; calledHelp = true;
  75                 setParameters();
  76                 vector<string> tempOutNames;
  77                 outputTypes["pcoa"] = tempOutNames;
  78                 outputTypes["loadings"] = tempOutNames;
  79         }
  80         catch(exception& e) {
  81                 m->errorOut(e, "PCOACommand", "PCOACommand");
  82                 exit(1);
  83         }
  84 }
  85 //**********************************************************************************************************************
  86
  87 PCOACommand::PCOACommand(string option)  {
  88         try {
  89                 abort = false; calledHelp = false;
  90
  91                 //allow user to run help
  92                 if(option == "help") { help(); abort = true; calledHelp = true; }
  93                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  94
  95                 else {
  96                         vector<string> myArray = setParameters();
  97
  98                         OptionParser parser(option);
  99                         map<string, string> parameters = parser. getParameters();
 100
 101                         ValidParameters validParameter;
 102                         map<string, string>::iterator it;
 103
 104                         //check to make sure all parameters are valid for command
 105                         for (it = parameters.begin(); it != parameters.end(); it++) {
 106                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 107                         }
 108                         //if the user changes the input directory command factory will send this info to us in the output parameter
 109                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 110                         if (inputDir == "not found"){   inputDir = "";          }
 111                         else {
 112                                 string path;
 113                                 it = parameters.find("phylip");
 114                                 //user has given a template file
 115                                 if(it != parameters.end()){
 116                                         path = m->hasPath(it->second);
 117                                         //if the user has not given a path then, add inputdir. else leave path alone.
 118                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 119                                 }
 120                         }
 121
 122                         //initialize outputTypes
 123                         vector<string> tempOutNames;
 124                         outputTypes["pcoa"] = tempOutNames;
 125                         outputTypes["loadings"] = tempOutNames;
 126
 127                         //required parameters
 128                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 129                         if (phylipfile == "not open") { abort = true; }
 130                         else if (phylipfile == "not found") {
 131                                 //if there is a current phylip file, use it
 132                                 phylipfile = m->getPhylipFile();
 133                                 if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 134                                 else {  m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
 135                         }else { m->setPhylipFile(phylipfile); }
 136
 137                         filename = phylipfile;
 138
 139                         //if the user changes the output directory command factory will send this info to us in the output parameter
 140                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 141                                 outputDir = "";
 142                                 outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it
 143                         }
 144
 145                         string temp = validParameter.validFile(parameters, "metric", false);    if (temp == "not found"){       temp = "T";                             }
 146                         metric = m->isTrue(temp);
 147                 }
 148
 149         }
 150         catch(exception& e) {
 151                 m->errorOut(e, "PCOACommand", "PCOACommand");
 152                 exit(1);
 153         }
 154 }
 155 //**********************************************************************************************************************
 156 int PCOACommand::execute(){
 157         try {
 158
 159                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 160
 161                 cout.setf(ios::fixed, ios::floatfield);
 162                 cout.setf(ios::showpoint);
 163                 cerr.setf(ios::fixed, ios::floatfield);
 164                 cerr.setf(ios::showpoint);
 165
 166                 vector<string> names;
 167                 vector<vector<double> > D;
 168
 169                 fbase = outputDir + m->getRootName(m->getSimpleName(filename));
 170
 171                 ReadPhylipVector readFile(filename);
 172                 names = readFile.read(D);
 173
 174                 if (m->control_pressed) { return 0; }
 175
 176                 double offset = 0.0000;
 177                 vector<double> d;
 178                 vector<double> e;
 179                 vector<vector<double> > G = D;
 180                 //vector<vector<double> > copy_G;
 181
 182                 m->mothurOut("\nProcessing...\n");
 183
 184                 for(int count=0;count<2;count++){
 185                         linearCalc.recenter(offset, D, G);              if (m->control_pressed) { return 0; }
 186                         linearCalc.tred2(G, d, e);                              if (m->control_pressed) { return 0; }
 187                         linearCalc.qtli(d, e, G);                               if (m->control_pressed) { return 0; }
 188                         offset = d[d.size()-1];
 189                         if(offset > 0.0) break;
 190                 }
 191
 192                 if (m->control_pressed) { return 0; }
 193
 194                 output(fbase, names, G, d);
 195
 196                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
 197
 198                 if (metric) {
 199
 200                         for (int i = 1; i < 4; i++) {
 201
 202                                 vector< vector<double> > EuclidDists = linearCalc.calculateEuclidianDistance(G, i); //G is the pcoa file
 203
 204                                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
 205
 206                                 double corr = linearCalc.calcPearson(EuclidDists, D); //G is the pcoa file, D is the users distance matrix
 207
 208                                 m->mothurOut("Rsq " + toString(i) + " axis: " + toString(corr * corr)); m->mothurOutEndLine();
 209
 210                                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
 211                         }
 212                 }
 213
 214                 m->mothurOutEndLine();
 215                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 216                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 217                 m->mothurOutEndLine();
 218
 219                 return 0;
 220         }
 221         catch(exception& e) {
 222                 m->errorOut(e, "PCOACommand", "execute");
 223                 exit(1);
 224         }
 225 }
 226 /*********************************************************************************************************************************/
 227
 228 void PCOACommand::get_comment(istream& f, char begin, char end){
 229         try {
 230                 char d=f.get();
 231                 while(d != end){        d = f.get();    }
 232                 d = f.peek();
 233         }
 234         catch(exception& e) {
 235                 m->errorOut(e, "PCOACommand", "get_comment");
 236                 exit(1);
 237         }
 238 }
 239 /*********************************************************************************************************************************/
 240
 241 void PCOACommand::output(string fnameRoot, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
 242         try {
 243                 int rank = name_list.size();
 244                 double dsum = 0.0000;
 245                 for(int i=0;i<rank;i++){
 246                         dsum += d[i];
 247                         for(int j=0;j<rank;j++){
 248                                 if(d[j] >= 0)   {       G[i][j] *= pow(d[j],0.5);       }
 249                                 else                    {       G[i][j] = 0.00000;                      }
 250                         }
 251                 }
 252
 253                 ofstream pcaData;
 254         string pcoaDataFile = fnameRoot+getOutputFileNameTag("pcoa");
 255         m->openOutputFile(pcoaDataFile, pcaData);
 256                 pcaData.setf(ios::fixed, ios::floatfield);
 257                 pcaData.setf(ios::showpoint);
 258                 outputNames.push_back(pcoaDataFile);
 259                 outputTypes["pcoa"].push_back(pcoaDataFile);
 260
 261                 ofstream pcaLoadings;
 262         string loadingsFile = fnameRoot+getOutputFileNameTag("loadings");
 263         m->openOutputFile(loadingsFile, pcaLoadings);
 264                 pcaLoadings.setf(ios::fixed, ios::floatfield);
 265                 pcaLoadings.setf(ios::showpoint);
 266                 outputNames.push_back(loadingsFile);
 267                 outputTypes["loadings"].push_back(loadingsFile);
 268
 269                 pcaLoadings << "axis\tloading\n";
 270                 for(int i=0;i<rank;i++){
 271                         pcaLoadings << i+1 << '\t' << d[i] * 100.0 / dsum << endl;
 272                 }
 273
 274                 pcaData << "group";
 275                 for(int i=0;i<rank;i++){
 276                         pcaData << '\t' << "axis" << i+1;
 277                 }
 278                 pcaData << endl;
 279
 280                 for(int i=0;i<rank;i++){
 281                         pcaData << name_list[i] << '\t';
 282                         for(int j=0;j<rank;j++){
 283                                 pcaData << G[i][j] << '\t';
 284                         }
 285                         pcaData << endl;
 286                 }
 287         }
 288         catch(exception& e) {
 289                 m->errorOut(e, "PCOACommand", "output");
 290                 exit(1);
 291         }
 292 }
 293
 294 /*********************************************************************************************************************************/
 295