phylotypecommand.cpp

   1 /*
   2  *  phylotypecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 11/20/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "phylotypecommand.h"
  11 #include "phylotree.h"
  12 #include "listvector.hpp"
  13 #include "rabundvector.hpp"
  14 #include "sabundvector.hpp"
  15
  16 //**********************************************************************************************************************
  17 vector<string> PhylotypeCommand::setParameters(){
  18         try {
  19                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","list-rabund-sabund",false,true,true); parameters.push_back(ptaxonomy);
  20                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pname);
  21                 CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pcutoff);
  22                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  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, "PhylotypeCommand", "setParameters");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 string PhylotypeCommand::getHelpString(){
  37         try {
  38                 string helpString = "";
  39                 helpString += "The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n";
  40                 helpString += "The phylotype command parameter options are taxonomy, cutoff and label. The taxonomy parameter is required.\n";
  41                 helpString += "The cutoff parameter allows you to specify the level you want to stop at.  The default is the highest level in your taxonomy file. \n";
  42                 helpString += "For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n";
  43                 helpString += "For the cutoff parameter levels count up from the root of the phylotree. This enables you to look at the grouping down to a specific resolution, say the genus level.\n";
  44                 helpString += "The label parameter allows you to specify which level you would like, and are separated by dashes.  The default all levels in your taxonomy file. \n";
  45                 helpString += "For the label parameter, levels count down from the root to keep the output similiar to mothur's other commands which report information from finer resolution to coarser resolutions.\n";
  46                 helpString += "The phylotype command should be in the following format: \n";
  47                 helpString += "phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n";
  48                 helpString += "Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n";
  49                 return helpString;
  50         }
  51         catch(exception& e) {
  52                 m->errorOut(e, "PhylotypeCommand", "getHelpString");
  53                 exit(1);
  54         }
  55 }
  56 //**********************************************************************************************************************
  57 string PhylotypeCommand::getOutputPattern(string type) {
  58     try {
  59         string pattern = "";
  60
  61         if (type == "list") {  pattern = "[filename],[tag],list"; }
  62         else if (type == "rabund") {  pattern = "[filename],[tag],rabund"; }
  63         else if (type == "sabund") {  pattern = "[filename],[tag],sabund"; }
  64         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  65
  66         return pattern;
  67     }
  68     catch(exception& e) {
  69         m->errorOut(e, "PhylotypeCommand", "getOutputPattern");
  70         exit(1);
  71     }
  72 }
  73 //**********************************************************************************************************************
  74 PhylotypeCommand::PhylotypeCommand(){
  75         try {
  76                 abort = true; calledHelp = true;
  77                 setParameters();
  78                 vector<string> tempOutNames;
  79                 outputTypes["list"] = tempOutNames;
  80                 outputTypes["sabund"] = tempOutNames;
  81                 outputTypes["rabund"] = tempOutNames;
  82         }
  83         catch(exception& e) {
  84                 m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
  85                 exit(1);
  86         }
  87 }
  88 /**********************************************************************************************************************/
  89 PhylotypeCommand::PhylotypeCommand(string option)  {
  90         try {
  91                 abort = false; calledHelp = false;
  92
  93                 //allow user to run help
  94                 if(option == "help") { help(); abort = true; calledHelp = true; }
  95                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  96
  97                 else {
  98                         vector<string> myArray = setParameters();
  99
 100                         OptionParser parser(option);
 101                         map<string, string> parameters = parser.getParameters();
 102
 103                         ValidParameters validParameter;
 104                         map<string, string>::iterator it;
 105
 106                         //check to make sure all parameters are valid for command
 107                         for (it = parameters.begin(); it != parameters.end(); it++) {
 108                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 109                         }
 110
 111                         //initialize outputTypes
 112                         vector<string> tempOutNames;
 113                         outputTypes["list"] = tempOutNames;
 114                         outputTypes["sabund"] = tempOutNames;
 115                         outputTypes["rabund"] = tempOutNames;
 116
 117                         //if the user changes the input directory command factory will send this info to us in the output parameter
 118                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 119                         if (inputDir == "not found"){   inputDir = "";          }
 120                         else {
 121                                 string path;
 122                                 it = parameters.find("taxonomy");
 123                                 //user has given a template file
 124                                 if(it != parameters.end()){
 125                                         path = m->hasPath(it->second);
 126                                         //if the user has not given a path then, add inputdir. else leave path alone.
 127                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 128                                 }
 129
 130                                 it = parameters.find("name");
 131                                 //user has given a template file
 132                                 if(it != parameters.end()){
 133                                         path = m->hasPath(it->second);
 134                                         //if the user has not given a path then, add inputdir. else leave path alone.
 135                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 136                                 }
 137                         }
 138
 139                         taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
 140                         if (taxonomyFileName == "not found") {
 141                                 taxonomyFileName = m->getTaxonomyFile();
 142                                 if (taxonomyFileName != "") {  m->mothurOut("Using " + taxonomyFileName + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
 143                                 else {
 144                                         m->mothurOut("No valid current files. taxonomy is a required parameter."); m->mothurOutEndLine();
 145                                         abort = true;
 146                                 }
 147                         }else if (taxonomyFileName == "not open") { taxonomyFileName = ""; abort = true; }
 148                         else { m->setTaxonomyFile(taxonomyFileName); }
 149
 150                         namefile = validParameter.validFile(parameters, "name", true);
 151                         if (namefile == "not open") { namefile = ""; abort = true; }
 152                         else if (namefile == "not found") { namefile = ""; }
 153                         else { readNamesFile(); m->setNameFile(namefile); }
 154
 155                         //if the user changes the output directory command factory will send this info to us in the output parameter
 156                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 157                                 outputDir = "";
 158                                 outputDir += m->hasPath(taxonomyFileName); //if user entered a file with a path then preserve it
 159                         }
 160
 161                         string temp = validParameter.validFile(parameters, "cutoff", false);
 162                         if (temp == "not found") { temp = "-1"; }
 163                         m->mothurConvert(temp, cutoff);
 164
 165                         label = validParameter.validFile(parameters, "label", false);
 166                         if (label == "not found") { label = ""; allLines = 1; }
 167                         else {
 168                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 169                                 else { allLines = 1;  }
 170                         }
 171
 172                         if (namefile == "") {
 173                                 vector<string> files; files.push_back(taxonomyFileName);
 174                                 parser.getNameFile(files);
 175                         }
 176
 177                 }
 178         }
 179         catch(exception& e) {
 180                 m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
 181                 exit(1);
 182         }
 183 }
 184 /**********************************************************************************************************************/
 185
 186 int PhylotypeCommand::execute(){
 187         try {
 188
 189                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 190
 191                 //reads in taxonomy file and makes all the taxonomies the same length
 192                 //by appending the last taxon to a given taxonomy as many times as needed to
 193                 //make it as long as the longest taxonomy in the file
 194                 TaxEqualizer* taxEqual = new TaxEqualizer(taxonomyFileName, cutoff, outputDir);
 195
 196                 if (m->control_pressed) { delete taxEqual; return 0; }
 197
 198                 string equalizedTaxFile = taxEqual->getEqualizedTaxFile();
 199
 200                 delete taxEqual;
 201
 202                 //build taxonomy tree from equalized file
 203                 PhyloTree* tree = new PhyloTree(equalizedTaxFile);
 204                 vector<int> leaves = tree->getGenusNodes();
 205
 206                 //store leaf nodes in current map
 207                 for (int i = 0; i < leaves.size(); i++)         {       currentNodes[leaves[i]] = leaves[i];    }
 208
 209                 bool done = false;
 210                 if (tree->get(leaves[0]).parent == -1) {  m->mothurOut("Empty Tree"); m->mothurOutEndLine();    done = true;    }
 211
 212                 if (m->control_pressed) { delete tree; return 0; }
 213
 214                 string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
 215                 map<string, string> variables;
 216         variables["[filename]"] = fileroot;
 217         variables["[tag]"] = "tx";
 218         ofstream outList;
 219                 string outputListFile = getOutputFileName("list",variables);
 220                 m->openOutputFile(outputListFile, outList);
 221                 ofstream outSabund;
 222                 string outputSabundFile = getOutputFileName("sabund",variables);
 223                 m->openOutputFile(outputSabundFile, outSabund);
 224                 ofstream outRabund;
 225                 string outputRabundFile = getOutputFileName("rabund",variables);
 226                 m->openOutputFile(outputRabundFile, outRabund);
 227
 228                 outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);
 229                 outputNames.push_back(outputSabundFile); outputTypes["sabund"].push_back(outputSabundFile);
 230                 outputNames.push_back(outputRabundFile); outputTypes["rabund"].push_back(outputRabundFile);
 231
 232                 int count = 1;
 233                 //start at leaves of tree and work towards root, processing the labels the user wants
 234                 while((!done) && ((allLines == 1) || (labels.size() != 0))) {
 235
 236                         string level = toString(count);
 237                         count++;
 238
 239                         if (m->control_pressed) {
 240                                 outRabund.close(); outSabund.close(); outList.close();
 241                                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 242                                 delete tree; return 0;
 243                         }
 244
 245                         //is this a level the user want output for
 246                         if(allLines == 1 || labels.count(level) == 1){
 247
 248                                 //output level
 249                                 m->mothurOut(level); m->mothurOutEndLine();
 250
 251                                 ListVector list;
 252                                 list.setLabel(level);
 253
 254                                 //go through nodes and build listvector
 255                                 for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 256
 257                                         //get parents
 258                                         TaxNode node = tree->get(itCurrent->first);
 259                                         parentNodes[node.parent] = node.parent;
 260
 261                                         vector<string> names = node.accessions;
 262
 263                                         //make the names compatable with listvector
 264                                         string name = "";
 265                                         for (int i = 0; i < names.size(); i++) {
 266
 267                         if (names[i] != "unknown") {
 268                             if (namefile != "") {
 269                                 map<string, string>::iterator itNames = namemap.find(names[i]);  //make sure this name is in namefile
 270
 271                                 if (itNames != namemap.end()) {  name += namemap[names[i]] + ",";   } //you found it in namefile
 272                                 else { m->mothurOut("[ERROR]: " + names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 273
 274                             }else{   name += names[i] + ",";    }
 275                         }
 276                                         }
 277
 278                     if (m->control_pressed) { break; }
 279
 280                                         name = name.substr(0, name.length()-1);  //rip off extra ','
 281                                         //add bin to list vector
 282                                         if (name != "") { list.push_back(name); } //caused by unknown
 283                                 }
 284
 285                                 //print listvector
 286                                 list.print(outList);
 287                                 //print rabund
 288                                 list.getRAbundVector().print(outRabund);
 289                                 //print sabund
 290                                 list.getSAbundVector().print(outSabund);
 291
 292                                 labels.erase(level);
 293
 294                         }else {
 295
 296                                 //just get parents
 297                                 for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 298                                         int parent = tree->get(itCurrent->first).parent;
 299                                         parentNodes[parent] = parent;
 300                                 }
 301                         }
 302
 303                         //move up a level
 304                         currentNodes = parentNodes;
 305                         parentNodes.clear();
 306
 307                         //have we reached the rootnode
 308                         if (tree->get(currentNodes.begin()->first).parent == -1)  {  done = true;  }
 309                 }
 310
 311                 outList.close();
 312                 outSabund.close();
 313                 outRabund.close();
 314
 315                 delete tree;
 316
 317                 if (m->control_pressed) {
 318                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 319                         return 0;
 320                 }
 321
 322                 //set list file as new current listfile
 323                 string current = "";
 324                 itTypes = outputTypes.find("list");
 325                 if (itTypes != outputTypes.end()) {
 326                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 327                 }
 328
 329                 //set rabund file as new current rabundfile
 330                 itTypes = outputTypes.find("rabund");
 331                 if (itTypes != outputTypes.end()) {
 332                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 333                 }
 334
 335                 //set sabund file as new current sabundfile
 336                 itTypes = outputTypes.find("sabund");
 337                 if (itTypes != outputTypes.end()) {
 338                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
 339                 }
 340
 341                 m->mothurOutEndLine();
 342                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 343                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 344                 m->mothurOutEndLine();
 345
 346                 return 0;
 347         }
 348
 349         catch(exception& e) {
 350                 m->errorOut(e, "PhylotypeCommand", "execute");
 351                 exit(1);
 352         }
 353 }
 354 /*****************************************************************/
 355 int PhylotypeCommand::readNamesFile() {
 356         try {
 357
 358                 ifstream in;
 359                 m->openInputFile(namefile, in);
 360
 361                 string first, second;
 362                 map<string, string>::iterator itNames;
 363
 364                 while(!in.eof()) {
 365                         in >> first >> second; m->gobble(in);
 366
 367                         itNames = namemap.find(first);
 368                         if (itNames == namemap.end()) {
 369                                 namemap[first] = second;
 370                         }else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); namemap.clear(); namefile = ""; return 1; }
 371                 }
 372                 in.close();
 373
 374                 return 0;
 375         }
 376         catch(exception& e) {
 377                 m->errorOut(e, "PhylotypeCommand", "readNamesFile");
 378                 exit(1);
 379         }
 380 }
 381
 382 /**********************************************************************************************************************/