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","fasta",false,false, true); parameters.push_back(pfasta);
  19         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false, true); parameters.push_back(pname);
  20         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none","count",false,false, true); parameters.push_back(pcount);
  21                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none","group",false,false, true); parameters.push_back(pgroup);
  22                 CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false, true); parameters.push_back(plist);
  23                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none","taxonomy",false,true, true); parameters.push_back(ptaxonomy);
  24                 CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none","alignreport",false,false); parameters.push_back(palignreport);
  25                 CommandParameter ptaxon("taxon", "String", "", "", "", "", "","",false,true, 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::getOutputPattern(string type) {
  64     try {
  65         string pattern = "";
  66
  67         if (type == "fasta")            {   pattern = "[filename],pick,[extension]";    }
  68         else if (type == "taxonomy")    {   pattern = "[filename],pick,[extension]";    }
  69         else if (type == "name")        {   pattern = "[filename],pick,[extension]";    }
  70         else if (type == "group")       {   pattern = "[filename],pick,[extension]";    }
  71         else if (type == "count")       {   pattern = "[filename],pick,[extension]";    }
  72         else if (type == "list")        {   pattern = "[filename],pick,[extension]";    }
  73         else if (type == "alignreport")      {   pattern = "[filename],pick.align.report";    }
  74         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  75
  76         return pattern;
  77     }
  78     catch(exception& e) {
  79         m->errorOut(e, "GetLineageCommand", "getOutputPattern");
  80         exit(1);
  81     }
  82 }
  83 //**********************************************************************************************************************
  84 GetLineageCommand::GetLineageCommand(){
  85         try {
  86                 abort = true; calledHelp = true;
  87                 setParameters();
  88                 vector<string> tempOutNames;
  89                 outputTypes["fasta"] = tempOutNames;
  90                 outputTypes["taxonomy"] = tempOutNames;
  91                 outputTypes["name"] = tempOutNames;
  92                 outputTypes["group"] = tempOutNames;
  93                 outputTypes["alignreport"] = tempOutNames;
  94                 outputTypes["list"] = tempOutNames;
  95         outputTypes["count"] = tempOutNames;
  96         }
  97         catch(exception& e) {
  98                 m->errorOut(e, "GetLineageCommand", "GetLineageCommand");
  99                 exit(1);
 100         }
 101 }
 102 //**********************************************************************************************************************
 103 GetLineageCommand::GetLineageCommand(string option)  {
 104         try {
 105                 abort = false; calledHelp = false;
 106
 107                 //allow user to run help
 108                 if(option == "help") { help(); abort = true; calledHelp = true; }
 109                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 110
 111                 else {
 112                         vector<string> myArray = setParameters();
 113
 114                         OptionParser parser(option);
 115                         map<string,string> parameters = parser.getParameters();
 116
 117                         ValidParameters validParameter;
 118                         map<string,string>::iterator it;
 119
 120                         //check to make sure all parameters are valid for command
 121                         for (it = parameters.begin(); it != parameters.end(); it++) {
 122                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 123                         }
 124
 125                         //initialize outputTypes
 126                         vector<string> tempOutNames;
 127                         outputTypes["fasta"] = tempOutNames;
 128                         outputTypes["taxonomy"] = tempOutNames;
 129                         outputTypes["name"] = tempOutNames;
 130                         outputTypes["group"] = tempOutNames;
 131                         outputTypes["alignreport"] = tempOutNames;
 132                         outputTypes["list"] = tempOutNames;
 133             outputTypes["count"] = tempOutNames;
 134
 135                         //if the user changes the output directory command factory will send this info to us in the output parameter
 136                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 137
 138                         //if the user changes the input directory command factory will send this info to us in the output parameter
 139                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 140                         if (inputDir == "not found"){   inputDir = "";          }
 141                         else {
 142                                 string path;
 143                                 it = parameters.find("alignreport");
 144                                 //user has given a template file
 145                                 if(it != parameters.end()){
 146                                         path = m->hasPath(it->second);
 147                                         //if the user has not given a path then, add inputdir. else leave path alone.
 148                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
 149                                 }
 150
 151                                 it = parameters.find("fasta");
 152                                 //user has given a template file
 153                                 if(it != parameters.end()){
 154                                         path = m->hasPath(it->second);
 155                                         //if the user has not given a path then, add inputdir. else leave path alone.
 156                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 157                                 }
 158
 159                                 it = parameters.find("list");
 160                                 //user has given a template file
 161                                 if(it != parameters.end()){
 162                                         path = m->hasPath(it->second);
 163                                         //if the user has not given a path then, add inputdir. else leave path alone.
 164                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 165                                 }
 166
 167                                 it = parameters.find("name");
 168                                 //user has given a template file
 169                                 if(it != parameters.end()){
 170                                         path = m->hasPath(it->second);
 171                                         //if the user has not given a path then, add inputdir. else leave path alone.
 172                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 173                                 }
 174
 175                                 it = parameters.find("group");
 176                                 //user has given a template file
 177                                 if(it != parameters.end()){
 178                                         path = m->hasPath(it->second);
 179                                         //if the user has not given a path then, add inputdir. else leave path alone.
 180                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 181                                 }
 182
 183                                 it = parameters.find("taxonomy");
 184                                 //user has given a template file
 185                                 if(it != parameters.end()){
 186                                         path = m->hasPath(it->second);
 187                                         //if the user has not given a path then, add inputdir. else leave path alone.
 188                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 189                                 }
 190
 191                 it = parameters.find("count");
 192                                 //user has given a template file
 193                                 if(it != parameters.end()){
 194                                         path = m->hasPath(it->second);
 195                                         //if the user has not given a path then, add inputdir. else leave path alone.
 196                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 197                                 }
 198                         }
 199
 200
 201                         //check for required parameters
 202                         fastafile = validParameter.validFile(parameters, "fasta", true);
 203                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 204                         else if (fastafile == "not found") {  fastafile = "";  }
 205                         else { m->setFastaFile(fastafile); }
 206
 207                         namefile = validParameter.validFile(parameters, "name", true);
 208                         if (namefile == "not open") { namefile = ""; abort = true; }
 209                         else if (namefile == "not found") {  namefile = "";  }
 210                         else { m->setNameFile(namefile); }
 211
 212                         groupfile = validParameter.validFile(parameters, "group", true);
 213                         if (groupfile == "not open") { abort = true; }
 214                         else if (groupfile == "not found") {  groupfile = "";  }
 215                         else { m->setGroupFile(groupfile); }
 216
 217                         alignfile = validParameter.validFile(parameters, "alignreport", true);
 218                         if (alignfile == "not open") { abort = true; }
 219                         else if (alignfile == "not found") {  alignfile = "";  }
 220
 221                         listfile = validParameter.validFile(parameters, "list", true);
 222                         if (listfile == "not open") { abort = true; }
 223                         else if (listfile == "not found") {  listfile = "";  }
 224                         else { m->setListFile(listfile); }
 225
 226                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 227                         if (taxfile == "not open") { taxfile = ""; abort = true; }
 228                         else if (taxfile == "not found") {
 229                                 taxfile = m->getTaxonomyFile();
 230                                 if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
 231                                 else {  m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
 232                         }else { m->setTaxonomyFile(taxfile); }
 233
 234                         string usedDups = "true";
 235                         string temp = validParameter.validFile(parameters, "dups", false);
 236                         if (temp == "not found") {
 237                                 if (namefile != "") {  temp = "true";                                   }
 238                                 else                            {  temp = "false"; usedDups = "";       }
 239                         }
 240                         dups = m->isTrue(temp);
 241
 242             countfile = validParameter.validFile(parameters, "count", true);
 243             if (countfile == "not open") { countfile = ""; abort = true; }
 244             else if (countfile == "not found") { countfile = "";  }
 245             else { m->setCountTableFile(countfile); }
 246
 247             if ((namefile != "") && (countfile != "")) {
 248                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 249             }
 250
 251             if ((groupfile != "") && (countfile != "")) {
 252                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 253             }
 254
 255                         taxons = validParameter.validFile(parameters, "taxon", false);
 256                         if (taxons == "not found") { taxons = "";  m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine();  abort = true;  }
 257                         else {
 258                                 //rip off quotes
 259                                 if (taxons[0] == '\'') {  taxons = taxons.substr(1); }
 260                                 if (taxons[(taxons.length()-1)] == '\'') {  taxons = taxons.substr(0, (taxons.length()-1)); }
 261                         }
 262                         m->splitAtChar(taxons, listOfTaxons, '-');
 263
 264                         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; }
 265
 266             if (countfile == "") {
 267                 if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
 268                     vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
 269                     parser.getNameFile(files);
 270                 }
 271             }
 272                 }
 273
 274         }
 275         catch(exception& e) {
 276                 m->errorOut(e, "GetLineageCommand", "GetLineageCommand");
 277                 exit(1);
 278         }
 279 }
 280 //**********************************************************************************************************************
 281
 282 int GetLineageCommand::execute(){
 283         try {
 284
 285                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 286
 287                 if (m->control_pressed) { return 0; }
 288
 289         if (countfile != "") {
 290             if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
 291                 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");
 292             }
 293         }
 294
 295                 //read through the correct file and output lines you want to keep
 296                 if (taxfile != "")                      {               readTax();              }  //fills the set of names to get
 297                 if (namefile != "")                     {               readName();             }
 298                 if (fastafile != "")            {               readFasta();    }
 299         if (countfile != "")            {               readCount();    }
 300                 if (groupfile != "")            {               readGroup();    }
 301                 if (alignfile != "")            {               readAlign();    }
 302                 if (listfile != "")                     {               readList();             }
 303
 304
 305                 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);  } return 0; }
 306
 307                 if (outputNames.size() != 0) {
 308                         m->mothurOutEndLine();
 309                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 310                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 311                         m->mothurOutEndLine();
 312
 313                         //set fasta file as new current fastafile
 314                         string current = "";
 315                         itTypes = outputTypes.find("fasta");
 316                         if (itTypes != outputTypes.end()) {
 317                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 318                         }
 319
 320                         itTypes = outputTypes.find("name");
 321                         if (itTypes != outputTypes.end()) {
 322                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 323                         }
 324
 325                         itTypes = outputTypes.find("group");
 326                         if (itTypes != outputTypes.end()) {
 327                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 328                         }
 329
 330                         itTypes = outputTypes.find("list");
 331                         if (itTypes != outputTypes.end()) {
 332                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 333                         }
 334
 335                         itTypes = outputTypes.find("taxonomy");
 336                         if (itTypes != outputTypes.end()) {
 337                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 338                         }
 339
 340             itTypes = outputTypes.find("count");
 341                         if (itTypes != outputTypes.end()) {
 342                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 343                         }
 344                 }
 345
 346                 return 0;
 347         }
 348
 349         catch(exception& e) {
 350                 m->errorOut(e, "GetLineageCommand", "execute");
 351                 exit(1);
 352         }
 353 }
 354
 355 //**********************************************************************************************************************
 356 int GetLineageCommand::readFasta(){
 357         try {
 358                 string thisOutputDir = outputDir;
 359                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 360                 map<string, string> variables;
 361         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
 362         variables["[extension]"] = m->getExtension(fastafile);
 363                 string outputFileName = getOutputFileName("fasta", variables);
 364                 ofstream out;
 365                 m->openOutputFile(outputFileName, out);
 366
 367
 368                 ifstream in;
 369                 m->openInputFile(fastafile, in);
 370                 string name;
 371
 372                 bool wroteSomething = false;
 373
 374                 while(!in.eof()){
 375
 376                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 377
 378                         Sequence currSeq(in);
 379                         name = currSeq.getName();
 380
 381                         if (name != "") {
 382                                 //if this name is in the accnos file
 383                                 if (names.count(name) != 0) {
 384                                         wroteSomething = true;
 385
 386                                         currSeq.printSequence(out);
 387                                 }
 388                         }
 389                         m->gobble(in);
 390                 }
 391                 in.close();
 392                 out.close();
 393
 394                 if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 395                 outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);
 396
 397                 return 0;
 398
 399         }
 400         catch(exception& e) {
 401                 m->errorOut(e, "GetLineageCommand", "readFasta");
 402                 exit(1);
 403         }
 404 }
 405 //**********************************************************************************************************************
 406 int GetLineageCommand::readCount(){
 407         try {
 408                 string thisOutputDir = outputDir;
 409                 if (outputDir == "") {  thisOutputDir += m->hasPath(countfile);  }
 410                 map<string, string> variables;
 411                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(countfile));
 412         variables["[extension]"] = m->getExtension(countfile);
 413                 string outputFileName = getOutputFileName("count", variables);
 414
 415                 ofstream out;
 416                 m->openOutputFile(outputFileName, out);
 417
 418                 ifstream in;
 419                 m->openInputFile(countfile, in);
 420
 421                 bool wroteSomething = false;
 422
 423         string headers = m->getline(in); m->gobble(in);
 424         out << headers << endl;
 425
 426         string name, rest; int thisTotal;
 427         while (!in.eof()) {
 428
 429             if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 430
 431             in >> name; m->gobble(in);
 432             in >> thisTotal; m->gobble(in);
 433             rest = m->getline(in); m->gobble(in);
 434             if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + rest + "\n"); }
 435
 436             if (names.count(name) != 0) {
 437                 out << name << '\t' << thisTotal << '\t' << rest << endl;
 438                 wroteSomething = true;
 439             }
 440         }
 441         in.close();
 442                 out.close();
 443
 444         //check for groups that have been eliminated
 445         CountTable ct;
 446         if (ct.testGroups(outputFileName)) {
 447             ct.readTable(outputFileName, true);
 448             ct.printTable(outputFileName);
 449         }
 450
 451
 452                 if (wroteSomething == false) {  m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 453                 outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
 454
 455                 return 0;
 456         }
 457         catch(exception& e) {
 458                 m->errorOut(e, "GetLineageCommand", "readCount");
 459                 exit(1);
 460         }
 461 }
 462 //**********************************************************************************************************************
 463 int GetLineageCommand::readList(){
 464         try {
 465                 string thisOutputDir = outputDir;
 466                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 467                 map<string, string> variables;
 468         variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
 469         variables["[extension]"] = m->getExtension(listfile);
 470                 string outputFileName = getOutputFileName("list", variables);
 471                 ofstream out;
 472                 m->openOutputFile(outputFileName, out);
 473
 474                 ifstream in;
 475                 m->openInputFile(listfile, in);
 476
 477                 bool wroteSomething = false;
 478
 479                 while(!in.eof()){
 480
 481                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 482
 483                         //read in list vector
 484                         ListVector list(in);
 485
 486                         //make a new list vector
 487                         ListVector newList;
 488                         newList.setLabel(list.getLabel());
 489
 490                         //for each bin
 491                         for (int i = 0; i < list.getNumBins(); i++) {
 492
 493                                 //parse out names that are in accnos file
 494                                 string binnames = list.get(i);
 495
 496                                 string newNames = "";
 497                                 while (binnames.find_first_of(',') != -1) {
 498                                         string name = binnames.substr(0,binnames.find_first_of(','));
 499                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 500
 501                                         //if that name is in the .accnos file, add it
 502                                         if (names.count(name) != 0) {  newNames += name + ",";  }
 503                                 }
 504
 505                                 //get last name
 506                                 if (names.count(binnames) != 0) {  newNames += binnames + ",";  }
 507
 508                                 //if there are names in this bin add to new list
 509                                 if (newNames != "") {
 510                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 511                                         newList.push_back(newNames);
 512                                 }
 513                         }
 514
 515                         //print new listvector
 516                         if (newList.getNumBins() != 0) {
 517                                 wroteSomething = true;
 518                                 newList.print(out);
 519                         }
 520
 521                         m->gobble(in);
 522                 }
 523                 in.close();
 524                 out.close();
 525
 526                 if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 527                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 528
 529                 return 0;
 530
 531         }
 532         catch(exception& e) {
 533                 m->errorOut(e, "GetLineageCommand", "readList");
 534                 exit(1);
 535         }
 536 }
 537 //**********************************************************************************************************************
 538 int GetLineageCommand::readName(){
 539         try {
 540                 string thisOutputDir = outputDir;
 541                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 542                 map<string, string> variables;
 543                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
 544         variables["[extension]"] = m->getExtension(namefile);
 545                 string outputFileName = getOutputFileName("name", variables);
 546                 ofstream out;
 547                 m->openOutputFile(outputFileName, out);
 548
 549
 550                 ifstream in;
 551                 m->openInputFile(namefile, in);
 552                 string name, firstCol, secondCol;
 553
 554                 bool wroteSomething = false;
 555
 556
 557                 while(!in.eof()){
 558
 559                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 560
 561                         in >> firstCol;
 562                         in >> secondCol;
 563
 564                         string hold = "";
 565                         if (dups) { hold = secondCol; }
 566
 567                         vector<string> parsedNames;
 568                         m->splitAtComma(secondCol, parsedNames);
 569
 570                         vector<string> validSecond;
 571                         for (int i = 0; i < parsedNames.size(); i++) {
 572                                 if (names.count(parsedNames[i]) != 0) {
 573                                         validSecond.push_back(parsedNames[i]);
 574                                 }
 575                         }
 576
 577                         if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
 578                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 579                                 out << firstCol << '\t' << hold << endl;
 580                                 wroteSomething = true;
 581                         }else {
 582                                 //if the name in the first column is in the set then print it and any other names in second column also in set
 583                                 if (names.count(firstCol) != 0) {
 584
 585                                         wroteSomething = true;
 586
 587                                         out << firstCol << '\t';
 588
 589                                         //you know you have at least one valid second since first column is valid
 590                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 591                                         out << validSecond[validSecond.size()-1] << endl;
 592
 593
 594                                 //make first name in set you come to first column and then add the remaining names to second column
 595                                 }else {
 596                                         //you want part of this row
 597                                         if (validSecond.size() != 0) {
 598
 599                                                 wroteSomething = true;
 600
 601                                                 out << validSecond[0] << '\t';
 602
 603                                                 //you know you have at least one valid second since first column is valid
 604                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 605                                                 out << validSecond[validSecond.size()-1] << endl;
 606                                         }
 607                                 }
 608                         }
 609                         m->gobble(in);
 610                 }
 611                 in.close();
 612                 out.close();
 613
 614                 if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 615                 outputNames.push_back(outputFileName);  outputTypes["name"].push_back(outputFileName);
 616
 617                 return 0;
 618
 619         }
 620         catch(exception& e) {
 621                 m->errorOut(e, "GetLineageCommand", "readName");
 622                 exit(1);
 623         }
 624 }
 625
 626 //**********************************************************************************************************************
 627 int GetLineageCommand::readGroup(){
 628         try {
 629                 string thisOutputDir = outputDir;
 630                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 631                 map<string, string> variables;
 632                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
 633         variables["[extension]"] = m->getExtension(groupfile);
 634                 string outputFileName = getOutputFileName("group", variables);
 635                 ofstream out;
 636                 m->openOutputFile(outputFileName, out);
 637
 638
 639                 ifstream in;
 640                 m->openInputFile(groupfile, in);
 641                 string name, group;
 642
 643                 bool wroteSomething = false;
 644
 645                 while(!in.eof()){
 646
 647                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 648
 649
 650                         in >> name;                             //read from first column
 651                         in >> group;                    //read from second column
 652
 653                         //if this name is in the accnos file
 654                         if (names.count(name) != 0) {
 655                                 wroteSomething = true;
 656
 657                                 out << name << '\t' << group << endl;
 658                         }
 659
 660                         m->gobble(in);
 661                 }
 662                 in.close();
 663                 out.close();
 664
 665                 if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 666                 outputNames.push_back(outputFileName);  outputTypes["group"].push_back(outputFileName);
 667
 668                 return 0;
 669
 670         }
 671         catch(exception& e) {
 672                 m->errorOut(e, "GetLineageCommand", "readGroup");
 673                 exit(1);
 674         }
 675 }
 676 //**********************************************************************************************************************
 677 int GetLineageCommand::readTax(){
 678         try {
 679                 string thisOutputDir = outputDir;
 680                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 681                 map<string, string> variables;
 682                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
 683         variables["[extension]"] = m->getExtension(taxfile);
 684                 string outputFileName = getOutputFileName("taxonomy", variables);
 685                 ofstream out;
 686                 m->openOutputFile(outputFileName, out);
 687
 688                 ifstream in;
 689                 m->openInputFile(taxfile, in);
 690                 string name, tax;
 691
 692                 //bool wroteSomething = false;
 693                 vector<bool> taxonsHasConfidence; taxonsHasConfidence.resize(listOfTaxons.size(), false);
 694                 vector< vector< map<string, float> > > searchTaxons; searchTaxons.resize(listOfTaxons.size());
 695                 vector<string> noConfidenceTaxons; noConfidenceTaxons.resize(listOfTaxons.size(), "");
 696
 697                 for (int i = 0; i < listOfTaxons.size(); i++) {
 698                         noConfidenceTaxons[i] = listOfTaxons[i];
 699                         int hasConPos = listOfTaxons[i].find_first_of('(');
 700                         if (hasConPos != string::npos) {
 701                                 taxonsHasConfidence[i] = true;
 702                                 searchTaxons[i] = getTaxons(listOfTaxons[i]);
 703                                 noConfidenceTaxons[i] = listOfTaxons[i];
 704                                 m->removeConfidences(noConfidenceTaxons[i]);
 705                         }
 706                 }
 707
 708
 709                 while(!in.eof()){
 710
 711                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 712
 713                         in >> name;                             //read from first column
 714                         in >> tax;                      //read from second column
 715
 716             string noQuotesTax = m->removeQuotes(tax);
 717
 718                         for (int j = 0; j < listOfTaxons.size(); j++) {
 719
 720                                 string newtax = noQuotesTax;
 721
 722                                 //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
 723                                 if (!taxonsHasConfidence[j]) {
 724                                         int hasConfidences = noQuotesTax.find_first_of('(');
 725                                         if (hasConfidences != string::npos) {
 726                                                 newtax = noQuotesTax;
 727                                                 m->removeConfidences(newtax);
 728                                         }
 729
 730                                         int pos = newtax.find(noConfidenceTaxons[j]);
 731
 732                                         if (pos != string::npos) { //this sequence contains the taxon the user wants
 733                                                 names.insert(name);
 734                                                 out << name << '\t' << tax << endl;
 735                                                 //since you belong to at least one of the taxons we want you are included so no need to search for other
 736                                                 break;
 737                                         }
 738                                 }else{//if listOfTaxons[i] has them and you don't them remove taxons
 739                                         int hasConfidences = noQuotesTax.find_first_of('(');
 740                                         if (hasConfidences == string::npos) {
 741
 742                                                 int pos = newtax.find(noConfidenceTaxons[j]);
 743
 744                                                 if (pos != string::npos) { //this sequence contains the taxon the user wants
 745                                                         names.insert(name);
 746                                                         out << name << '\t' << tax << endl;
 747                                                         //since you belong to at least one of the taxons we want you are included so no need to search for other
 748                                                         break;
 749                                                 }
 750                                         }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
 751                                                 //first remove confidences from both and see if the taxonomy exists
 752
 753                                                 string noNewTax = noQuotesTax;
 754                                                 int hasConfidences = noQuotesTax.find_first_of('(');
 755                                                 if (hasConfidences != string::npos) {
 756                                                         noNewTax = noQuotesTax;
 757                                                         m->removeConfidences(noNewTax);
 758                                                 }
 759
 760                                                 int pos = noNewTax.find(noConfidenceTaxons[j]);
 761
 762                                                 if (pos != string::npos) { //if yes, then are the confidences okay
 763
 764                                                         bool good = true;
 765                                                         vector< map<string, float> > usersTaxon = getTaxons(newtax);
 766
 767                                                         //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
 768                                                         //we want to "line them up", so we will find the the index where the searchstring starts
 769                                                         int index = 0;
 770                                                         for (int i = 0; i < usersTaxon.size(); i++) {
 771
 772                                                                 if (usersTaxon[i].begin()->first == searchTaxons[j][0].begin()->first) {
 773                                                                         index = i;
 774                                                                         int spot = 0;
 775                                                                         bool goodspot = true;
 776                                                                         //is this really the start, or are we dealing with a taxon of the same name?
 777                                                                         while ((spot < searchTaxons[j].size()) && ((i+spot) < usersTaxon.size())) {
 778                                                                                 if (usersTaxon[i+spot].begin()->first != searchTaxons[j][spot].begin()->first) { goodspot = false; break; }
 779                                                                                 else { spot++; }
 780                                                                         }
 781
 782                                                                         if (goodspot) { break; }
 783                                                                 }
 784                                                         }
 785
 786                                                         for (int i = 0; i < searchTaxons[j].size(); i++) {
 787
 788                                                                 if ((i+index) < usersTaxon.size()) { //just in case, should never be false
 789                                                                         if (usersTaxon[i+index].begin()->second < searchTaxons[j][i].begin()->second) { //is the users cutoff less than the search taxons
 790                                                                                 good = false;
 791                                                                                 break;
 792                                                                         }
 793                                                                 }else {
 794                                                                         good = false;
 795                                                                         break;
 796                                                                 }
 797                                                         }
 798
 799                                                         //passed the test so add you
 800                                                         if (good) {
 801                                                                 names.insert(name);
 802                                                                 out << name << '\t' << tax << endl;
 803                                                                 break;
 804                                                         }
 805                                                 }
 806                                         }
 807                                 }
 808
 809                         }
 810
 811                         m->gobble(in);
 812                 }
 813                 in.close();
 814                 out.close();
 815
 816                 if (names.size() == 0) { m->mothurOut("Your taxonomy file does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 817                 outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
 818
 819                 return 0;
 820
 821         }
 822         catch(exception& e) {
 823                 m->errorOut(e, "GetLineageCommand", "readTax");
 824                 exit(1);
 825         }
 826 }
 827 /**************************************************************************************************/
 828 vector< map<string, float> > GetLineageCommand::getTaxons(string tax) {
 829         try {
 830
 831                 vector< map<string, float> > t;
 832                 string taxon = "";
 833                 int taxLength = tax.length();
 834
 835                 for(int i=0;i<taxLength;i++){
 836                         if(tax[i] == ';'){
 837
 838                                 int openParen = taxon.find_last_of('(');
 839                                 int closeParen = taxon.find_last_of(')');
 840
 841                                 string newtaxon, confidence;
 842                                 if ((openParen != string::npos) && (closeParen != string::npos)) {
 843                     string confidenceScore = taxon.substr(openParen+1, (closeParen-(openParen+1)));
 844                     if (m->isNumeric1(confidenceScore)) {  //its a confidence
 845                         newtaxon = taxon.substr(0, openParen); //rip off confidence
 846                         confidence = taxon.substr((openParen+1), (closeParen-openParen-1));
 847                     }else { //its part of the taxon
 848                         newtaxon = taxon;
 849                         confidence = "0";
 850                     }
 851                                 }else{
 852                                         newtaxon = taxon;
 853                                         confidence = "0";
 854                                 }
 855                                 float con = 0;
 856                                 convert(confidence, con);
 857
 858                                 map<string, float> temp;
 859                                 temp[newtaxon] = con;
 860
 861                                 t.push_back(temp);
 862                                 taxon = "";
 863                         }
 864                         else{
 865                                 taxon += tax[i];
 866
 867                         }
 868                 }
 869
 870                 return t;
 871         }
 872         catch(exception& e) {
 873                 m->errorOut(e, "GetLineageCommand", "getTaxons");
 874                 exit(1);
 875         }
 876 }
 877 //**********************************************************************************************************************
 878 //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
 879 int GetLineageCommand::readAlign(){
 880         try {
 881                 string thisOutputDir = outputDir;
 882                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 883         map<string, string> variables;
 884                 variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(alignfile));
 885         variables["[extension]"] = m->getExtension(alignfile);
 886                 string outputFileName = getOutputFileName("alignreport", variables);
 887
 888                 ofstream out;
 889                 m->openOutputFile(outputFileName, out);
 890
 891
 892                 ifstream in;
 893                 m->openInputFile(alignfile, in);
 894                 string name, junk;
 895
 896                 bool wroteSomething = false;
 897
 898                 //read column headers
 899                 for (int i = 0; i < 16; i++) {
 900                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 901                         else                    {       break;                  }
 902                 }
 903                 out << endl;
 904
 905                 while(!in.eof()){
 906
 907                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 908
 909
 910                         in >> name;                             //read from first column
 911
 912                         //if this name is in the accnos file
 913                         if (names.count(name) != 0) {
 914                                 wroteSomething = true;
 915
 916                                 out << name << '\t';
 917
 918                                 //read rest
 919                                 for (int i = 0; i < 15; i++) {
 920                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 921                                         else                    {       break;                  }
 922                                 }
 923                                 out << endl;
 924
 925                         }else {//still read just don't do anything with it
 926                                 //read rest
 927                                 for (int i = 0; i < 15; i++) {
 928                                         if (!in.eof())  {       in >> junk;             }
 929                                         else                    {       break;                  }
 930                                 }
 931                         }
 932
 933                         m->gobble(in);
 934                 }
 935                 in.close();
 936                 out.close();
 937
 938                 if (wroteSomething == false) { m->mothurOut("Your file contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 939                 outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
 940
 941                 return 0;
 942
 943         }
 944         catch(exception& e) {
 945                 m->errorOut(e, "GetLineageCommand", "readAlign");
 946                 exit(1);
 947         }
 948 }
 949 //**********************************************************************************************************************
 950
 951
 952
 953