getlineagecommand.cpp

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