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