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::getValidParameters(){
  18         try {
  19                 string Array[] =  {"taxonomy","cutoff","label","name","outputdir","inputdir"};
  20                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  21                 return myArray;
  22         }
  23         catch(exception& e) {
  24                 m->errorOut(e, "PhylotypeCommand", "getValidParameters");
  25                 exit(1);
  26         }
  27 }
  28 //**********************************************************************************************************************
  29 PhylotypeCommand::PhylotypeCommand(){
  30         try {
  31                 abort = true;
  32                 //initialize outputTypes
  33                 vector<string> tempOutNames;
  34                 outputTypes["list"] = tempOutNames;
  35                 outputTypes["sabund"] = tempOutNames;
  36                 outputTypes["rabund"] = tempOutNames;
  37         }
  38         catch(exception& e) {
  39                 m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
  40                 exit(1);
  41         }
  42 }
  43 //**********************************************************************************************************************
  44 vector<string> PhylotypeCommand::getRequiredParameters(){
  45         try {
  46                 string Array[] =  {"taxonomy"};
  47                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  48                 return myArray;
  49         }
  50         catch(exception& e) {
  51                 m->errorOut(e, "PhylotypeCommand", "getRequiredParameters");
  52                 exit(1);
  53         }
  54 }
  55 //**********************************************************************************************************************
  56 vector<string> PhylotypeCommand::getRequiredFiles(){
  57         try {
  58                 vector<string> myArray;
  59                 return myArray;
  60         }
  61         catch(exception& e) {
  62                 m->errorOut(e, "PhylotypeCommand", "getRequiredFiles");
  63                 exit(1);
  64         }
  65 }
  66 /**********************************************************************************************************************/
  67 PhylotypeCommand::PhylotypeCommand(string option)  {
  68         try {
  69                 abort = false;
  70
  71                 //allow user to run help
  72                 if(option == "help") { help(); abort = true; }
  73
  74                 else {
  75
  76                         //valid paramters for this command
  77                         string AlignArray[] =  {"taxonomy","cutoff","label","name","outputdir","inputdir"};
  78                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  79
  80                         OptionParser parser(option);
  81                         map<string, string> parameters = parser.getParameters();
  82
  83                         ValidParameters validParameter;
  84                         map<string, string>::iterator it;
  85
  86                         //check to make sure all parameters are valid for command
  87                         for (it = parameters.begin(); it != parameters.end(); it++) {
  88                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  89                         }
  90
  91                         //initialize outputTypes
  92                         vector<string> tempOutNames;
  93                         outputTypes["list"] = tempOutNames;
  94                         outputTypes["sabund"] = tempOutNames;
  95                         outputTypes["rabund"] = tempOutNames;
  96
  97                         //if the user changes the input directory command factory will send this info to us in the output parameter
  98                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  99                         if (inputDir == "not found"){   inputDir = "";          }
 100                         else {
 101                                 string path;
 102                                 it = parameters.find("taxonomy");
 103                                 //user has given a template file
 104                                 if(it != parameters.end()){
 105                                         path = m->hasPath(it->second);
 106                                         //if the user has not given a path then, add inputdir. else leave path alone.
 107                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 108                                 }
 109
 110                                 it = parameters.find("name");
 111                                 //user has given a template file
 112                                 if(it != parameters.end()){
 113                                         path = m->hasPath(it->second);
 114                                         //if the user has not given a path then, add inputdir. else leave path alone.
 115                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 116                                 }
 117                         }
 118
 119                         taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
 120                         if (taxonomyFileName == "not found") {
 121                                 m->mothurOut("taxonomy is a required parameter for the phylotype command.");
 122                                 m->mothurOutEndLine();
 123                                 abort = true;
 124                         }else if (taxonomyFileName == "not open") { abort = true; }
 125
 126                         namefile = validParameter.validFile(parameters, "name", true);
 127                         if (namefile == "not open") { abort = true; }
 128                         else if (namefile == "not found") { namefile = ""; }
 129                         else { readNamesFile(); }
 130
 131                         //if the user changes the output directory command factory will send this info to us in the output parameter
 132                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 133                                 outputDir = "";
 134                                 outputDir += m->hasPath(taxonomyFileName); //if user entered a file with a path then preserve it
 135                         }
 136
 137                         string temp = validParameter.validFile(parameters, "cutoff", false);
 138                         if (temp == "not found") { temp = "-1"; }
 139                         convert(temp, cutoff);
 140
 141                         label = validParameter.validFile(parameters, "label", false);
 142                         if (label == "not found") { label = ""; allLines = 1; }
 143                         else {
 144                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 145                                 else { allLines = 1;  }
 146                         }
 147
 148                 }
 149         }
 150         catch(exception& e) {
 151                 m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
 152                 exit(1);
 153         }
 154 }
 155 /**********************************************************************************************************************/
 156
 157 void PhylotypeCommand::help(){
 158         try {
 159                 m->mothurOut("The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n");
 160                 m->mothurOut("The phylotype command parameter options are taxonomy, cutoff and label. The taxonomy parameter is required.\n");
 161                 m->mothurOut("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");
 162                 m->mothurOut("For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n");
 163                 m->mothurOut("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");
 164                 m->mothurOut("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");
 165                 m->mothurOut("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");
 166                 m->mothurOut("The phylotype command should be in the following format: \n");
 167                 m->mothurOut("phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n");
 168                 m->mothurOut("Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n\n");
 169         }
 170         catch(exception& e) {
 171                 m->errorOut(e, "PhylotypeCommand", "help");
 172                 exit(1);
 173         }
 174 }
 175 /**********************************************************************************************************************/
 176
 177 PhylotypeCommand::~PhylotypeCommand(){}
 178
 179 /**********************************************************************************************************************/
 180
 181 int PhylotypeCommand::execute(){
 182         try {
 183
 184                 if (abort == true) { return 0; }
 185
 186                 //reads in taxonomy file and makes all the taxonomies the same length
 187                 //by appending the last taxon to a given taxonomy as many times as needed to
 188                 //make it as long as the longest taxonomy in the file
 189                 TaxEqualizer* taxEqual = new TaxEqualizer(taxonomyFileName, cutoff, outputDir);
 190
 191                 if (m->control_pressed) { delete taxEqual; return 0; }
 192
 193                 string equalizedTaxFile = taxEqual->getEqualizedTaxFile();
 194
 195                 delete taxEqual;
 196
 197                 //build taxonomy tree from equalized file
 198                 PhyloTree* tree = new PhyloTree(equalizedTaxFile);
 199                 vector<int> leaves = tree->getGenusNodes();
 200
 201                 //store leaf nodes in current map
 202                 for (int i = 0; i < leaves.size(); i++)         {       currentNodes[leaves[i]] = leaves[i];    }
 203
 204                 bool done = false;
 205                 if (tree->get(leaves[0]).parent == -1) {  m->mothurOut("Empty Tree"); m->mothurOutEndLine();    done = true;    }
 206
 207                 if (m->control_pressed) { delete tree; return 0; }
 208
 209                 string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
 210
 211                 ofstream outList;
 212                 string outputListFile = fileroot + "tx.list";
 213                 m->openOutputFile(outputListFile, outList);
 214                 ofstream outSabund;
 215                 string outputSabundFile = fileroot + "tx.sabund";
 216                 m->openOutputFile(outputSabundFile, outSabund);
 217                 ofstream outRabund;
 218                 string outputRabundFile = fileroot + "tx.rabund";
 219                 m->openOutputFile(outputRabundFile, outRabund);
 220
 221                 outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);
 222                 outputNames.push_back(outputSabundFile); outputTypes["sabund"].push_back(outputSabundFile);
 223                 outputNames.push_back(outputRabundFile); outputTypes["rabund"].push_back(outputRabundFile);
 224
 225                 int count = 1;
 226                 //start at leaves of tree and work towards root, processing the labels the user wants
 227                 while((!done) && ((allLines == 1) || (labels.size() != 0))) {
 228
 229                         string level = toString(count);
 230                         count++;
 231
 232                         if (m->control_pressed) {
 233                                 outRabund.close(); outSabund.close(); outList.close();
 234                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 235                                 delete tree; return 0;
 236                         }
 237
 238                         //is this a level the user want output for
 239                         if(allLines == 1 || labels.count(level) == 1){
 240
 241                                 //output level
 242                                 m->mothurOut(level); m->mothurOutEndLine();
 243
 244                                 ListVector list;
 245                                 list.setLabel(level);
 246                                 //go through nodes and build listvector
 247                                 for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 248
 249                                         //get parents
 250                                         TaxNode node = tree->get(itCurrent->first);
 251                                         parentNodes[node.parent] = node.parent;
 252
 253                                         vector<string> names = node.accessions;
 254
 255                                         //make the names compatable with listvector
 256                                         string name = "";
 257                                         for (int i = 0; i < names.size(); i++) {
 258                                                 if (namefile != "") {
 259                                                         map<string, string>::iterator itNames = namemap.find(names[i]);  //make sure this name is in namefile
 260
 261                                                         if (itNames != namemap.end()) {  name += namemap[names[i]] + ",";   } //you found it in namefile
 262                                                         else { m->mothurOut(names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); exit(1);  }
 263
 264                                                 }else{   name += names[i] + ",";        }
 265                                         }
 266                                         name = name.substr(0, name.length()-1);  //rip off extra ','
 267
 268                                         //add bin to list vector
 269                                         list.push_back(name);
 270                                 }
 271
 272                                 //print listvector
 273                                 list.print(outList);
 274                                 //print rabund
 275                                 list.getRAbundVector().print(outRabund);
 276                                 //print sabund
 277                                 list.getSAbundVector().print(outSabund);
 278
 279                                 labels.erase(level);
 280
 281                         }else {
 282
 283                                 //just get parents
 284                                 for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 285                                         int parent = tree->get(itCurrent->first).parent;
 286                                         parentNodes[parent] = parent;
 287                                 }
 288                         }
 289
 290                         //move up a level
 291                         currentNodes = parentNodes;
 292                         parentNodes.clear();
 293
 294                         //have we reached the rootnode
 295                         if (tree->get(currentNodes.begin()->first).parent == -1)  {  done = true;  }
 296                 }
 297
 298                 outList.close();
 299                 outSabund.close();
 300                 outRabund.close();
 301
 302                 delete tree;
 303
 304                 if (m->control_pressed) {
 305                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 306                         return 0;
 307                 }
 308
 309                 m->mothurOutEndLine();
 310                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 311                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 312                 m->mothurOutEndLine();
 313
 314                 return 0;
 315         }
 316
 317         catch(exception& e) {
 318                 m->errorOut(e, "PhylotypeCommand", "execute");
 319                 exit(1);
 320         }
 321 }
 322 /*****************************************************************/
 323 int PhylotypeCommand::readNamesFile() {
 324         try {
 325
 326                 ifstream in;
 327                 m->openInputFile(namefile, in);
 328
 329                 string first, second;
 330                 map<string, string>::iterator itNames;
 331
 332                 while(!in.eof()) {
 333                         in >> first >> second; m->gobble(in);
 334
 335                         itNames = namemap.find(first);
 336                         if (itNames == namemap.end()) {
 337                                 namemap[first] = second;
 338                         }else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); namemap.clear(); namefile = ""; return 1; }
 339                 }
 340                 in.close();
 341
 342                 return 0;
 343         }
 344         catch(exception& e) {
 345                 m->errorOut(e, "PhylotypeCommand", "readNamesFile");
 346                 exit(1);
 347         }
 348 }
 349
 350 /**********************************************************************************************************************/