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 //**********************************************************************************************************************
  51 PCOACommand::PCOACommand(){
  52         try {
  53                 abort = true; calledHelp = true;
  54                 setParameters();
  55                 vector<string> tempOutNames;
  56                 outputTypes["pcoa"] = tempOutNames;
  57                 outputTypes["loadings"] = tempOutNames;
  58         }
  59         catch(exception& e) {
  60                 m->errorOut(e, "PCOACommand", "PCOACommand");
  61                 exit(1);
  62         }
  63 }
  64 //**********************************************************************************************************************
  65
  66 PCOACommand::PCOACommand(string option)  {
  67         try {
  68                 abort = false; calledHelp = false;
  69
  70                 //allow user to run help
  71                 if(option == "help") { help(); abort = true; calledHelp = true; }
  72                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  73
  74                 else {
  75                         vector<string> myArray = setParameters();
  76
  77                         OptionParser parser(option);
  78                         map<string, string> parameters = parser. getParameters();
  79
  80                         ValidParameters validParameter;
  81                         map<string, string>::iterator it;
  82
  83                         //check to make sure all parameters are valid for command
  84                         for (it = parameters.begin(); it != parameters.end(); it++) {
  85                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  86                         }
  87                         //if the user changes the input directory command factory will send this info to us in the output parameter
  88                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  89                         if (inputDir == "not found"){   inputDir = "";          }
  90                         else {
  91                                 string path;
  92                                 it = parameters.find("phylip");
  93                                 //user has given a template file
  94                                 if(it != parameters.end()){
  95                                         path = m->hasPath(it->second);
  96                                         //if the user has not given a path then, add inputdir. else leave path alone.
  97                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
  98                                 }
  99                         }
 100
 101                         //initialize outputTypes
 102                         vector<string> tempOutNames;
 103                         outputTypes["pcoa"] = tempOutNames;
 104                         outputTypes["loadings"] = tempOutNames;
 105
 106                         //required parameters
 107                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 108                         if (phylipfile == "not open") { abort = true; }
 109                         else if (phylipfile == "not found") {
 110                                 //if there is a current phylip file, use it
 111                                 phylipfile = m->getPhylipFile();
 112                                 if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 113                                 else {  m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
 114                         }else { m->setPhylipFile(phylipfile); }
 115
 116                         filename = phylipfile;
 117
 118                         //if the user changes the output directory command factory will send this info to us in the output parameter
 119                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 120                                 outputDir = "";
 121                                 outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it
 122                         }
 123
 124                         string temp = validParameter.validFile(parameters, "metric", false);    if (temp == "not found"){       temp = "T";                             }
 125                         metric = m->isTrue(temp);
 126                 }
 127
 128         }
 129         catch(exception& e) {
 130                 m->errorOut(e, "PCOACommand", "PCOACommand");
 131                 exit(1);
 132         }
 133 }
 134 //**********************************************************************************************************************
 135 int PCOACommand::execute(){
 136         try {
 137
 138                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 139
 140                 cout.setf(ios::fixed, ios::floatfield);
 141                 cout.setf(ios::showpoint);
 142                 cerr.setf(ios::fixed, ios::floatfield);
 143                 cerr.setf(ios::showpoint);
 144
 145                 vector<string> names;
 146                 vector<vector<double> > D;
 147
 148                 fbase = outputDir + m->getRootName(m->getSimpleName(filename));
 149
 150                 ReadPhylipVector readFile(filename);
 151                 names = readFile.read(D);
 152
 153                 if (m->control_pressed) { return 0; }
 154
 155                 double offset = 0.0000;
 156                 vector<double> d;
 157                 vector<double> e;
 158                 vector<vector<double> > G = D;
 159                 //vector<vector<double> > copy_G;
 160
 161                 m->mothurOut("\nProcessing...\n");
 162
 163                 for(int count=0;count<2;count++){
 164                         linearCalc.recenter(offset, D, G);              if (m->control_pressed) { return 0; }
 165                         linearCalc.tred2(G, d, e);                              if (m->control_pressed) { return 0; }
 166                         linearCalc.qtli(d, e, G);                               if (m->control_pressed) { return 0; }
 167                         offset = d[d.size()-1];
 168                         if(offset > 0.0) break;
 169                 }
 170
 171                 if (m->control_pressed) { return 0; }
 172
 173                 output(fbase, names, G, d);
 174
 175                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
 176
 177                 if (metric) {
 178
 179                         for (int i = 1; i < 4; i++) {
 180
 181                                 vector< vector<double> > EuclidDists = linearCalc.calculateEuclidianDistance(G, i); //G is the pcoa file
 182
 183                                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
 184
 185                                 double corr = linearCalc.calcPearson(EuclidDists, D); //G is the pcoa file, D is the users distance matrix
 186
 187                                 m->mothurOut("Rsq " + toString(i) + " axis: " + toString(corr * corr)); m->mothurOutEndLine();
 188
 189                                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
 190                         }
 191                 }
 192
 193                 m->mothurOutEndLine();
 194                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 195                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 196                 m->mothurOutEndLine();
 197
 198                 return 0;
 199         }
 200         catch(exception& e) {
 201                 m->errorOut(e, "PCOACommand", "execute");
 202                 exit(1);
 203         }
 204 }
 205 /*********************************************************************************************************************************/
 206
 207 void PCOACommand::get_comment(istream& f, char begin, char end){
 208         try {
 209                 char d=f.get();
 210                 while(d != end){        d = f.get();    }
 211                 d = f.peek();
 212         }
 213         catch(exception& e) {
 214                 m->errorOut(e, "PCOACommand", "get_comment");
 215                 exit(1);
 216         }
 217 }
 218 /*********************************************************************************************************************************/
 219
 220 void PCOACommand::output(string fnameRoot, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
 221         try {
 222                 int rank = name_list.size();
 223                 double dsum = 0.0000;
 224                 for(int i=0;i<rank;i++){
 225                         dsum += d[i];
 226                         for(int j=0;j<rank;j++){
 227                                 if(d[j] >= 0)   {       G[i][j] *= pow(d[j],0.5);       }
 228                                 else                    {       G[i][j] = 0.00000;                      }
 229                         }
 230                 }
 231
 232                 ofstream pcaData((fnameRoot+"pcoa.axes").c_str(), ios::trunc);
 233                 pcaData.setf(ios::fixed, ios::floatfield);
 234                 pcaData.setf(ios::showpoint);
 235                 outputNames.push_back(fnameRoot+"pcoa.axes");
 236                 outputTypes["pcoa"].push_back(fnameRoot+"pcoa.axes");
 237
 238                 ofstream pcaLoadings((fnameRoot+"pcoa.loadings").c_str(), ios::trunc);
 239                 pcaLoadings.setf(ios::fixed, ios::floatfield);
 240                 pcaLoadings.setf(ios::showpoint);
 241                 outputNames.push_back(fnameRoot+"pcoa.loadings");
 242                 outputTypes["loadings"].push_back(fnameRoot+"pcoa.loadings");
 243
 244                 pcaLoadings << "axis\tloading\n";
 245                 for(int i=0;i<rank;i++){
 246                         pcaLoadings << i+1 << '\t' << d[i] * 100.0 / dsum << endl;
 247                 }
 248
 249                 pcaData << "group";
 250                 for(int i=0;i<rank;i++){
 251                         pcaData << '\t' << "axis" << i+1;
 252                 }
 253                 pcaData << endl;
 254
 255                 for(int i=0;i<rank;i++){
 256                         pcaData << name_list[i] << '\t';
 257                         for(int j=0;j<rank;j++){
 258                                 pcaData << G[i][j] << '\t';
 259                         }
 260                         pcaData << endl;
 261                 }
 262         }
 263         catch(exception& e) {
 264                 m->errorOut(e, "PCOACommand", "output");
 265                 exit(1);
 266         }
 267 }
 268
 269 /*********************************************************************************************************************************/
 270