removelineagecommand.cpp

   1 /*
   2  *  removelineagecommand.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 "removelineagecommand.h"
  11 #include "sequence.hpp"
  12 #include "listvector.hpp"
  13
  14 //**********************************************************************************************************************
  15 vector<string> RemoveLineageCommand::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, "RemoveLineageCommand", "setParameters");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 string RemoveLineageCommand::getHelpString(){
  39         try {
  40                 string helpString = "";
  41                 helpString += "The remove.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 not from the taxon you requested to be removed.\n";
  43                 helpString += "The remove.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 remove, and is required.\n";
  46                 helpString += "You may enter your taxons with confidence scores, doing so will remove only those sequences that belong to the taxonomy and whose cofidence scores fall below the scores you give.\n";
  47                 helpString += "If they belong to the taxonomy and have confidences above those you provide the sequence will not be removed.\n";
  48                 helpString += "The remove.lineage command should be in the following format: remove.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n";
  49                 helpString += "Example remove.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 remove.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, "RemoveLineageCommand", "getHelpString");
  57                 exit(1);
  58         }
  59 }
  60 //**********************************************************************************************************************
  61 string RemoveLineageCommand::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, "RemoveLineageCommand", "getOutputFileNameTag");
  82                 exit(1);
  83         }
  84 }
  85 //**********************************************************************************************************************
  86 RemoveLineageCommand::RemoveLineageCommand(){
  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, "RemoveLineageCommand", "RemoveLineageCommand");
 100                 exit(1);
 101         }
 102 }
 103 //**********************************************************************************************************************
 104 RemoveLineageCommand::RemoveLineageCommand(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 ((usedDups != "") && (namefile == "")) {  m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine();  abort = true; }
 246
 247                         if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
 248                                 vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
 249                                 parser.getNameFile(files);
 250                         }
 251
 252                 }
 253
 254         }
 255         catch(exception& e) {
 256                 m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand");
 257                 exit(1);
 258         }
 259 }
 260 //**********************************************************************************************************************
 261
 262 int RemoveLineageCommand::execute(){
 263         try {
 264
 265                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 266
 267                 if (m->control_pressed) { return 0; }
 268
 269                 //read through the correct file and output lines you want to keep
 270                 if (taxfile != "")                      {               readTax();              }  //fills the set of names to remove
 271                 if (namefile != "")                     {               readName();             }
 272                 if (fastafile != "")            {               readFasta();    }
 273                 if (groupfile != "")            {               readGroup();    }
 274                 if (alignfile != "")            {               readAlign();    }
 275                 if (listfile != "")                     {               readList();             }
 276
 277
 278                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
 279
 280                 if (outputNames.size() != 0) {
 281                         m->mothurOutEndLine();
 282                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 283                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 284                         m->mothurOutEndLine();
 285
 286                         //set fasta file as new current fastafile
 287                         string current = "";
 288                         itTypes = outputTypes.find("fasta");
 289                         if (itTypes != outputTypes.end()) {
 290                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 291                         }
 292
 293                         itTypes = outputTypes.find("name");
 294                         if (itTypes != outputTypes.end()) {
 295                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 296                         }
 297
 298                         itTypes = outputTypes.find("group");
 299                         if (itTypes != outputTypes.end()) {
 300                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 301                         }
 302
 303                         itTypes = outputTypes.find("list");
 304                         if (itTypes != outputTypes.end()) {
 305                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 306                         }
 307
 308                         itTypes = outputTypes.find("taxonomy");
 309                         if (itTypes != outputTypes.end()) {
 310                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 311                         }
 312                 }
 313
 314                 return 0;
 315         }
 316
 317         catch(exception& e) {
 318                 m->errorOut(e, "RemoveLineageCommand", "execute");
 319                 exit(1);
 320         }
 321 }
 322
 323 //**********************************************************************************************************************
 324 int RemoveLineageCommand::readFasta(){
 325         try {
 326                 string thisOutputDir = outputDir;
 327                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 328                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
 329                 ofstream out;
 330                 m->openOutputFile(outputFileName, out);
 331
 332                 ifstream in;
 333                 m->openInputFile(fastafile, in);
 334                 string name;
 335
 336                 bool wroteSomething = false;
 337
 338                 while(!in.eof()){
 339                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 340
 341                         Sequence currSeq(in);
 342                         name = currSeq.getName();
 343
 344                         if (name != "") {
 345                                 //if this name is in the accnos file
 346                                 if (names.count(name) == 0) {
 347                                         wroteSomething = true;
 348
 349                                         currSeq.printSequence(out);
 350                                 }
 351                         }
 352                         m->gobble(in);
 353                 }
 354                 in.close();
 355                 out.close();
 356
 357                 if (wroteSomething == false) {  m->mothurOut("Your fasta file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 358                 outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
 359
 360                 return 0;
 361
 362         }
 363         catch(exception& e) {
 364                 m->errorOut(e, "RemoveLineageCommand", "readFasta");
 365                 exit(1);
 366         }
 367 }
 368 //**********************************************************************************************************************
 369 int RemoveLineageCommand::readList(){
 370         try {
 371                 string thisOutputDir = outputDir;
 372                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 373                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
 374                 ofstream out;
 375                 m->openOutputFile(outputFileName, out);
 376
 377                 ifstream in;
 378                 m->openInputFile(listfile, in);
 379
 380                 bool wroteSomething = false;
 381
 382                 while(!in.eof()){
 383                         //read in list vector
 384                         ListVector list(in);
 385
 386                         //make a new list vector
 387                         ListVector newList;
 388                         newList.setLabel(list.getLabel());
 389
 390                         //for each bin
 391                         for (int i = 0; i < list.getNumBins(); i++) {
 392                                 if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 393
 394                                 //parse out names that are in accnos file
 395                                 string binnames = list.get(i);
 396
 397                                 string newNames = "";
 398                                 while (binnames.find_first_of(',') != -1) {
 399                                         string name = binnames.substr(0,binnames.find_first_of(','));
 400                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 401
 402                                         //if that name is in the .accnos file, add it
 403                                         if (names.count(name) == 0) {  newNames += name + ",";  }
 404                                 }
 405
 406                                 //get last name
 407                                 if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
 408
 409                                 //if there are names in this bin add to new list
 410                                 if (newNames != "") {
 411                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 412                                         newList.push_back(newNames);
 413                                 }
 414                         }
 415
 416                         //print new listvector
 417                         if (newList.getNumBins() != 0) {
 418                                 wroteSomething = true;
 419                                 newList.print(out);
 420                         }
 421
 422                         m->gobble(in);
 423                 }
 424                 in.close();
 425                 out.close();
 426
 427                 if (wroteSomething == false) {  m->mothurOut("Your list file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 428                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 429
 430                 return 0;
 431
 432         }
 433         catch(exception& e) {
 434                 m->errorOut(e, "RemoveLineageCommand", "readList");
 435                 exit(1);
 436         }
 437 }
 438 //**********************************************************************************************************************
 439 int RemoveLineageCommand::readName(){
 440         try {
 441                 string thisOutputDir = outputDir;
 442                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 443                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
 444                 ofstream out;
 445                 m->openOutputFile(outputFileName, out);
 446
 447                 ifstream in;
 448                 m->openInputFile(namefile, in);
 449                 string name, firstCol, secondCol;
 450
 451                 bool wroteSomething = false;
 452
 453                 while(!in.eof()){
 454                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 455
 456                         in >> firstCol;
 457                         in >> secondCol;
 458
 459                         vector<string> parsedNames;
 460                         m->splitAtComma(secondCol, parsedNames);
 461
 462                         vector<string> validSecond;  validSecond.clear();
 463                         for (int i = 0; i < parsedNames.size(); i++) {
 464                                 if (names.count(parsedNames[i]) == 0) {
 465                                         validSecond.push_back(parsedNames[i]);
 466                                 }
 467                         }
 468
 469                         if ((dups) && (validSecond.size() != parsedNames.size())) {  //if dups is true and we want to get rid of anyone, get rid of everyone
 470                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 471                         }else {
 472                                         //if the name in the first column is in the set then print it and any other names in second column also in set
 473                                 if (names.count(firstCol) == 0) {
 474
 475                                         wroteSomething = true;
 476
 477                                         out << firstCol << '\t';
 478
 479                                         //you know you have at least one valid second since first column is valid
 480                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 481                                         out << validSecond[validSecond.size()-1] << endl;
 482
 483                                         //make first name in set you come to first column and then add the remaining names to second column
 484                                 }else {
 485
 486                                         //you want part of this row
 487                                         if (validSecond.size() != 0) {
 488
 489                                                 wroteSomething = true;
 490
 491                                                 out << validSecond[0] << '\t';
 492
 493                                                 //you know you have at least one valid second since first column is valid
 494                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 495                                                 out << validSecond[validSecond.size()-1] << endl;
 496                                         }
 497                                 }
 498                         }
 499                         m->gobble(in);
 500                 }
 501                 in.close();
 502                 out.close();
 503
 504                 if (wroteSomething == false) {  m->mothurOut("Your name file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 505                 outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
 506
 507                 return 0;
 508         }
 509         catch(exception& e) {
 510                 m->errorOut(e, "RemoveLineageCommand", "readName");
 511                 exit(1);
 512         }
 513 }
 514
 515 //**********************************************************************************************************************
 516 int RemoveLineageCommand::readGroup(){
 517         try {
 518                 string thisOutputDir = outputDir;
 519                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 520                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
 521                 ofstream out;
 522                 m->openOutputFile(outputFileName, out);
 523
 524                 ifstream in;
 525                 m->openInputFile(groupfile, in);
 526                 string name, group;
 527
 528                 bool wroteSomething = false;
 529
 530                 while(!in.eof()){
 531                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 532
 533                         in >> name;                             //read from first column
 534                         in >> group;                    //read from second column
 535
 536                         //if this name is in the accnos file
 537                         if (names.count(name) == 0) {
 538                                 wroteSomething = true;
 539                                 out << name << '\t' << group << endl;
 540                         }
 541
 542                         m->gobble(in);
 543                 }
 544                 in.close();
 545                 out.close();
 546
 547                 if (wroteSomething == false) {  m->mothurOut("Your group file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 548                 outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName);
 549
 550                 return 0;
 551         }
 552         catch(exception& e) {
 553                 m->errorOut(e, "RemoveLineageCommand", "readGroup");
 554                 exit(1);
 555         }
 556 }
 557 //**********************************************************************************************************************
 558 int RemoveLineageCommand::readTax(){
 559         try {
 560                 string thisOutputDir = outputDir;
 561                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 562                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
 563                 ofstream out;
 564                 m->openOutputFile(outputFileName, out);
 565
 566                 ifstream in;
 567                 m->openInputFile(taxfile, in);
 568                 string name, tax;
 569
 570                 bool wroteSomething = false;
 571
 572                 vector<bool> taxonsHasConfidence; taxonsHasConfidence.resize(listOfTaxons.size(), false);
 573                 vector< vector< map<string, float> > > searchTaxons; searchTaxons.resize(listOfTaxons.size());
 574                 vector<string> noConfidenceTaxons; noConfidenceTaxons.resize(listOfTaxons.size(), "");
 575
 576                 for (int i = 0; i < listOfTaxons.size(); i++) {
 577                         noConfidenceTaxons[i] = listOfTaxons[i];
 578                         int hasConPos = listOfTaxons[i].find_first_of('(');
 579                         if (hasConPos != string::npos) {
 580                                 taxonsHasConfidence[i] = true;
 581                                 searchTaxons[i] = getTaxons(listOfTaxons[i]);
 582                                 noConfidenceTaxons[i] = listOfTaxons[i];
 583                                 m->removeConfidences(noConfidenceTaxons[i]);
 584                         }
 585                 }
 586
 587
 588                 while(!in.eof()){
 589
 590                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 591
 592                         in >> name;                             //read from first column
 593                         in >> tax;                      //read from second column
 594
 595                         bool remove = false;
 596
 597                         for (int j = 0; j < listOfTaxons.size(); j++) {
 598                                 string newtax = tax;
 599
 600                                 //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
 601                                 if (!taxonsHasConfidence[j]) {
 602
 603                                         int hasConfidences = tax.find_first_of('(');
 604                                         if (hasConfidences != string::npos) {
 605                                                 newtax = tax;
 606                                                 m->removeConfidences(newtax);
 607                                         }
 608
 609                                         int pos = newtax.find(noConfidenceTaxons[j]);
 610
 611                                         if (pos == string::npos) {
 612                                                 //wroteSomething = true;
 613                                                 //out << name << '\t' << tax << endl;
 614                                         }else{ //this sequence contains the taxon the user wants to remove
 615                                                 names.insert(name);
 616                                                 remove=true; break;
 617                                         }
 618
 619                                 }else{//if taxons has them and you don't them remove taxons
 620                                         int hasConfidences = tax.find_first_of('(');
 621                                         if (hasConfidences == string::npos) {
 622
 623                                                 int pos = newtax.find(noConfidenceTaxons[j]);
 624
 625                                                 if (pos == string::npos) {
 626                                                         //wroteSomething = true;
 627                                                         //out << name << '\t' << tax << endl;
 628                                                 }else{ //this sequence contains the taxon the user wants to remove
 629                                                         names.insert(name);
 630                                                         remove=true; break;
 631                                                 }
 632                                         }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
 633                                                 //first remove confidences from both and see if the taxonomy exists
 634
 635                                                 string noNewTax = tax;
 636                                                 int hasConfidences = tax.find_first_of('(');
 637                                                 if (hasConfidences != string::npos) {
 638                                                         noNewTax = tax;
 639                                                         m->removeConfidences(noNewTax);
 640                                                 }
 641
 642                                                 int pos = noNewTax.find(noConfidenceTaxons[j]);
 643
 644                                                 if (pos != string::npos) { //if yes, then are the confidences okay
 645
 646                                                         vector< map<string, float> > usersTaxon = getTaxons(newtax);
 647
 648                                                         //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
 649                                                         //we want to "line them up", so we will find the the index where the searchstring starts
 650                                                         int index = 0;
 651                                                         for (int i = 0; i < usersTaxon.size(); i++) {
 652
 653                                                                 if (usersTaxon[i].begin()->first == searchTaxons[j][0].begin()->first) {
 654                                                                         index = i;
 655                                                                         int spot = 0;
 656                                                                         bool goodspot = true;
 657                                                                         //is this really the start, or are we dealing with a taxon of the same name?
 658                                                                         while ((spot < searchTaxons[j].size()) && ((i+spot) < usersTaxon.size())) {
 659                                                                                 if (usersTaxon[i+spot].begin()->first != searchTaxons[j][spot].begin()->first) { goodspot = false; break; }
 660                                                                                 else { spot++; }
 661                                                                         }
 662
 663                                                                         if (goodspot) { break; }
 664                                                                 }
 665                                                         }
 666
 667                                                         for (int i = 0; i < searchTaxons[j].size(); i++) {
 668
 669                                                                 if ((i+index) < usersTaxon.size()) { //just in case, should never be false
 670                                                                         if (usersTaxon[i+index].begin()->second < searchTaxons[j][i].begin()->second) { //is the users cutoff less than the search taxons
 671                                                                                 remove = true;
 672                                                                                 break;
 673                                                                         }
 674                                                                 }else {
 675                                                                         remove = true;
 676                                                                         break;
 677                                                                 }
 678                                                         }
 679
 680                                                         //passed the test so remove you
 681                                                         if (remove) {
 682                                                                 names.insert(name);
 683                                                                 remove=true; break;
 684                                                         }else {
 685                                                                 //wroteSomething = true;
 686                                                                 //out << name << '\t' << tax << endl;
 687                                                         }
 688                                                 }else {
 689                                                         //wroteSomething = true;
 690                                                         //out << name << '\t' << tax << endl;
 691                                                 }
 692                                         }
 693                                 }
 694
 695                         }
 696
 697                         if (!remove) {  wroteSomething = true; out << name << '\t' << tax << endl; }
 698                         m->gobble(in);
 699                 }
 700                 in.close();
 701                 out.close();
 702
 703                 if (!wroteSomething) { m->mothurOut("Your taxonomy file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 704                 outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
 705
 706                 return 0;
 707
 708         }
 709         catch(exception& e) {
 710                 m->errorOut(e, "RemoveLineageCommand", "readTax");
 711                 exit(1);
 712         }
 713 }
 714 /**************************************************************************************************/
 715 vector< map<string, float> > RemoveLineageCommand::getTaxons(string tax) {
 716         try {
 717
 718                 vector< map<string, float> > t;
 719                 string taxon = "";
 720                 int taxLength = tax.length();
 721                 for(int i=0;i<taxLength;i++){
 722                         if(tax[i] == ';'){
 723
 724                                 int openParen = taxon.find_first_of('(');
 725                                 int closeParen = taxon.find_last_of(')');
 726
 727                                 string newtaxon, confidence;
 728                                 if ((openParen != string::npos) && (closeParen != string::npos)) {
 729                                         newtaxon = taxon.substr(0, openParen); //rip off confidence
 730                                         confidence = taxon.substr((openParen+1), (closeParen-openParen-1));
 731                                 }else{
 732                                         newtaxon = taxon;
 733                                         confidence = "0";
 734                                 }
 735                                 float con = 0;
 736                                 convert(confidence, con);
 737
 738                                 map<string, float> temp;
 739                                 temp[newtaxon] = con;
 740                                 t.push_back(temp);
 741
 742                                 taxon = "";
 743                         }
 744                         else{
 745                                 taxon += tax[i];
 746                         }
 747                 }
 748
 749                 return t;
 750         }
 751         catch(exception& e) {
 752                 m->errorOut(e, "RemoveLineageCommand", "getTaxons");
 753                 exit(1);
 754         }
 755 }
 756 //**********************************************************************************************************************
 757 //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
 758 int RemoveLineageCommand::readAlign(){
 759         try {
 760                 string thisOutputDir = outputDir;
 761                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 762                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + getOutputFileNameTag("alignreport");
 763
 764                 ofstream out;
 765                 m->openOutputFile(outputFileName, out);
 766
 767                 ifstream in;
 768                 m->openInputFile(alignfile, in);
 769                 string name, junk;
 770
 771                 bool wroteSomething = false;
 772
 773                 //read column headers
 774                 for (int i = 0; i < 16; i++) {
 775                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 776                         else                    {       break;                  }
 777                 }
 778                 out << endl;
 779
 780                 while(!in.eof()){
 781                         if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 782
 783                         in >> name;                             //read from first column
 784
 785                         //if this name is in the accnos file
 786                         if (names.count(name) == 0) {
 787                                 wroteSomething = true;
 788
 789                                 out << name << '\t';
 790
 791                                 //read rest
 792                                 for (int i = 0; i < 15; i++) {
 793                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 794                                         else                    {       break;                  }
 795                                 }
 796                                 out << endl;
 797
 798                         }else {//still read just don't do anything with it
 799
 800                                 //read rest
 801                                 for (int i = 0; i < 15; i++) {
 802                                         if (!in.eof())  {       in >> junk;             }
 803                                         else                    {       break;                  }
 804                                 }
 805                         }
 806
 807                         m->gobble(in);
 808                 }
 809                 in.close();
 810                 out.close();
 811
 812                 if (wroteSomething == false) {  m->mothurOut("Your align file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
 813                 outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
 814
 815                 return 0;
 816
 817         }
 818         catch(exception& e) {
 819                 m->errorOut(e, "RemoveLineageCommand", "readAlign");
 820                 exit(1);
 821         }
 822 }
 823 //**********************************************************************************************************************
 824