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