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 #include "counttable.h"
  14
  15 //**********************************************************************************************************************
  16 vector<string> GetLineageCommand::setParameters(){
  17         try {
  18                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
  19         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none",false,false); parameters.push_back(pname);
  20         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none",false,false); parameters.push_back(pcount);
  21                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none",false,false); parameters.push_back(pgroup);
  22                 CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
  23                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(ptaxonomy);
  24                 CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);
  25                 CommandParameter ptaxon("taxon", "String", "", "", "", "", "",false,true); parameters.push_back(ptaxon);
  26                 CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
  27                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  28                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  29
  30                 vector<string> myArray;
  31                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  32                 return myArray;
  33         }
  34         catch(exception& e) {
  35                 m->errorOut(e, "GetLineageCommand", "setParameters");
  36                 exit(1);
  37         }
  38 }
  39 //**********************************************************************************************************************
  40 string GetLineageCommand::getHelpString(){
  41         try {
  42                 string helpString = "";
  43                 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";
  44                 helpString += "It outputs a file containing only the sequences from the taxonomy file that are from the taxon requested.\n";
  45                 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";
  46                 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";
  47                 helpString += "The taxon parameter allows you to select the taxons you would like to get and is required.\n";
  48                 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";
  49                 helpString += "If they belong to the taxonomy and have confidences below those you provide the sequence will not be selected.\n";
  50                 helpString += "The get.lineage command should be in the following format: get.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n";
  51                 helpString += "Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n";
  52                 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";
  53                 helpString += "Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n";
  54                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  55                 return helpString;
  56         }
  57         catch(exception& e) {
  58                 m->errorOut(e, "GetLineageCommand", "getHelpString");
  59                 exit(1);
  60         }
  61 }
  62 //**********************************************************************************************************************
  63 string GetLineageCommand::getOutputFileNameTag(string type, string inputName=""){
  64         try {
  65         string outputFileName = "";
  66                 map<string, vector<string> >::iterator it;
  67
  68         //is this a type this command creates
  69         it = outputTypes.find(type);
  70         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  71         else {
  72             if (type == "fasta")            {   outputFileName =  "pick" + m->getExtension(inputName);   }
  73             else if (type == "taxonomy")    {   outputFileName =  "pick" + m->getExtension(inputName);   }
  74             else if (type == "name")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
  75             else if (type == "count")       {   outputFileName =  "pick.count_table";                    }
  76             else if (type == "group")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
  77             else if (type == "list")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
  78             else if (type == "alignreport") {   outputFileName =  "pick.align.report";   }
  79             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  80         }
  81         return outputFileName;
  82         }
  83         catch(exception& e) {
  84                 m->errorOut(e, "GetLineageCommand", "getOutputFileNameTag");
  85                 exit(1);
  86         }
  87 }
  88 //**********************************************************************************************************************
  89 GetLineageCommand::GetLineageCommand(){
  90         try {
  91                 abort = true; calledHelp = true;
  92                 setParameters();
  93                 vector<string> tempOutNames;
  94                 outputTypes["fasta"] = tempOutNames;
  95                 outputTypes["taxonomy"] = tempOutNames;
  96                 outputTypes["name"] = tempOutNames;
  97                 outputTypes["group"] = tempOutNames;
  98                 outputTypes["alignreport"] = tempOutNames;
  99                 outputTypes["list"] = tempOutNames;
 100         outputTypes["count"] = tempOutNames;
 101         }
 102         catch(exception& e) {
 103                 m->errorOut(e, "GetLineageCommand", "GetLineageCommand");
 104                 exit(1);
 105         }
 106 }
 107 //**********************************************************************************************************************
 108 GetLineageCommand::GetLineageCommand(string option)  {
 109         try {
 110                 abort = false; calledHelp = false;
 111
 112                 //allow user to run help
 113                 if(option == "help") { help(); abort = true; calledHelp = true; }
 114                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 115
 116                 else {
 117                         vector<string> myArray = setParameters();
 118
 119                         OptionParser parser(option);
 120                         map<string,string> parameters = parser.getParameters();
 121
 122                         ValidParameters validParameter;
 123                         map<string,string>::iterator it;
 124
 125                         //check to make sure all parameters are valid for command
 126                         for (it = parameters.begin(); it != parameters.end(); it++) {
 127                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 128                         }
 129
 130                         //initialize outputTypes
 131                         vector<string> tempOutNames;
 132                         outputTypes["fasta"] = tempOutNames;
 133                         outputTypes["taxonomy"] = tempOutNames;
 134                         outputTypes["name"] = tempOutNames;
 135                         outputTypes["group"] = tempOutNames;
 136                         outputTypes["alignreport"] = tempOutNames;
 137                         outputTypes["list"] = tempOutNames;
 138             outputTypes["count"] = tempOutNames;
 139
 140                         //if the user changes the output directory command factory will send this info to us in the output parameter
 141                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 142
 143                         //if the user changes the input directory command factory will send this info to us in the output parameter
 144                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 145                         if (inputDir == "not found"){   inputDir = "";          }
 146                         else {
 147                                 string path;
 148                                 it = parameters.find("alignreport");
 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["alignreport"] = inputDir + it->second;              }
 154                                 }
 155
 156                                 it = parameters.find("fasta");
 157                                 //user has given a template file
 158                                 if(it != parameters.end()){
 159                                         path = m->hasPath(it->second);
 160                                         //if the user has not given a path then, add inputdir. else leave path alone.
 161                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 162                                 }
 163
 164                                 it = parameters.find("list");
 165                                 //user has given a template file
 166                                 if(it != parameters.end()){
 167                                         path = m->hasPath(it->second);
 168                                         //if the user has not given a path then, add inputdir. else leave path alone.
 169                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 170                                 }
 171
 172                                 it = parameters.find("name");
 173                                 //user has given a template file
 174                                 if(it != parameters.end()){
 175                                         path = m->hasPath(it->second);
 176                                         //if the user has not given a path then, add inputdir. else leave path alone.
 177                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 178                                 }
 179
 180                                 it = parameters.find("group");
 181                                 //user has given a template file
 182                                 if(it != parameters.end()){
 183                                         path = m->hasPath(it->second);
 184                                         //if the user has not given a path then, add inputdir. else leave path alone.
 185                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 186                                 }
 187
 188                                 it = parameters.find("taxonomy");
 189                                 //user has given a template file
 190                                 if(it != parameters.end()){
 191                                         path = m->hasPath(it->second);
 192                                         //if the user has not given a path then, add inputdir. else leave path alone.
 193                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 194                                 }
 195
 196                 it = parameters.find("count");
 197                                 //user has given a template file
 198                                 if(it != parameters.end()){
 199                                         path = m->hasPath(it->second);
 200                                         //if the user has not given a path then, add inputdir. else leave path alone.
 201                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 202                                 }
 203                         }
 204
 205
 206                         //check for required parameters
 207                         fastafile = validParameter.validFile(parameters, "fasta", true);
 208                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 209                         else if (fastafile == "not found") {  fastafile = "";  }
 210                         else { m->setFastaFile(fastafile); }
 211
 212                         namefile = validParameter.validFile(parameters, "name", true);
 213                         if (namefile == "not open") { namefile = ""; abort = true; }
 214                         else if (namefile == "not found") {  namefile = "";  }
 215                         else { m->setNameFile(namefile); }
 216
 217                         groupfile = validParameter.validFile(parameters, "group", true);
 218                         if (groupfile == "not open") { abort = true; }
 219                         else if (groupfile == "not found") {  groupfile = "";  }
 220                         else { m->setGroupFile(groupfile); }
 221
 222                         alignfile = validParameter.validFile(parameters, "alignreport", true);
 223                         if (alignfile == "not open") { abort = true; }
 224                         else if (alignfile == "not found") {  alignfile = "";  }
 225
 226                         listfile = validParameter.validFile(parameters, "list", true);
 227                         if (listfile == "not open") { abort = true; }
 228                         else if (listfile == "not found") {  listfile = "";  }
 229                         else { m->setListFile(listfile); }
 230
 231                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 232                         if (taxfile == "not open") { taxfile = ""; abort = true; }
 233                         else if (taxfile == "not found") {
 234                                 taxfile = m->getTaxonomyFile();
 235                                 if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
 236                                 else {  m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
 237                         }else { m->setTaxonomyFile(taxfile); }
 238
 239                         string usedDups = "true";
 240                         string temp = validParameter.validFile(parameters, "dups", false);
 241                         if (temp == "not found") {
 242                                 if (namefile != "") {  temp = "true";                                   }
 243                                 else                            {  temp = "false"; usedDups = "";       }
 244                         }
 245                         dups = m->isTrue(temp);
 246
 247             countfile = validParameter.validFile(parameters, "count", true);
 248             if (countfile == "not open") { countfile = ""; abort = true; }
 249             else if (countfile == "not found") { countfile = "";  }
 250             else { m->setCountTableFile(countfile); }
 251
 252             if ((namefile != "") && (countfile != "")) {
 253                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 254             }
 255
 256             if ((groupfile != "") && (countfile != "")) {
 257                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 258             }
 259
 260                         taxons = validParameter.validFile(parameters, "taxon", false);
 261                         if (taxons == "not found") { taxons = "";  m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine();  abort = true;  }
 262                         else {
 263                                 //rip off quotes
 264                                 if (taxons[0] == '\'') {  taxons = taxons.substr(1); }
 265                                 if (taxons[(taxons.length()-1)] == '\'') {  taxons = taxons.substr(0, (taxons.length()-1)); }
 266                         }
 267                         m->splitAtChar(taxons, listOfTaxons, '-');
 268
 269                         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; }
 270
 271             if (countfile == "") {
 272                 if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
 273                     vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
 274                     parser.getNameFile(files);
 275                 }
 276             }
 277                 }
 278
 279         }
 280         catch(exception& e) {
 281                 m->errorOut(e, "GetLineageCommand", "GetLineageCommand");
 282                 exit(1);
 283         }
 284 }
 285 //**********************************************************************************************************************
 286
 287 int GetLineageCommand::execute(){
 288         try {
 289
 290                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 291
 292                 if (m->control_pressed) { return 0; }
 293
 294         if (countfile != "") {
 295             if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
 296                 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");
 297             }
 298         }
 299
 300                 //read through the correct file and output lines you want to keep
 301                 if (taxfile != "")                      {               readTax();              }  //fills the set of names to get
 302                 if (namefile != "")                     {               readName();             }
 303                 if (fastafile != "")            {               readFasta();    }
 304         if (countfile != "")            {               readCount();    }
 305                 if (groupfile != "")            {               readGroup();    }
 306                 if (alignfile != "")            {               readAlign();    }
 307                 if (listfile != "")                     {               readList();             }
 308
 309
 310                 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);  } return 0; }
 311
 312                 if (outputNames.size() != 0) {
 313                         m->mothurOutEndLine();
 314                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 315                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 316                         m->mothurOutEndLine();
 317
 318                         //set fasta file as new current fastafile
 319                         string current = "";
 320                         itTypes = outputTypes.find("fasta");
 321                         if (itTypes != outputTypes.end()) {
 322                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 323                         }
 324
 325                         itTypes = outputTypes.find("name");
 326                         if (itTypes != outputTypes.end()) {
 327                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 328                         }
 329
 330                         itTypes = outputTypes.find("group");
 331                         if (itTypes != outputTypes.end()) {
 332                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 333                         }
 334
 335                         itTypes = outputTypes.find("list");
 336                         if (itTypes != outputTypes.end()) {
 337                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 338                         }
 339
 340                         itTypes = outputTypes.find("taxonomy");
 341                         if (itTypes != outputTypes.end()) {
 342                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 343                         }
 344
 345             itTypes = outputTypes.find("count");
 346                         if (itTypes != outputTypes.end()) {
 347                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 348                         }
 349                 }
 350
 351                 return 0;
 352         }
 353
 354         catch(exception& e) {
 355                 m->errorOut(e, "GetLineageCommand", "execute");
 356                 exit(1);
 357         }
 358 }
 359
 360 //**********************************************************************************************************************
 361 int GetLineageCommand::readFasta(){
 362         try {
 363                 string thisOutputDir = outputDir;
 364                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 365                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
 366                 ofstream out;
 367                 m->openOutputFile(outputFileName, out);
 368
 369
 370                 ifstream in;
 371                 m->openInputFile(fastafile, in);
 372                 string name;
 373
 374                 bool wroteSomething = false;
 375
 376                 while(!in.eof()){
 377
 378                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 379
 380                         Sequence currSeq(in);
 381                         name = currSeq.getName();
 382
 383                         if (name != "") {
 384                                 //if this name is in the accnos file
 385                                 if (names.count(name) != 0) {
 386                                         wroteSomething = true;
 387
 388                                         currSeq.printSequence(out);
 389                                 }
 390                         }
 391                         m->gobble(in);
 392                 }
 393                 in.close();
 394                 out.close();
 395
 396                 if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 397                 outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);
 398
 399                 return 0;
 400
 401         }
 402         catch(exception& e) {
 403                 m->errorOut(e, "GetLineageCommand", "readFasta");
 404                 exit(1);
 405         }
 406 }
 407 //**********************************************************************************************************************
 408 int GetLineageCommand::readCount(){
 409         try {
 410                 string thisOutputDir = outputDir;
 411                 if (outputDir == "") {  thisOutputDir += m->hasPath(countfile);  }
 412                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
 413
 414                 ofstream out;
 415                 m->openOutputFile(outputFileName, out);
 416
 417                 ifstream in;
 418                 m->openInputFile(countfile, in);
 419
 420                 bool wroteSomething = false;
 421
 422         string headers = m->getline(in); m->gobble(in);
 423         out << headers << endl;
 424
 425         string name, rest; int thisTotal;
 426         while (!in.eof()) {
 427
 428             if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 429
 430             in >> name; m->gobble(in);
 431             in >> thisTotal; m->gobble(in);
 432             rest = m->getline(in); m->gobble(in);
 433             if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + rest + "\n"); }
 434
 435             if (names.count(name) != 0) {
 436                 out << name << '\t' << thisTotal << '\t' << rest << endl;
 437                 wroteSomething = true;
 438             }
 439         }
 440         in.close();
 441                 out.close();
 442
 443         //check for groups that have been eliminated
 444         CountTable ct;
 445         if (ct.testGroups(outputFileName)) {
 446             ct.readTable(outputFileName);
 447             ct.printTable(outputFileName);
 448         }
 449
 450
 451                 if (wroteSomething == false) {  m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 452                 outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
 453
 454                 return 0;
 455         }
 456         catch(exception& e) {
 457                 m->errorOut(e, "GetLineageCommand", "readCount");
 458                 exit(1);
 459         }
 460 }
 461 //**********************************************************************************************************************
 462 int GetLineageCommand::readList(){
 463         try {
 464                 string thisOutputDir = outputDir;
 465                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 466                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
 467                 ofstream out;
 468                 m->openOutputFile(outputFileName, out);
 469
 470                 ifstream in;
 471                 m->openInputFile(listfile, in);
 472
 473                 bool wroteSomething = false;
 474
 475                 while(!in.eof()){
 476
 477                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 478
 479                         //read in list vector
 480                         ListVector list(in);
 481
 482                         //make a new list vector
 483                         ListVector newList;
 484                         newList.setLabel(list.getLabel());
 485
 486                         //for each bin
 487                         for (int i = 0; i < list.getNumBins(); i++) {
 488
 489                                 //parse out names that are in accnos file
 490                                 string binnames = list.get(i);
 491
 492                                 string newNames = "";
 493                                 while (binnames.find_first_of(',') != -1) {
 494                                         string name = binnames.substr(0,binnames.find_first_of(','));
 495                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 496
 497                                         //if that name is in the .accnos file, add it
 498                                         if (names.count(name) != 0) {  newNames += name + ",";  }
 499                                 }
 500
 501                                 //get last name
 502                                 if (names.count(binnames) != 0) {  newNames += binnames + ",";  }
 503
 504                                 //if there are names in this bin add to new list
 505                                 if (newNames != "") {
 506                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 507                                         newList.push_back(newNames);
 508                                 }
 509                         }
 510
 511                         //print new listvector
 512                         if (newList.getNumBins() != 0) {
 513                                 wroteSomething = true;
 514                                 newList.print(out);
 515                         }
 516
 517                         m->gobble(in);
 518                 }
 519                 in.close();
 520                 out.close();
 521
 522                 if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 523                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 524
 525                 return 0;
 526
 527         }
 528         catch(exception& e) {
 529                 m->errorOut(e, "GetLineageCommand", "readList");
 530                 exit(1);
 531         }
 532 }
 533 //**********************************************************************************************************************
 534 int GetLineageCommand::readName(){
 535         try {
 536                 string thisOutputDir = outputDir;
 537                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 538                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
 539                 ofstream out;
 540                 m->openOutputFile(outputFileName, out);
 541
 542
 543                 ifstream in;
 544                 m->openInputFile(namefile, in);
 545                 string name, firstCol, secondCol;
 546
 547                 bool wroteSomething = false;
 548
 549
 550                 while(!in.eof()){
 551
 552                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 553
 554                         in >> firstCol;
 555                         in >> secondCol;
 556
 557                         string hold = "";
 558                         if (dups) { hold = secondCol; }
 559
 560                         vector<string> parsedNames;
 561                         m->splitAtComma(secondCol, parsedNames);
 562
 563                         vector<string> validSecond;
 564                         for (int i = 0; i < parsedNames.size(); i++) {
 565                                 if (names.count(parsedNames[i]) != 0) {
 566                                         validSecond.push_back(parsedNames[i]);
 567                                 }
 568                         }
 569
 570                         if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
 571                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 572                                 out << firstCol << '\t' << hold << endl;
 573                                 wroteSomething = true;
 574                         }else {
 575                                 //if the name in the first column is in the set then print it and any other names in second column also in set
 576                                 if (names.count(firstCol) != 0) {
 577
 578                                         wroteSomething = true;
 579
 580                                         out << firstCol << '\t';
 581
 582                                         //you know you have at least one valid second since first column is valid
 583                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 584                                         out << validSecond[validSecond.size()-1] << endl;
 585
 586
 587                                 //make first name in set you come to first column and then add the remaining names to second column
 588                                 }else {
 589                                         //you want part of this row
 590                                         if (validSecond.size() != 0) {
 591
 592                                                 wroteSomething = true;
 593
 594                                                 out << validSecond[0] << '\t';
 595
 596                                                 //you know you have at least one valid second since first column is valid
 597                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 598                                                 out << validSecond[validSecond.size()-1] << endl;
 599                                         }
 600                                 }
 601                         }
 602                         m->gobble(in);
 603                 }
 604                 in.close();
 605                 out.close();
 606
 607                 if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 608                 outputNames.push_back(outputFileName);  outputTypes["name"].push_back(outputFileName);
 609
 610                 return 0;
 611
 612         }
 613         catch(exception& e) {
 614                 m->errorOut(e, "GetLineageCommand", "readName");
 615                 exit(1);
 616         }
 617 }
 618
 619 //**********************************************************************************************************************
 620 int GetLineageCommand::readGroup(){
 621         try {
 622                 string thisOutputDir = outputDir;
 623                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 624                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
 625                 ofstream out;
 626                 m->openOutputFile(outputFileName, out);
 627
 628
 629                 ifstream in;
 630                 m->openInputFile(groupfile, in);
 631                 string name, group;
 632
 633                 bool wroteSomething = false;
 634
 635                 while(!in.eof()){
 636
 637                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 638
 639
 640                         in >> name;                             //read from first column
 641                         in >> group;                    //read from second column
 642
 643                         //if this name is in the accnos file
 644                         if (names.count(name) != 0) {
 645                                 wroteSomething = true;
 646
 647                                 out << name << '\t' << group << endl;
 648                         }
 649
 650                         m->gobble(in);
 651                 }
 652                 in.close();
 653                 out.close();
 654
 655                 if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 656                 outputNames.push_back(outputFileName);  outputTypes["group"].push_back(outputFileName);
 657
 658                 return 0;
 659
 660         }
 661         catch(exception& e) {
 662                 m->errorOut(e, "GetLineageCommand", "readGroup");
 663                 exit(1);
 664         }
 665 }
 666 //**********************************************************************************************************************
 667 int GetLineageCommand::readTax(){
 668         try {
 669                 string thisOutputDir = outputDir;
 670                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 671                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
 672                 ofstream out;
 673                 m->openOutputFile(outputFileName, out);
 674
 675                 ifstream in;
 676                 m->openInputFile(taxfile, in);
 677                 string name, tax;
 678
 679                 //bool wroteSomething = false;
 680                 vector<bool> taxonsHasConfidence; taxonsHasConfidence.resize(listOfTaxons.size(), false);
 681                 vector< vector< map<string, float> > > searchTaxons; searchTaxons.resize(listOfTaxons.size());
 682                 vector<string> noConfidenceTaxons; noConfidenceTaxons.resize(listOfTaxons.size(), "");
 683
 684                 for (int i = 0; i < listOfTaxons.size(); i++) {
 685                         noConfidenceTaxons[i] = listOfTaxons[i];
 686                         int hasConPos = listOfTaxons[i].find_first_of('(');
 687                         if (hasConPos != string::npos) {
 688                                 taxonsHasConfidence[i] = true;
 689                                 searchTaxons[i] = getTaxons(listOfTaxons[i]);
 690                                 noConfidenceTaxons[i] = listOfTaxons[i];
 691                                 m->removeConfidences(noConfidenceTaxons[i]);
 692                         }
 693                 }
 694
 695
 696                 while(!in.eof()){
 697
 698                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 699
 700                         in >> name;                             //read from first column
 701                         in >> tax;                      //read from second column
 702
 703             string noQuotesTax = m->removeQuotes(tax);
 704
 705                         for (int j = 0; j < listOfTaxons.size(); j++) {
 706
 707                                 string newtax = noQuotesTax;
 708
 709                                 //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
 710                                 if (!taxonsHasConfidence[j]) {
 711                                         int hasConfidences = noQuotesTax.find_first_of('(');
 712                                         if (hasConfidences != string::npos) {
 713                                                 newtax = noQuotesTax;
 714                                                 m->removeConfidences(newtax);
 715                                         }
 716
 717                                         int pos = newtax.find(noConfidenceTaxons[j]);
 718
 719                                         if (pos != string::npos) { //this sequence contains the taxon the user wants
 720                                                 names.insert(name);
 721                                                 out << name << '\t' << tax << endl;
 722                                                 //since you belong to at least one of the taxons we want you are included so no need to search for other
 723                                                 break;
 724                                         }
 725                                 }else{//if listOfTaxons[i] has them and you don't them remove taxons
 726                                         int hasConfidences = noQuotesTax.find_first_of('(');
 727                                         if (hasConfidences == string::npos) {
 728
 729                                                 int pos = newtax.find(noConfidenceTaxons[j]);
 730
 731                                                 if (pos != string::npos) { //this sequence contains the taxon the user wants
 732                                                         names.insert(name);
 733                                                         out << name << '\t' << tax << endl;
 734                                                         //since you belong to at least one of the taxons we want you are included so no need to search for other
 735                                                         break;
 736                                                 }
 737                                         }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
 738                                                 //first remove confidences from both and see if the taxonomy exists
 739
 740                                                 string noNewTax = noQuotesTax;
 741                                                 int hasConfidences = noQuotesTax.find_first_of('(');
 742                                                 if (hasConfidences != string::npos) {
 743                                                         noNewTax = noQuotesTax;
 744                                                         m->removeConfidences(noNewTax);
 745                                                 }
 746
 747                                                 int pos = noNewTax.find(noConfidenceTaxons[j]);
 748
 749                                                 if (pos != string::npos) { //if yes, then are the confidences okay
 750
 751                                                         bool good = true;
 752                                                         vector< map<string, float> > usersTaxon = getTaxons(newtax);
 753
 754                                                         //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
 755                                                         //we want to "line them up", so we will find the the index where the searchstring starts
 756                                                         int index = 0;
 757                                                         for (int i = 0; i < usersTaxon.size(); i++) {
 758
 759                                                                 if (usersTaxon[i].begin()->first == searchTaxons[j][0].begin()->first) {
 760                                                                         index = i;
 761                                                                         int spot = 0;
 762                                                                         bool goodspot = true;
 763                                                                         //is this really the start, or are we dealing with a taxon of the same name?
 764                                                                         while ((spot < searchTaxons[j].size()) && ((i+spot) < usersTaxon.size())) {
 765                                                                                 if (usersTaxon[i+spot].begin()->first != searchTaxons[j][spot].begin()->first) { goodspot = false; break; }
 766                                                                                 else { spot++; }
 767                                                                         }
 768
 769                                                                         if (goodspot) { break; }
 770                                                                 }
 771                                                         }
 772
 773                                                         for (int i = 0; i < searchTaxons[j].size(); i++) {
 774
 775                                                                 if ((i+index) < usersTaxon.size()) { //just in case, should never be false
 776                                                                         if (usersTaxon[i+index].begin()->second < searchTaxons[j][i].begin()->second) { //is the users cutoff less than the search taxons
 777                                                                                 good = false;
 778                                                                                 break;
 779                                                                         }
 780                                                                 }else {
 781                                                                         good = false;
 782                                                                         break;
 783                                                                 }
 784                                                         }
 785
 786                                                         //passed the test so add you
 787                                                         if (good) {
 788                                                                 names.insert(name);
 789                                                                 out << name << '\t' << tax << endl;
 790                                                                 break;
 791                                                         }
 792                                                 }
 793                                         }
 794                                 }
 795
 796                         }
 797
 798                         m->gobble(in);
 799                 }
 800                 in.close();
 801                 out.close();
 802
 803                 if (names.size() == 0) { m->mothurOut("Your taxonomy file does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 804                 outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
 805
 806                 return 0;
 807
 808         }
 809         catch(exception& e) {
 810                 m->errorOut(e, "GetLineageCommand", "readTax");
 811                 exit(1);
 812         }
 813 }
 814 /**************************************************************************************************/
 815 vector< map<string, float> > GetLineageCommand::getTaxons(string tax) {
 816         try {
 817
 818                 vector< map<string, float> > t;
 819                 string taxon = "";
 820                 int taxLength = tax.length();
 821
 822                 for(int i=0;i<taxLength;i++){
 823                         if(tax[i] == ';'){
 824
 825                                 int openParen = taxon.find_last_of('(');
 826                                 int closeParen = taxon.find_last_of(')');
 827
 828                                 string newtaxon, confidence;
 829                                 if ((openParen != string::npos) && (closeParen != string::npos)) {
 830                     string confidenceScore = taxon.substr(openParen+1, (closeParen-(openParen+1)));
 831                     if (m->isNumeric1(confidenceScore)) {  //its a confidence
 832                         newtaxon = taxon.substr(0, openParen); //rip off confidence
 833                         confidence = taxon.substr((openParen+1), (closeParen-openParen-1));
 834                     }else { //its part of the taxon
 835                         newtaxon = taxon;
 836                         confidence = "0";
 837                     }
 838                                 }else{
 839                                         newtaxon = taxon;
 840                                         confidence = "0";
 841                                 }
 842                                 float con = 0;
 843                                 convert(confidence, con);
 844
 845                                 map<string, float> temp;
 846                                 temp[newtaxon] = con;
 847
 848                                 t.push_back(temp);
 849                                 taxon = "";
 850                         }
 851                         else{
 852                                 taxon += tax[i];
 853
 854                         }
 855                 }
 856
 857                 return t;
 858         }
 859         catch(exception& e) {
 860                 m->errorOut(e, "GetLineageCommand", "getTaxons");
 861                 exit(1);
 862         }
 863 }
 864 //**********************************************************************************************************************
 865 //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
 866 int GetLineageCommand::readAlign(){
 867         try {
 868                 string thisOutputDir = outputDir;
 869                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 870                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + getOutputFileNameTag("alignreport");
 871                 ofstream out;
 872                 m->openOutputFile(outputFileName, out);
 873
 874
 875                 ifstream in;
 876                 m->openInputFile(alignfile, in);
 877                 string name, junk;
 878
 879                 bool wroteSomething = false;
 880
 881                 //read column headers
 882                 for (int i = 0; i < 16; i++) {
 883                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 884                         else                    {       break;                  }
 885                 }
 886                 out << endl;
 887
 888                 while(!in.eof()){
 889
 890                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 891
 892
 893                         in >> name;                             //read from first column
 894
 895                         //if this name is in the accnos file
 896                         if (names.count(name) != 0) {
 897                                 wroteSomething = true;
 898
 899                                 out << name << '\t';
 900
 901                                 //read rest
 902                                 for (int i = 0; i < 15; i++) {
 903                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 904                                         else                    {       break;                  }
 905                                 }
 906                                 out << endl;
 907
 908                         }else {//still read just don't do anything with it
 909                                 //read rest
 910                                 for (int i = 0; i < 15; i++) {
 911                                         if (!in.eof())  {       in >> junk;             }
 912                                         else                    {       break;                  }
 913                                 }
 914                         }
 915
 916                         m->gobble(in);
 917                 }
 918                 in.close();
 919                 out.close();
 920
 921                 if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 922                 outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
 923
 924                 return 0;
 925
 926         }
 927         catch(exception& e) {
 928                 m->errorOut(e, "GetLineageCommand", "readAlign");
 929                 exit(1);
 930         }
 931 }
 932 //**********************************************************************************************************************
 933
 934
 935
 936