getlineagecommand.cpp

   1 /*
   2  *  getlineagecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 9/24/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "getlineagecommand.h"
  11 #include "sequence.hpp"
  12 #include "listvector.hpp"
  13
  14 //**********************************************************************************************************************
  15 vector<string> GetLineageCommand::setParameters(){
  16         try {
  17                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
  18         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none",false,false); parameters.push_back(pname);
  19         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none",false,false); parameters.push_back(pcount);
  20                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none",false,false); parameters.push_back(pgroup);
  21                 CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
  22                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(ptaxonomy);
  23                 CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);
  24                 CommandParameter ptaxon("taxon", "String", "", "", "", "", "",false,true); parameters.push_back(ptaxon);
  25                 CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
  26                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  27                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  28
  29                 vector<string> myArray;
  30                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  31                 return myArray;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "GetLineageCommand", "setParameters");
  35                 exit(1);
  36         }
  37 }
  38 //**********************************************************************************************************************
  39 string GetLineageCommand::getHelpString(){
  40         try {
  41                 string helpString = "";
  42                 helpString += "The get.lineage command reads a taxonomy file and any of the following file types: fasta, name, group, count, list or alignreport file.\n";
  43                 helpString += "It outputs a file containing only the sequences from the taxonomy file that are from the taxon requested.\n";
  44                 helpString += "The get.lineage command parameters are taxon, fasta, name, group, count, list, taxonomy, alignreport and dups.  You must provide taxonomy unless you have a valid current taxonomy file.\n";
  45                 helpString += "The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n";
  46                 helpString += "The taxon parameter allows you to select the taxons you would like to get and is required.\n";
  47                 helpString += "You may enter your taxons with confidence scores, doing so will get only those sequences that belong to the taxonomy and whose cofidence scores is above the scores you give.\n";
  48                 helpString += "If they belong to the taxonomy and have confidences below those you provide the sequence will not be selected.\n";
  49                 helpString += "The get.lineage command should be in the following format: get.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n";
  50                 helpString += "Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n";
  51                 helpString += "Note: If you are running mothur in script mode you must wrap the taxon in ' characters so mothur will ignore the ; in the taxon.\n";
  52                 helpString += "Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n";
  53                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  54                 return helpString;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "GetLineageCommand", "getHelpString");
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 string GetLineageCommand::getOutputFileNameTag(string type, string inputName=""){
  63         try {
  64         string outputFileName = "";
  65                 map<string, vector<string> >::iterator it;
  66
  67         //is this a type this command creates
  68         it = outputTypes.find(type);
  69         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  70         else {
  71             if (type == "fasta")            {   outputFileName =  "pick" + m->getExtension(inputName);   }
  72             else if (type == "taxonomy")    {   outputFileName =  "pick" + m->getExtension(inputName);   }
  73             else if (type == "name")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
  74             else if (type == "count")       {   outputFileName =  "pick.count.table";                    }
  75             else if (type == "group")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
  76             else if (type == "list")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
  77             else if (type == "alignreport") {   outputFileName =  "pick.align.report";   }
  78             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  79         }
  80         return outputFileName;
  81         }
  82         catch(exception& e) {
  83                 m->errorOut(e, "GetLineageCommand", "getOutputFileNameTag");
  84                 exit(1);
  85         }
  86 }
  87 //**********************************************************************************************************************
  88 GetLineageCommand::GetLineageCommand(){
  89         try {
  90                 abort = true; calledHelp = true;
  91                 setParameters();
  92                 vector<string> tempOutNames;
  93                 outputTypes["fasta"] = tempOutNames;
  94                 outputTypes["taxonomy"] = tempOutNames;
  95                 outputTypes["name"] = tempOutNames;
  96                 outputTypes["group"] = tempOutNames;
  97                 outputTypes["alignreport"] = tempOutNames;
  98                 outputTypes["list"] = tempOutNames;
  99         outputTypes["count"] = tempOutNames;
 100         }
 101         catch(exception& e) {
 102                 m->errorOut(e, "GetLineageCommand", "GetLineageCommand");
 103                 exit(1);
 104         }
 105 }
 106 //**********************************************************************************************************************
 107 GetLineageCommand::GetLineageCommand(string option)  {
 108         try {
 109                 abort = false; calledHelp = false;
 110
 111                 //allow user to run help
 112                 if(option == "help") { help(); abort = true; calledHelp = true; }
 113                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 114
 115                 else {
 116                         vector<string> myArray = setParameters();
 117
 118                         OptionParser parser(option);
 119                         map<string,string> parameters = parser.getParameters();
 120
 121                         ValidParameters validParameter;
 122                         map<string,string>::iterator it;
 123
 124                         //check to make sure all parameters are valid for command
 125                         for (it = parameters.begin(); it != parameters.end(); it++) {
 126                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 127                         }
 128
 129                         //initialize outputTypes
 130                         vector<string> tempOutNames;
 131                         outputTypes["fasta"] = tempOutNames;
 132                         outputTypes["taxonomy"] = tempOutNames;
 133                         outputTypes["name"] = tempOutNames;
 134                         outputTypes["group"] = tempOutNames;
 135                         outputTypes["alignreport"] = tempOutNames;
 136                         outputTypes["list"] = tempOutNames;
 137             outputTypes["count"] = tempOutNames;
 138
 139                         //if the user changes the output directory command factory will send this info to us in the output parameter
 140                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 141
 142                         //if the user changes the input directory command factory will send this info to us in the output parameter
 143                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 144                         if (inputDir == "not found"){   inputDir = "";          }
 145                         else {
 146                                 string path;
 147                                 it = parameters.find("alignreport");
 148                                 //user has given a template file
 149                                 if(it != parameters.end()){
 150                                         path = m->hasPath(it->second);
 151                                         //if the user has not given a path then, add inputdir. else leave path alone.
 152                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
 153                                 }
 154
 155                                 it = parameters.find("fasta");
 156                                 //user has given a template file
 157                                 if(it != parameters.end()){
 158                                         path = m->hasPath(it->second);
 159                                         //if the user has not given a path then, add inputdir. else leave path alone.
 160                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 161                                 }
 162
 163                                 it = parameters.find("list");
 164                                 //user has given a template file
 165                                 if(it != parameters.end()){
 166                                         path = m->hasPath(it->second);
 167                                         //if the user has not given a path then, add inputdir. else leave path alone.
 168                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 169                                 }
 170
 171                                 it = parameters.find("name");
 172                                 //user has given a template file
 173                                 if(it != parameters.end()){
 174                                         path = m->hasPath(it->second);
 175                                         //if the user has not given a path then, add inputdir. else leave path alone.
 176                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 177                                 }
 178
 179                                 it = parameters.find("group");
 180                                 //user has given a template file
 181                                 if(it != parameters.end()){
 182                                         path = m->hasPath(it->second);
 183                                         //if the user has not given a path then, add inputdir. else leave path alone.
 184                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 185                                 }
 186
 187                                 it = parameters.find("taxonomy");
 188                                 //user has given a template file
 189                                 if(it != parameters.end()){
 190                                         path = m->hasPath(it->second);
 191                                         //if the user has not given a path then, add inputdir. else leave path alone.
 192                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 193                                 }
 194
 195                 it = parameters.find("count");
 196                                 //user has given a template file
 197                                 if(it != parameters.end()){
 198                                         path = m->hasPath(it->second);
 199                                         //if the user has not given a path then, add inputdir. else leave path alone.
 200                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 201                                 }
 202                         }
 203
 204
 205                         //check for required parameters
 206                         fastafile = validParameter.validFile(parameters, "fasta", true);
 207                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 208                         else if (fastafile == "not found") {  fastafile = "";  }
 209                         else { m->setFastaFile(fastafile); }
 210
 211                         namefile = validParameter.validFile(parameters, "name", true);
 212                         if (namefile == "not open") { namefile = ""; abort = true; }
 213                         else if (namefile == "not found") {  namefile = "";  }
 214                         else { m->setNameFile(namefile); }
 215
 216                         groupfile = validParameter.validFile(parameters, "group", true);
 217                         if (groupfile == "not open") { abort = true; }
 218                         else if (groupfile == "not found") {  groupfile = "";  }
 219                         else { m->setGroupFile(groupfile); }
 220
 221                         alignfile = validParameter.validFile(parameters, "alignreport", true);
 222                         if (alignfile == "not open") { abort = true; }
 223                         else if (alignfile == "not found") {  alignfile = "";  }
 224
 225                         listfile = validParameter.validFile(parameters, "list", true);
 226                         if (listfile == "not open") { abort = true; }
 227                         else if (listfile == "not found") {  listfile = "";  }
 228                         else { m->setListFile(listfile); }
 229
 230                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 231                         if (taxfile == "not open") { taxfile = ""; abort = true; }
 232                         else if (taxfile == "not found") {
 233                                 taxfile = m->getTaxonomyFile();
 234                                 if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
 235                                 else {  m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
 236                         }else { m->setTaxonomyFile(taxfile); }
 237
 238                         string usedDups = "true";
 239                         string temp = validParameter.validFile(parameters, "dups", false);
 240                         if (temp == "not found") {
 241                                 if (namefile != "") {  temp = "true";                                   }
 242                                 else                            {  temp = "false"; usedDups = "";       }
 243                         }
 244                         dups = m->isTrue(temp);
 245
 246             countfile = validParameter.validFile(parameters, "count", true);
 247             if (countfile == "not open") { countfile = ""; abort = true; }
 248             else if (countfile == "not found") { countfile = "";  }
 249             else { m->setCountTableFile(countfile); }
 250
 251             if ((namefile != "") && (countfile != "")) {
 252                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 253             }
 254
 255             if ((groupfile != "") && (countfile != "")) {
 256                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 257             }
 258
 259                         taxons = validParameter.validFile(parameters, "taxon", false);
 260                         if (taxons == "not found") { taxons = "";  m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine();  abort = true;  }
 261                         else {
 262                                 //rip off quotes
 263                                 if (taxons[0] == '\'') {  taxons = taxons.substr(1); }
 264                                 if (taxons[(taxons.length()-1)] == '\'') {  taxons = taxons.substr(0, (taxons.length()-1)); }
 265                         }
 266                         m->splitAtChar(taxons, listOfTaxons, '-');
 267
 268                         if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (countfile == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, count, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; }
 269
 270             if (countfile == "") {
 271                 if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
 272                     vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
 273                     parser.getNameFile(files);
 274                 }
 275             }
 276                 }
 277
 278         }
 279         catch(exception& e) {
 280                 m->errorOut(e, "GetLineageCommand", "GetLineageCommand");
 281                 exit(1);
 282         }
 283 }
 284 //**********************************************************************************************************************
 285
 286 int GetLineageCommand::execute(){
 287         try {
 288
 289                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 290
 291                 if (m->control_pressed) { return 0; }
 292
 293         if (countfile != "") {
 294             if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
 295                 m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
 296             }
 297         }
 298
 299                 //read through the correct file and output lines you want to keep
 300                 if (taxfile != "")                      {               readTax();              }  //fills the set of names to get
 301                 if (namefile != "")                     {               readName();             }
 302                 if (fastafile != "")            {               readFasta();    }
 303         if (countfile != "")            {               readCount();    }
 304                 if (groupfile != "")            {               readGroup();    }
 305                 if (alignfile != "")            {               readAlign();    }
 306                 if (listfile != "")                     {               readList();             }
 307
 308
 309                 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);  } return 0; }
 310
 311                 if (outputNames.size() != 0) {
 312                         m->mothurOutEndLine();
 313                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 314                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 315                         m->mothurOutEndLine();
 316
 317                         //set fasta file as new current fastafile
 318                         string current = "";
 319                         itTypes = outputTypes.find("fasta");
 320                         if (itTypes != outputTypes.end()) {
 321                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 322                         }
 323
 324                         itTypes = outputTypes.find("name");
 325                         if (itTypes != outputTypes.end()) {
 326                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 327                         }
 328
 329                         itTypes = outputTypes.find("group");
 330                         if (itTypes != outputTypes.end()) {
 331                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 332                         }
 333
 334                         itTypes = outputTypes.find("list");
 335                         if (itTypes != outputTypes.end()) {
 336                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 337                         }
 338
 339                         itTypes = outputTypes.find("taxonomy");
 340                         if (itTypes != outputTypes.end()) {
 341                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 342                         }
 343
 344             itTypes = outputTypes.find("count");
 345                         if (itTypes != outputTypes.end()) {
 346                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 347                         }
 348                 }
 349
 350                 return 0;
 351         }
 352
 353         catch(exception& e) {
 354                 m->errorOut(e, "GetLineageCommand", "execute");
 355                 exit(1);
 356         }
 357 }
 358
 359 //**********************************************************************************************************************
 360 int GetLineageCommand::readFasta(){
 361         try {
 362                 string thisOutputDir = outputDir;
 363                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 364                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
 365                 ofstream out;
 366                 m->openOutputFile(outputFileName, out);
 367
 368
 369                 ifstream in;
 370                 m->openInputFile(fastafile, in);
 371                 string name;
 372
 373                 bool wroteSomething = false;
 374
 375                 while(!in.eof()){
 376
 377                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 378
 379                         Sequence currSeq(in);
 380                         name = currSeq.getName();
 381
 382                         if (name != "") {
 383                                 //if this name is in the accnos file
 384                                 if (names.count(name) != 0) {
 385                                         wroteSomething = true;
 386
 387                                         currSeq.printSequence(out);
 388                                 }
 389                         }
 390                         m->gobble(in);
 391                 }
 392                 in.close();
 393                 out.close();
 394
 395                 if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 396                 outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);
 397
 398                 return 0;
 399
 400         }
 401         catch(exception& e) {
 402                 m->errorOut(e, "GetLineageCommand", "readFasta");
 403                 exit(1);
 404         }
 405 }
 406 //**********************************************************************************************************************
 407 int GetLineageCommand::readCount(){
 408         try {
 409                 string thisOutputDir = outputDir;
 410                 if (outputDir == "") {  thisOutputDir += m->hasPath(countfile);  }
 411                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
 412
 413                 ofstream out;
 414                 m->openOutputFile(outputFileName, out);
 415
 416                 ifstream in;
 417                 m->openInputFile(countfile, in);
 418
 419                 bool wroteSomething = false;
 420
 421         string headers = m->getline(in); m->gobble(in);
 422         out << headers << endl;
 423
 424         string name, rest; int thisTotal;
 425         while (!in.eof()) {
 426
 427             if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 428
 429             in >> name; m->gobble(in);
 430             in >> thisTotal; m->gobble(in);
 431             rest = m->getline(in); m->gobble(in);
 432             if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + rest + "\n"); }
 433
 434             if (names.count(name) != 0) {
 435                 out << name << '\t' << thisTotal << '\t' << rest << endl;
 436                 wroteSomething = true;
 437             }
 438         }
 439         in.close();
 440                 out.close();
 441
 442                 if (wroteSomething == false) {  m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 443                 outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
 444
 445                 return 0;
 446         }
 447         catch(exception& e) {
 448                 m->errorOut(e, "GetLineageCommand", "readCount");
 449                 exit(1);
 450         }
 451 }
 452 //**********************************************************************************************************************
 453 int GetLineageCommand::readList(){
 454         try {
 455                 string thisOutputDir = outputDir;
 456                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 457                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
 458                 ofstream out;
 459                 m->openOutputFile(outputFileName, out);
 460
 461                 ifstream in;
 462                 m->openInputFile(listfile, in);
 463
 464                 bool wroteSomething = false;
 465
 466                 while(!in.eof()){
 467
 468                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 469
 470                         //read in list vector
 471                         ListVector list(in);
 472
 473                         //make a new list vector
 474                         ListVector newList;
 475                         newList.setLabel(list.getLabel());
 476
 477                         //for each bin
 478                         for (int i = 0; i < list.getNumBins(); i++) {
 479
 480                                 //parse out names that are in accnos file
 481                                 string binnames = list.get(i);
 482
 483                                 string newNames = "";
 484                                 while (binnames.find_first_of(',') != -1) {
 485                                         string name = binnames.substr(0,binnames.find_first_of(','));
 486                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 487
 488                                         //if that name is in the .accnos file, add it
 489                                         if (names.count(name) != 0) {  newNames += name + ",";  }
 490                                 }
 491
 492                                 //get last name
 493                                 if (names.count(binnames) != 0) {  newNames += binnames + ",";  }
 494
 495                                 //if there are names in this bin add to new list
 496                                 if (newNames != "") {
 497                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 498                                         newList.push_back(newNames);
 499                                 }
 500                         }
 501
 502                         //print new listvector
 503                         if (newList.getNumBins() != 0) {
 504                                 wroteSomething = true;
 505                                 newList.print(out);
 506                         }
 507
 508                         m->gobble(in);
 509                 }
 510                 in.close();
 511                 out.close();
 512
 513                 if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 514                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 515
 516                 return 0;
 517
 518         }
 519         catch(exception& e) {
 520                 m->errorOut(e, "GetLineageCommand", "readList");
 521                 exit(1);
 522         }
 523 }
 524 //**********************************************************************************************************************
 525 int GetLineageCommand::readName(){
 526         try {
 527                 string thisOutputDir = outputDir;
 528                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 529                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
 530                 ofstream out;
 531                 m->openOutputFile(outputFileName, out);
 532
 533
 534                 ifstream in;
 535                 m->openInputFile(namefile, in);
 536                 string name, firstCol, secondCol;
 537
 538                 bool wroteSomething = false;
 539
 540
 541                 while(!in.eof()){
 542
 543                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 544
 545                         in >> firstCol;
 546                         in >> secondCol;
 547
 548                         string hold = "";
 549                         if (dups) { hold = secondCol; }
 550
 551                         vector<string> parsedNames;
 552                         m->splitAtComma(secondCol, parsedNames);
 553
 554                         vector<string> validSecond;
 555                         for (int i = 0; i < parsedNames.size(); i++) {
 556                                 if (names.count(parsedNames[i]) != 0) {
 557                                         validSecond.push_back(parsedNames[i]);
 558                                 }
 559                         }
 560
 561                         if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
 562                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 563                                 out << firstCol << '\t' << hold << endl;
 564                                 wroteSomething = true;
 565                         }else {
 566                                 //if the name in the first column is in the set then print it and any other names in second column also in set
 567                                 if (names.count(firstCol) != 0) {
 568
 569                                         wroteSomething = true;
 570
 571                                         out << firstCol << '\t';
 572
 573                                         //you know you have at least one valid second since first column is valid
 574                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 575                                         out << validSecond[validSecond.size()-1] << endl;
 576
 577
 578                                 //make first name in set you come to first column and then add the remaining names to second column
 579                                 }else {
 580                                         //you want part of this row
 581                                         if (validSecond.size() != 0) {
 582
 583                                                 wroteSomething = true;
 584
 585                                                 out << validSecond[0] << '\t';
 586
 587                                                 //you know you have at least one valid second since first column is valid
 588                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 589                                                 out << validSecond[validSecond.size()-1] << endl;
 590                                         }
 591                                 }
 592                         }
 593                         m->gobble(in);
 594                 }
 595                 in.close();
 596                 out.close();
 597
 598                 if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 599                 outputNames.push_back(outputFileName);  outputTypes["name"].push_back(outputFileName);
 600
 601                 return 0;
 602
 603         }
 604         catch(exception& e) {
 605                 m->errorOut(e, "GetLineageCommand", "readName");
 606                 exit(1);
 607         }
 608 }
 609
 610 //**********************************************************************************************************************
 611 int GetLineageCommand::readGroup(){
 612         try {
 613                 string thisOutputDir = outputDir;
 614                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 615                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
 616                 ofstream out;
 617                 m->openOutputFile(outputFileName, out);
 618
 619
 620                 ifstream in;
 621                 m->openInputFile(groupfile, in);
 622                 string name, group;
 623
 624                 bool wroteSomething = false;
 625
 626                 while(!in.eof()){
 627
 628                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 629
 630
 631                         in >> name;                             //read from first column
 632                         in >> group;                    //read from second column
 633
 634                         //if this name is in the accnos file
 635                         if (names.count(name) != 0) {
 636                                 wroteSomething = true;
 637
 638                                 out << name << '\t' << group << endl;
 639                         }
 640
 641                         m->gobble(in);
 642                 }
 643                 in.close();
 644                 out.close();
 645
 646                 if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 647                 outputNames.push_back(outputFileName);  outputTypes["group"].push_back(outputFileName);
 648
 649                 return 0;
 650
 651         }
 652         catch(exception& e) {
 653                 m->errorOut(e, "GetLineageCommand", "readGroup");
 654                 exit(1);
 655         }
 656 }
 657 //**********************************************************************************************************************
 658 int GetLineageCommand::readTax(){
 659         try {
 660                 string thisOutputDir = outputDir;
 661                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 662                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
 663                 ofstream out;
 664                 m->openOutputFile(outputFileName, out);
 665
 666                 ifstream in;
 667                 m->openInputFile(taxfile, in);
 668                 string name, tax;
 669
 670                 //bool wroteSomething = false;
 671                 vector<bool> taxonsHasConfidence; taxonsHasConfidence.resize(listOfTaxons.size(), false);
 672                 vector< vector< map<string, float> > > searchTaxons; searchTaxons.resize(listOfTaxons.size());
 673                 vector<string> noConfidenceTaxons; noConfidenceTaxons.resize(listOfTaxons.size(), "");
 674
 675                 for (int i = 0; i < listOfTaxons.size(); i++) {
 676                         noConfidenceTaxons[i] = listOfTaxons[i];
 677                         int hasConPos = listOfTaxons[i].find_first_of('(');
 678                         if (hasConPos != string::npos) {
 679                                 taxonsHasConfidence[i] = true;
 680                                 searchTaxons[i] = getTaxons(listOfTaxons[i]);
 681                                 noConfidenceTaxons[i] = listOfTaxons[i];
 682                                 m->removeConfidences(noConfidenceTaxons[i]);
 683                         }
 684                 }
 685
 686
 687                 while(!in.eof()){
 688
 689                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 690
 691                         in >> name;                             //read from first column
 692                         in >> tax;                      //read from second column
 693
 694                         for (int j = 0; j < listOfTaxons.size(); j++) {
 695
 696                                 string newtax = tax;
 697
 698                                 //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
 699                                 if (!taxonsHasConfidence[j]) {
 700                                         int hasConfidences = tax.find_first_of('(');
 701                                         if (hasConfidences != string::npos) {
 702                                                 newtax = tax;
 703                                                 m->removeConfidences(newtax);
 704                                         }
 705
 706                                         int pos = newtax.find(noConfidenceTaxons[j]);
 707
 708                                         if (pos != string::npos) { //this sequence contains the taxon the user wants
 709                                                 names.insert(name);
 710                                                 out << name << '\t' << tax << endl;
 711                                                 //since you belong to at least one of the taxons we want you are included so no need to search for other
 712                                                 break;
 713                                         }
 714                                 }else{//if listOfTaxons[i] has them and you don't them remove taxons
 715                                         int hasConfidences = tax.find_first_of('(');
 716                                         if (hasConfidences == string::npos) {
 717
 718                                                 int pos = newtax.find(noConfidenceTaxons[j]);
 719
 720                                                 if (pos != string::npos) { //this sequence contains the taxon the user wants
 721                                                         names.insert(name);
 722                                                         out << name << '\t' << tax << endl;
 723                                                         //since you belong to at least one of the taxons we want you are included so no need to search for other
 724                                                         break;
 725                                                 }
 726                                         }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
 727                                                 //first remove confidences from both and see if the taxonomy exists
 728
 729                                                 string noNewTax = tax;
 730                                                 int hasConfidences = tax.find_first_of('(');
 731                                                 if (hasConfidences != string::npos) {
 732                                                         noNewTax = tax;
 733                                                         m->removeConfidences(noNewTax);
 734                                                 }
 735
 736                                                 int pos = noNewTax.find(noConfidenceTaxons[j]);
 737
 738                                                 if (pos != string::npos) { //if yes, then are the confidences okay
 739
 740                                                         bool good = true;
 741                                                         vector< map<string, float> > usersTaxon = getTaxons(newtax);
 742
 743                                                         //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
 744                                                         //we want to "line them up", so we will find the the index where the searchstring starts
 745                                                         int index = 0;
 746                                                         for (int i = 0; i < usersTaxon.size(); i++) {
 747
 748                                                                 if (usersTaxon[i].begin()->first == searchTaxons[j][0].begin()->first) {
 749                                                                         index = i;
 750                                                                         int spot = 0;
 751                                                                         bool goodspot = true;
 752                                                                         //is this really the start, or are we dealing with a taxon of the same name?
 753                                                                         while ((spot < searchTaxons[j].size()) && ((i+spot) < usersTaxon.size())) {
 754                                                                                 if (usersTaxon[i+spot].begin()->first != searchTaxons[j][spot].begin()->first) { goodspot = false; break; }
 755                                                                                 else { spot++; }
 756                                                                         }
 757
 758                                                                         if (goodspot) { break; }
 759                                                                 }
 760                                                         }
 761
 762                                                         for (int i = 0; i < searchTaxons[j].size(); i++) {
 763
 764                                                                 if ((i+index) < usersTaxon.size()) { //just in case, should never be false
 765                                                                         if (usersTaxon[i+index].begin()->second < searchTaxons[j][i].begin()->second) { //is the users cutoff less than the search taxons
 766                                                                                 good = false;
 767                                                                                 break;
 768                                                                         }
 769                                                                 }else {
 770                                                                         good = false;
 771                                                                         break;
 772                                                                 }
 773                                                         }
 774
 775                                                         //passed the test so add you
 776                                                         if (good) {
 777                                                                 names.insert(name);
 778                                                                 out << name << '\t' << tax << endl;
 779                                                                 break;
 780                                                         }
 781                                                 }
 782                                         }
 783                                 }
 784
 785                         }
 786
 787                         m->gobble(in);
 788                 }
 789                 in.close();
 790                 out.close();
 791
 792                 if (names.size() == 0) { m->mothurOut("Your taxonomy file does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 793                 outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
 794
 795                 return 0;
 796
 797         }
 798         catch(exception& e) {
 799                 m->errorOut(e, "GetLineageCommand", "readTax");
 800                 exit(1);
 801         }
 802 }
 803 /**************************************************************************************************/
 804 vector< map<string, float> > GetLineageCommand::getTaxons(string tax) {
 805         try {
 806
 807                 vector< map<string, float> > t;
 808                 string taxon = "";
 809                 int taxLength = tax.length();
 810                 for(int i=0;i<taxLength;i++){
 811                         if(tax[i] == ';'){
 812
 813                                 int openParen = taxon.find_first_of('(');
 814                                 int closeParen = taxon.find_last_of(')');
 815
 816                                 string newtaxon, confidence;
 817                                 if ((openParen != string::npos) && (closeParen != string::npos)) {
 818                                         newtaxon = taxon.substr(0, openParen); //rip off confidence
 819                                         confidence = taxon.substr((openParen+1), (closeParen-openParen-1));
 820                                 }else{
 821                                         newtaxon = taxon;
 822                                         confidence = "0";
 823                                 }
 824                                 float con = 0;
 825                                 convert(confidence, con);
 826
 827                                 map<string, float> temp;
 828                                 temp[newtaxon] = con;
 829                                 t.push_back(temp);
 830
 831                                 taxon = "";
 832                         }
 833                         else{
 834                                 taxon += tax[i];
 835                         }
 836                 }
 837
 838                 return t;
 839         }
 840         catch(exception& e) {
 841                 m->errorOut(e, "GetLineageCommand", "getTaxons");
 842                 exit(1);
 843         }
 844 }
 845 //**********************************************************************************************************************
 846 //alignreport file has a column header line then all other lines contain 16 columns.  we just want the first column since that contains the name
 847 int GetLineageCommand::readAlign(){
 848         try {
 849                 string thisOutputDir = outputDir;
 850                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 851                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + getOutputFileNameTag("alignreport");
 852                 ofstream out;
 853                 m->openOutputFile(outputFileName, out);
 854
 855
 856                 ifstream in;
 857                 m->openInputFile(alignfile, in);
 858                 string name, junk;
 859
 860                 bool wroteSomething = false;
 861
 862                 //read column headers
 863                 for (int i = 0; i < 16; i++) {
 864                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 865                         else                    {       break;                  }
 866                 }
 867                 out << endl;
 868
 869                 while(!in.eof()){
 870
 871                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 872
 873
 874                         in >> name;                             //read from first column
 875
 876                         //if this name is in the accnos file
 877                         if (names.count(name) != 0) {
 878                                 wroteSomething = true;
 879
 880                                 out << name << '\t';
 881
 882                                 //read rest
 883                                 for (int i = 0; i < 15; i++) {
 884                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 885                                         else                    {       break;                  }
 886                                 }
 887                                 out << endl;
 888
 889                         }else {//still read just don't do anything with it
 890                                 //read rest
 891                                 for (int i = 0; i < 15; i++) {
 892                                         if (!in.eof())  {       in >> junk;             }
 893                                         else                    {       break;                  }
 894                                 }
 895                         }
 896
 897                         m->gobble(in);
 898                 }
 899                 in.close();
 900                 out.close();
 901
 902                 if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 903                 outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
 904
 905                 return 0;
 906
 907         }
 908         catch(exception& e) {
 909                 m->errorOut(e, "GetLineageCommand", "readAlign");
 910                 exit(1);
 911         }
 912 }
 913 //**********************************************************************************************************************
 914
 915
 916
 917