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",false,true); parameters.push_back(ptaxonomy);
  20                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  21                 CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "",false,false); 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\n";
  49                 return helpString;
  50         }
  51         catch(exception& e) {
  52                 m->errorOut(e, "PhylotypeCommand", "getHelpString");
  53                 exit(1);
  54         }
  55 }
  56
  57 //**********************************************************************************************************************
  58 PhylotypeCommand::PhylotypeCommand(){
  59         try {
  60                 abort = true; calledHelp = true;
  61                 setParameters();
  62                 vector<string> tempOutNames;
  63                 outputTypes["list"] = tempOutNames;
  64                 outputTypes["sabund"] = tempOutNames;
  65                 outputTypes["rabund"] = tempOutNames;
  66         }
  67         catch(exception& e) {
  68                 m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
  69                 exit(1);
  70         }
  71 }
  72 /**********************************************************************************************************************/
  73 PhylotypeCommand::PhylotypeCommand(string option)  {
  74         try {
  75                 abort = false; calledHelp = false;
  76
  77                 //allow user to run help
  78                 if(option == "help") { help(); abort = true; calledHelp = true; }
  79
  80                 else {
  81                         vector<string> myArray = setParameters();
  82
  83                         OptionParser parser(option);
  84                         map<string, string> parameters = parser.getParameters();
  85
  86                         ValidParameters validParameter;
  87                         map<string, string>::iterator it;
  88
  89                         //check to make sure all parameters are valid for command
  90                         for (it = parameters.begin(); it != parameters.end(); it++) {
  91                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  92                         }
  93
  94                         //initialize outputTypes
  95                         vector<string> tempOutNames;
  96                         outputTypes["list"] = tempOutNames;
  97                         outputTypes["sabund"] = tempOutNames;
  98                         outputTypes["rabund"] = tempOutNames;
  99
 100                         //if the user changes the input directory command factory will send this info to us in the output parameter
 101                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 102                         if (inputDir == "not found"){   inputDir = "";          }
 103                         else {
 104                                 string path;
 105                                 it = parameters.find("taxonomy");
 106                                 //user has given a template file
 107                                 if(it != parameters.end()){
 108                                         path = m->hasPath(it->second);
 109                                         //if the user has not given a path then, add inputdir. else leave path alone.
 110                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 111                                 }
 112
 113                                 it = parameters.find("name");
 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["name"] = inputDir + it->second;             }
 119                                 }
 120                         }
 121
 122                         taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
 123                         if (taxonomyFileName == "not found") {
 124                                 taxonomyFileName = m->getTaxonomyFile();
 125                                 if (taxonomyFileName != "") {  m->mothurOut("Using " + taxonomyFileName + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
 126                                 else {
 127                                         m->mothurOut("No valid current files. taxonomy is a required parameter."); m->mothurOutEndLine();
 128                                         abort = true;
 129                                 }
 130                         }else if (taxonomyFileName == "not open") { abort = true; }
 131
 132                         namefile = validParameter.validFile(parameters, "name", true);
 133                         if (namefile == "not open") { abort = true; }
 134                         else if (namefile == "not found") { namefile = ""; }
 135                         else { readNamesFile(); }
 136
 137                         //if the user changes the output directory command factory will send this info to us in the output parameter
 138                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 139                                 outputDir = "";
 140                                 outputDir += m->hasPath(taxonomyFileName); //if user entered a file with a path then preserve it
 141                         }
 142
 143                         string temp = validParameter.validFile(parameters, "cutoff", false);
 144                         if (temp == "not found") { temp = "-1"; }
 145                         convert(temp, cutoff);
 146
 147                         label = validParameter.validFile(parameters, "label", false);
 148                         if (label == "not found") { label = ""; allLines = 1; }
 149                         else {
 150                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 151                                 else { allLines = 1;  }
 152                         }
 153
 154                 }
 155         }
 156         catch(exception& e) {
 157                 m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
 158                 exit(1);
 159         }
 160 }
 161 /**********************************************************************************************************************/
 162
 163 int PhylotypeCommand::execute(){
 164         try {
 165
 166                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 167
 168                 //reads in taxonomy file and makes all the taxonomies the same length
 169                 //by appending the last taxon to a given taxonomy as many times as needed to
 170                 //make it as long as the longest taxonomy in the file
 171                 TaxEqualizer* taxEqual = new TaxEqualizer(taxonomyFileName, cutoff, outputDir);
 172
 173                 if (m->control_pressed) { delete taxEqual; return 0; }
 174
 175                 string equalizedTaxFile = taxEqual->getEqualizedTaxFile();
 176
 177                 delete taxEqual;
 178
 179                 //build taxonomy tree from equalized file
 180                 PhyloTree* tree = new PhyloTree(equalizedTaxFile);
 181                 vector<int> leaves = tree->getGenusNodes();
 182
 183                 //store leaf nodes in current map
 184                 for (int i = 0; i < leaves.size(); i++)         {       currentNodes[leaves[i]] = leaves[i];    }
 185
 186                 bool done = false;
 187                 if (tree->get(leaves[0]).parent == -1) {  m->mothurOut("Empty Tree"); m->mothurOutEndLine();    done = true;    }
 188
 189                 if (m->control_pressed) { delete tree; return 0; }
 190
 191                 string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
 192
 193                 ofstream outList;
 194                 string outputListFile = fileroot + "tx.list";
 195                 m->openOutputFile(outputListFile, outList);
 196                 ofstream outSabund;
 197                 string outputSabundFile = fileroot + "tx.sabund";
 198                 m->openOutputFile(outputSabundFile, outSabund);
 199                 ofstream outRabund;
 200                 string outputRabundFile = fileroot + "tx.rabund";
 201                 m->openOutputFile(outputRabundFile, outRabund);
 202
 203                 outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);
 204                 outputNames.push_back(outputSabundFile); outputTypes["sabund"].push_back(outputSabundFile);
 205                 outputNames.push_back(outputRabundFile); outputTypes["rabund"].push_back(outputRabundFile);
 206
 207                 int count = 1;
 208                 //start at leaves of tree and work towards root, processing the labels the user wants
 209                 while((!done) && ((allLines == 1) || (labels.size() != 0))) {
 210
 211                         string level = toString(count);
 212                         count++;
 213
 214                         if (m->control_pressed) {
 215                                 outRabund.close(); outSabund.close(); outList.close();
 216                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 217                                 delete tree; return 0;
 218                         }
 219
 220                         //is this a level the user want output for
 221                         if(allLines == 1 || labels.count(level) == 1){
 222
 223                                 //output level
 224                                 m->mothurOut(level); m->mothurOutEndLine();
 225
 226                                 ListVector list;
 227                                 list.setLabel(level);
 228                                 //go through nodes and build listvector
 229                                 for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 230
 231                                         //get parents
 232                                         TaxNode node = tree->get(itCurrent->first);
 233                                         parentNodes[node.parent] = node.parent;
 234
 235                                         vector<string> names = node.accessions;
 236
 237                                         //make the names compatable with listvector
 238                                         string name = "";
 239                                         for (int i = 0; i < names.size(); i++) {
 240                                                 if (namefile != "") {
 241                                                         map<string, string>::iterator itNames = namemap.find(names[i]);  //make sure this name is in namefile
 242
 243                                                         if (itNames != namemap.end()) {  name += namemap[names[i]] + ",";   } //you found it in namefile
 244                                                         else { m->mothurOut(names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); exit(1);  }
 245
 246                                                 }else{   name += names[i] + ",";        }
 247                                         }
 248                                         name = name.substr(0, name.length()-1);  //rip off extra ','
 249
 250                                         //add bin to list vector
 251                                         list.push_back(name);
 252                                 }
 253
 254                                 //print listvector
 255                                 list.print(outList);
 256                                 //print rabund
 257                                 list.getRAbundVector().print(outRabund);
 258                                 //print sabund
 259                                 list.getSAbundVector().print(outSabund);
 260
 261                                 labels.erase(level);
 262
 263                         }else {
 264
 265                                 //just get parents
 266                                 for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 267                                         int parent = tree->get(itCurrent->first).parent;
 268                                         parentNodes[parent] = parent;
 269                                 }
 270                         }
 271
 272                         //move up a level
 273                         currentNodes = parentNodes;
 274                         parentNodes.clear();
 275
 276                         //have we reached the rootnode
 277                         if (tree->get(currentNodes.begin()->first).parent == -1)  {  done = true;  }
 278                 }
 279
 280                 outList.close();
 281                 outSabund.close();
 282                 outRabund.close();
 283
 284                 delete tree;
 285
 286                 if (m->control_pressed) {
 287                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 288                         return 0;
 289                 }
 290
 291                 //set list file as new current listfile
 292                 string current = "";
 293                 itTypes = outputTypes.find("list");
 294                 if (itTypes != outputTypes.end()) {
 295                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 296                 }
 297
 298                 //set rabund file as new current rabundfile
 299                 itTypes = outputTypes.find("rabund");
 300                 if (itTypes != outputTypes.end()) {
 301                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 302                 }
 303
 304                 //set sabund file as new current sabundfile
 305                 itTypes = outputTypes.find("sabund");
 306                 if (itTypes != outputTypes.end()) {
 307                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
 308                 }
 309
 310                 m->mothurOutEndLine();
 311                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 312                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 313                 m->mothurOutEndLine();
 314
 315                 return 0;
 316         }
 317
 318         catch(exception& e) {
 319                 m->errorOut(e, "PhylotypeCommand", "execute");
 320                 exit(1);
 321         }
 322 }
 323 /*****************************************************************/
 324 int PhylotypeCommand::readNamesFile() {
 325         try {
 326
 327                 ifstream in;
 328                 m->openInputFile(namefile, in);
 329
 330                 string first, second;
 331                 map<string, string>::iterator itNames;
 332
 333                 while(!in.eof()) {
 334                         in >> first >> second; m->gobble(in);
 335
 336                         itNames = namemap.find(first);
 337                         if (itNames == namemap.end()) {
 338                                 namemap[first] = second;
 339                         }else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); namemap.clear(); namefile = ""; return 1; }
 340                 }
 341                 in.close();
 342
 343                 return 0;
 344         }
 345         catch(exception& e) {
 346                 m->errorOut(e, "PhylotypeCommand", "readNamesFile");
 347                 exit(1);
 348         }
 349 }
 350
 351 /**********************************************************************************************************************/