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", "", "", "NameCount", "none", "ColumnName","rabund-sabund",false,false,true); parameters.push_back(pname);
  21                 CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pcount);
  22                 CommandParameter pcutoff("cutoff", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pcutoff);
  23                 CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
  24                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  25                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  26
  27                 vector<string> myArray;
  28                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  29                 return myArray;
  30         }
  31         catch(exception& e) {
  32                 m->errorOut(e, "PhylotypeCommand", "setParameters");
  33                 exit(1);
  34         }
  35 }
  36 //**********************************************************************************************************************
  37 string PhylotypeCommand::getHelpString(){
  38         try {
  39                 string helpString = "";
  40                 helpString += "The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n";
  41                 helpString += "The phylotype command parameter options are taxonomy, name, count, cutoff and label. The taxonomy parameter is required.\n";
  42                 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";
  43                 helpString += "For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n";
  44                 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";
  45                 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";
  46                 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";
  47                 helpString += "The phylotype command should be in the following format: \n";
  48                 helpString += "phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n";
  49                 helpString += "Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n";
  50                 return helpString;
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "PhylotypeCommand", "getHelpString");
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58 string PhylotypeCommand::getOutputPattern(string type) {
  59     try {
  60         string pattern = "";
  61
  62         if (type == "list") {  pattern = "[filename],[clustertag],list-[filename],[clustertag],[tag2],list"; }
  63         else if (type == "rabund") {  pattern = "[filename],[clustertag],rabund"; }
  64         else if (type == "sabund") {  pattern = "[filename],[clustertag],sabund"; }
  65         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  66
  67         return pattern;
  68     }
  69     catch(exception& e) {
  70         m->errorOut(e, "PhylotypeCommand", "getOutputPattern");
  71         exit(1);
  72     }
  73 }
  74 //**********************************************************************************************************************
  75 PhylotypeCommand::PhylotypeCommand(){
  76         try {
  77                 abort = true; calledHelp = true;
  78                 setParameters();
  79                 vector<string> tempOutNames;
  80                 outputTypes["list"] = tempOutNames;
  81                 outputTypes["sabund"] = tempOutNames;
  82                 outputTypes["rabund"] = tempOutNames;
  83         }
  84         catch(exception& e) {
  85                 m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
  86                 exit(1);
  87         }
  88 }
  89 /**********************************************************************************************************************/
  90 PhylotypeCommand::PhylotypeCommand(string option)  {
  91         try {
  92                 abort = false; calledHelp = false;
  93
  94                 //allow user to run help
  95                 if(option == "help") { help(); abort = true; calledHelp = true; }
  96                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  97
  98                 else {
  99                         vector<string> myArray = setParameters();
 100
 101                         OptionParser parser(option);
 102                         map<string, string> parameters = parser.getParameters();
 103
 104                         ValidParameters validParameter;
 105                         map<string, string>::iterator it;
 106
 107                         //check to make sure all parameters are valid for command
 108                         for (it = parameters.begin(); it != parameters.end(); it++) {
 109                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 110                         }
 111
 112                         //initialize outputTypes
 113                         vector<string> tempOutNames;
 114                         outputTypes["list"] = tempOutNames;
 115                         outputTypes["sabund"] = tempOutNames;
 116                         outputTypes["rabund"] = tempOutNames;
 117
 118                         //if the user changes the input directory command factory will send this info to us in the output parameter
 119                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 120                         if (inputDir == "not found"){   inputDir = "";          }
 121                         else {
 122                                 string path;
 123                                 it = parameters.find("taxonomy");
 124                                 //user has given a template file
 125                                 if(it != parameters.end()){
 126                                         path = m->hasPath(it->second);
 127                                         //if the user has not given a path then, add inputdir. else leave path alone.
 128                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 129                                 }
 130
 131                                 it = parameters.find("name");
 132                                 //user has given a template file
 133                                 if(it != parameters.end()){
 134                                         path = m->hasPath(it->second);
 135                                         //if the user has not given a path then, add inputdir. else leave path alone.
 136                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 137                                 }
 138
 139                 it = parameters.find("count");
 140                                 //user has given a template file
 141                                 if(it != parameters.end()){
 142                                         path = m->hasPath(it->second);
 143                                         //if the user has not given a path then, add inputdir. else leave path alone.
 144                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 145                                 }
 146                         }
 147
 148                         taxonomyFileName = validParameter.validFile(parameters, "taxonomy", true);
 149                         if (taxonomyFileName == "not found") {
 150                                 taxonomyFileName = m->getTaxonomyFile();
 151                                 if (taxonomyFileName != "") {  m->mothurOut("Using " + taxonomyFileName + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
 152                                 else {
 153                                         m->mothurOut("No valid current files. taxonomy is a required parameter."); m->mothurOutEndLine();
 154                                         abort = true;
 155                                 }
 156                         }else if (taxonomyFileName == "not open") { taxonomyFileName = ""; abort = true; }
 157                         else { m->setTaxonomyFile(taxonomyFileName); }
 158
 159                         namefile = validParameter.validFile(parameters, "name", true);
 160                         if (namefile == "not open") { namefile = ""; abort = true; }
 161                         else if (namefile == "not found") { namefile = ""; }
 162                         else { readNamesFile(); m->setNameFile(namefile); }
 163
 164             countfile = validParameter.validFile(parameters, "count", true);
 165                         if (countfile == "not open") { abort = true; countfile = ""; }
 166                         else if (countfile == "not found") { countfile = ""; }
 167                         else { m->setCountTableFile(countfile); }
 168
 169                         //if the user changes the output directory command factory will send this info to us in the output parameter
 170                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 171                                 outputDir = "";
 172                                 outputDir += m->hasPath(taxonomyFileName); //if user entered a file with a path then preserve it
 173                         }
 174
 175             if ((countfile != "") && (namefile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
 176
 177                         string temp = validParameter.validFile(parameters, "cutoff", false);
 178                         if (temp == "not found") { temp = "-1"; }
 179                         m->mothurConvert(temp, cutoff);
 180
 181                         label = validParameter.validFile(parameters, "label", false);
 182                         if (label == "not found") { label = ""; allLines = 1; }
 183                         else {
 184                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 185                                 else { allLines = 1;  }
 186                         }
 187
 188             if (countfile == "") {
 189                 if (namefile == "") {
 190                     vector<string> files; files.push_back(taxonomyFileName);
 191                     parser.getNameFile(files);
 192                 }
 193                         }
 194                 }
 195         }
 196         catch(exception& e) {
 197                 m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
 198                 exit(1);
 199         }
 200 }
 201 /**********************************************************************************************************************/
 202
 203 int PhylotypeCommand::execute(){
 204         try {
 205
 206                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 207
 208                 //reads in taxonomy file and makes all the taxonomies the same length
 209                 //by appending the last taxon to a given taxonomy as many times as needed to
 210                 //make it as long as the longest taxonomy in the file
 211                 TaxEqualizer* taxEqual = new TaxEqualizer(taxonomyFileName, cutoff, outputDir);
 212
 213                 if (m->control_pressed) { delete taxEqual; return 0; }
 214
 215                 string equalizedTaxFile = taxEqual->getEqualizedTaxFile();
 216
 217                 delete taxEqual;
 218
 219                 //build taxonomy tree from equalized file
 220                 PhyloTree* tree = new PhyloTree(equalizedTaxFile);
 221                 vector<int> leaves = tree->getGenusNodes();
 222
 223                 //store leaf nodes in current map
 224                 for (int i = 0; i < leaves.size(); i++)         {       currentNodes[leaves[i]] = leaves[i];    }
 225
 226                 bool done = false;
 227                 if (tree->get(leaves[0]).parent == -1) {  m->mothurOut("Empty Tree"); m->mothurOutEndLine();    done = true;    }
 228
 229                 if (m->control_pressed) { delete tree; return 0; }
 230
 231                 ofstream outList, outRabund, outSabund;
 232         map<string, string> variables;
 233         string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
 234         variables["[filename]"] = fileroot;
 235         variables["[clustertag]"] = "tx";
 236         string sabundFileName = getOutputFileName("sabund", variables);
 237         string rabundFileName = getOutputFileName("rabund", variables);
 238         if (countfile != "") { variables["[tag2]"] = "unique_list"; }
 239         string listFileName = getOutputFileName("list", variables);
 240
 241         if (countfile == "") {
 242             m->openOutputFile(sabundFileName,   outSabund);
 243             m->openOutputFile(rabundFileName,   outRabund);
 244             outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
 245             outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
 246
 247         }
 248                 m->openOutputFile(listFileName, outList);
 249         outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
 250
 251
 252                 int count = 1;
 253                 //start at leaves of tree and work towards root, processing the labels the user wants
 254                 while((!done) && ((allLines == 1) || (labels.size() != 0))) {
 255
 256                         string level = toString(count);
 257                         count++;
 258
 259                         if (m->control_pressed) {
 260                                 if (countfile == "") { outRabund.close(); outSabund.close(); } outList.close();
 261                                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 262                                 delete tree; return 0;
 263                         }
 264
 265                         //is this a level the user want output for
 266                         if(allLines == 1 || labels.count(level) == 1){
 267
 268                                 //output level
 269                                 m->mothurOut(level); m->mothurOutEndLine();
 270
 271                                 ListVector list;
 272                                 list.setLabel(level);
 273
 274                                 //go through nodes and build listvector
 275                                 for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 276
 277                                         //get parents
 278                                         TaxNode node = tree->get(itCurrent->first);
 279                                         parentNodes[node.parent] = node.parent;
 280
 281                                         vector<string> names = node.accessions;
 282
 283                                         //make the names compatable with listvector
 284                                         string name = "";
 285                                         for (int i = 0; i < names.size(); i++) {
 286
 287                         if (names[i] != "unknown") {
 288                             if (namefile != "") {
 289                                 map<string, string>::iterator itNames = namemap.find(names[i]);  //make sure this name is in namefile
 290
 291                                 if (itNames != namemap.end()) {  name += namemap[names[i]] + ",";   } //you found it in namefile
 292                                 else { m->mothurOut("[ERROR]: " + names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 293
 294                             }else{   name += names[i] + ",";    }
 295                         }
 296                                         }
 297
 298                     if (m->control_pressed) { break; }
 299
 300                                         name = name.substr(0, name.length()-1);  //rip off extra ','
 301                                         //add bin to list vector
 302                                         if (name != "") { list.push_back(name); } //caused by unknown
 303                                 }
 304
 305                                 //print listvector
 306                                 list.print(outList);
 307                 if (countfile == "") {
 308                     //print rabund
 309                     list.getRAbundVector().print(outRabund);
 310                     //print sabund
 311                     list.getSAbundVector().print(outSabund);
 312                 }
 313                                 labels.erase(level);
 314
 315                         }else {
 316
 317                                 //just get parents
 318                                 for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 319                                         int parent = tree->get(itCurrent->first).parent;
 320                                         parentNodes[parent] = parent;
 321                                 }
 322                         }
 323
 324                         //move up a level
 325                         currentNodes = parentNodes;
 326                         parentNodes.clear();
 327
 328                         //have we reached the rootnode
 329                         if (tree->get(currentNodes.begin()->first).parent == -1)  {  done = true;  }
 330                 }
 331
 332                 outList.close();
 333         if (countfile == "") {
 334             outSabund.close();
 335             outRabund.close();
 336         }
 337
 338                 delete tree;
 339
 340                 if (m->control_pressed) {
 341                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  }
 342                         return 0;
 343                 }
 344
 345                 //set list file as new current listfile
 346                 string current = "";
 347                 itTypes = outputTypes.find("list");
 348                 if (itTypes != outputTypes.end()) {
 349                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 350                 }
 351
 352                 //set rabund file as new current rabundfile
 353                 itTypes = outputTypes.find("rabund");
 354                 if (itTypes != outputTypes.end()) {
 355                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
 356                 }
 357
 358                 //set sabund file as new current sabundfile
 359                 itTypes = outputTypes.find("sabund");
 360                 if (itTypes != outputTypes.end()) {
 361                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
 362                 }
 363
 364                 m->mothurOutEndLine();
 365                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 366                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 367                 m->mothurOutEndLine();
 368
 369                 return 0;
 370         }
 371
 372         catch(exception& e) {
 373                 m->errorOut(e, "PhylotypeCommand", "execute");
 374                 exit(1);
 375         }
 376 }
 377 /*****************************************************************/
 378 int PhylotypeCommand::readNamesFile() {
 379         try {
 380
 381                 ifstream in;
 382                 m->openInputFile(namefile, in);
 383
 384                 string first, second;
 385                 map<string, string>::iterator itNames;
 386
 387                 while(!in.eof()) {
 388                         in >> first >> second; m->gobble(in);
 389
 390                         itNames = namemap.find(first);
 391                         if (itNames == namemap.end()) {
 392                                 namemap[first] = second;
 393                         }else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); namemap.clear(); namefile = ""; return 1; }
 394                 }
 395                 in.close();
 396
 397                 return 0;
 398         }
 399         catch(exception& e) {
 400                 m->errorOut(e, "PhylotypeCommand", "readNamesFile");
 401                 exit(1);
 402         }
 403 }
 404
 405 /**********************************************************************************************************************/