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