getseqscommand.cpp

   1 /*
   2  *  getseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 7/8/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "getseqscommand.h"
  11 #include "sequence.hpp"
  12 #include "listvector.hpp"
  13
  14 //**********************************************************************************************************************
  15 vector<string> GetSeqsCommand::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,false); parameters.push_back(ptaxonomy);
  22                 CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);
  23                 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pqfile);
  24                 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos);
  25                 CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
  26                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  27                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  28                 CommandParameter paccnos2("accnos2", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos2);
  29
  30                 vector<string> myArray;
  31                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  32                 return myArray;
  33         }
  34         catch(exception& e) {
  35                 m->errorOut(e, "GetSeqsCommand", "setParameters");
  36                 exit(1);
  37         }
  38 }
  39 //**********************************************************************************************************************
  40 string GetSeqsCommand::getHelpString(){
  41         try {
  42                 string helpString = "";
  43                 helpString += "The get.seqs command reads an .accnos file and any of the following file types: fasta, name, group, list, taxonomy, quality or alignreport file.\n";
  44                 helpString += "It outputs a file containing only the sequences in the .accnos file.\n";
  45                 helpString += "The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups.  You must provide accnos unless you have a valid current accnos file, and at least one of the other parameters.\n";
  46                 helpString += "The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n";
  47                 helpString += "The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n";
  48                 helpString += "Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n";
  49                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  50                 return helpString;
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "GetSeqsCommand", "getHelpString");
  54                 exit(1);
  55         }
  56 }
  57
  58 //**********************************************************************************************************************
  59 GetSeqsCommand::GetSeqsCommand(){
  60         try {
  61                 abort = true; calledHelp = true;
  62                 setParameters();
  63                 vector<string> tempOutNames;
  64                 outputTypes["fasta"] = tempOutNames;
  65                 outputTypes["taxonomy"] = tempOutNames;
  66                 outputTypes["name"] = tempOutNames;
  67                 outputTypes["group"] = tempOutNames;
  68                 outputTypes["alignreport"] = tempOutNames;
  69                 outputTypes["list"] = tempOutNames;
  70                 outputTypes["qfile"] = tempOutNames;
  71                 outputTypes["accnosreport"] = tempOutNames;
  72         }
  73         catch(exception& e) {
  74                 m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
  75                 exit(1);
  76         }
  77 }
  78 //**********************************************************************************************************************
  79 GetSeqsCommand::GetSeqsCommand(string option)  {
  80         try {
  81                 abort = false; calledHelp = false;
  82
  83                 //allow user to run help
  84                 if(option == "help") { help(); abort = true; calledHelp = true; }
  85                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  86
  87                 else {
  88                         vector<string> myArray = setParameters();
  89
  90                         OptionParser parser(option);
  91                         map<string,string> parameters = parser.getParameters();
  92
  93                         ValidParameters validParameter;
  94                         map<string,string>::iterator it;
  95
  96                         //check to make sure all parameters are valid for command
  97                         for (it = parameters.begin(); it != parameters.end(); it++) {
  98                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  99                         }
 100
 101                         //initialize outputTypes
 102                         vector<string> tempOutNames;
 103                         outputTypes["fasta"] = tempOutNames;
 104                         outputTypes["taxonomy"] = tempOutNames;
 105                         outputTypes["name"] = tempOutNames;
 106                         outputTypes["group"] = tempOutNames;
 107                         outputTypes["alignreport"] = tempOutNames;
 108                         outputTypes["list"] = tempOutNames;
 109                         outputTypes["qfile"] = tempOutNames;
 110                         outputTypes["accnosreport"] = tempOutNames;
 111
 112                         //if the user changes the output directory command factory will send this info to us in the output parameter
 113                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 114
 115                         //if the user changes the input directory command factory will send this info to us in the output parameter
 116                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 117                         if (inputDir == "not found"){   inputDir = "";          }
 118                         else {
 119                                 string path;
 120                                 it = parameters.find("alignreport");
 121                                 //user has given a template file
 122                                 if(it != parameters.end()){
 123                                         path = m->hasPath(it->second);
 124                                         //if the user has not given a path then, add inputdir. else leave path alone.
 125                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
 126                                 }
 127
 128                                 it = parameters.find("fasta");
 129                                 //user has given a template file
 130                                 if(it != parameters.end()){
 131                                         path = m->hasPath(it->second);
 132                                         //if the user has not given a path then, add inputdir. else leave path alone.
 133                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 134                                 }
 135
 136                                 it = parameters.find("accnos");
 137                                 //user has given a template file
 138                                 if(it != parameters.end()){
 139                                         path = m->hasPath(it->second);
 140                                         //if the user has not given a path then, add inputdir. else leave path alone.
 141                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 142                                 }
 143
 144                                 it = parameters.find("accnos2");
 145                                 //user has given a template file
 146                                 if(it != parameters.end()){
 147                                         path = m->hasPath(it->second);
 148                                         //if the user has not given a path then, add inputdir. else leave path alone.
 149                                         if (path == "") {       parameters["accnos2"] = inputDir + it->second;          }
 150                                 }
 151
 152                                 it = parameters.find("list");
 153                                 //user has given a template file
 154                                 if(it != parameters.end()){
 155                                         path = m->hasPath(it->second);
 156                                         //if the user has not given a path then, add inputdir. else leave path alone.
 157                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 158                                 }
 159
 160                                 it = parameters.find("name");
 161                                 //user has given a template file
 162                                 if(it != parameters.end()){
 163                                         path = m->hasPath(it->second);
 164                                         //if the user has not given a path then, add inputdir. else leave path alone.
 165                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 166                                 }
 167
 168                                 it = parameters.find("group");
 169                                 //user has given a template file
 170                                 if(it != parameters.end()){
 171                                         path = m->hasPath(it->second);
 172                                         //if the user has not given a path then, add inputdir. else leave path alone.
 173                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 174                                 }
 175
 176                                 it = parameters.find("taxonomy");
 177                                 //user has given a template file
 178                                 if(it != parameters.end()){
 179                                         path = m->hasPath(it->second);
 180                                         //if the user has not given a path then, add inputdir. else leave path alone.
 181                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 182                                 }
 183
 184                                 it = parameters.find("qfile");
 185                                 //user has given a template file
 186                                 if(it != parameters.end()){
 187                                         path = m->hasPath(it->second);
 188                                         //if the user has not given a path then, add inputdir. else leave path alone.
 189                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 190                                 }
 191                         }
 192
 193
 194                         //check for required parameters
 195                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 196                         if (accnosfile == "not open") { abort = true; }
 197                         else if (accnosfile == "not found") {
 198                                 accnosfile = m->getAccnosFile();
 199                                 if (accnosfile != "") {  m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); }
 200                                 else {
 201                                         m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine();
 202                                         abort = true;
 203                                 }
 204                         }else { m->setAccnosFile(accnosfile); }
 205
 206                         if (accnosfile2 == "not found") { accnosfile2 = ""; }
 207
 208                         fastafile = validParameter.validFile(parameters, "fasta", true);
 209                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 210                         else if (fastafile == "not found") {  fastafile = "";  }
 211                         else { m->setFastaFile(fastafile); }
 212
 213                         namefile = validParameter.validFile(parameters, "name", true);
 214                         if (namefile == "not open") { namefile = ""; abort = true; }
 215                         else if (namefile == "not found") {  namefile = "";  }
 216                         else { m->setNameFile(namefile); }
 217
 218                         groupfile = validParameter.validFile(parameters, "group", true);
 219                         if (groupfile == "not open") { abort = true; }
 220                         else if (groupfile == "not found") {  groupfile = "";  }
 221                         else { m->setGroupFile(groupfile); }
 222
 223                         alignfile = validParameter.validFile(parameters, "alignreport", true);
 224                         if (alignfile == "not open") { abort = true; }
 225                         else if (alignfile == "not found") {  alignfile = "";  }
 226
 227                         listfile = validParameter.validFile(parameters, "list", true);
 228                         if (listfile == "not open") { abort = true; }
 229                         else if (listfile == "not found") {  listfile = "";  }
 230                         else { m->setListFile(listfile); }
 231
 232                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 233                         if (taxfile == "not open") { taxfile = ""; abort = true; }
 234                         else if (taxfile == "not found") {  taxfile = "";  }
 235                         else { m->setTaxonomyFile(taxfile); }
 236
 237                         qualfile = validParameter.validFile(parameters, "qfile", true);
 238                         if (qualfile == "not open") { abort = true; }
 239                         else if (qualfile == "not found") {  qualfile = "";  }
 240                         else { m->setQualFile(qualfile); }
 241
 242                         accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
 243                         if (accnosfile2 == "not open") { abort = true; }
 244                         else if (accnosfile2 == "not found") {  accnosfile2 = "";  }
 245
 246
 247                         string usedDups = "true";
 248                         string temp = validParameter.validFile(parameters, "dups", false);      if (temp == "not found") { temp = "true"; usedDups = ""; }
 249                         dups = m->isTrue(temp);
 250
 251                         if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == "") && (accnosfile2 == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy, quality or listfile."); m->mothurOutEndLine(); abort = true; }
 252
 253                         if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
 254                                 vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
 255                                 parser.getNameFile(files);
 256                         }
 257                 }
 258
 259         }
 260         catch(exception& e) {
 261                 m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
 262                 exit(1);
 263         }
 264 }
 265 //**********************************************************************************************************************
 266
 267 int GetSeqsCommand::execute(){
 268         try {
 269
 270                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 271
 272                 //get names you want to keep
 273                 readAccnos();
 274
 275                 if (m->control_pressed) { return 0; }
 276
 277                 //read through the correct file and output lines you want to keep
 278                 if (namefile != "")                     {               readName();                     }
 279                 if (fastafile != "")            {               readFasta();            }
 280                 if (groupfile != "")            {               readGroup();            }
 281                 if (alignfile != "")            {               readAlign();            }
 282                 if (listfile != "")                     {               readList();                     }
 283                 if (taxfile != "")                      {               readTax();                      }
 284                 if (qualfile != "")                     {               readQual();                     }
 285                 if (accnosfile2 != "")          {               compareAccnos();        }
 286
 287         if (m->debug) { runSanityCheck(); }
 288
 289                 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);  } return 0; }
 290
 291
 292                 if (outputNames.size() != 0) {
 293                         m->mothurOutEndLine();
 294                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 295                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 296                         m->mothurOutEndLine();
 297
 298                         //set fasta file as new current fastafile
 299                         string current = "";
 300                         itTypes = outputTypes.find("fasta");
 301                         if (itTypes != outputTypes.end()) {
 302                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 303                         }
 304
 305                         itTypes = outputTypes.find("name");
 306                         if (itTypes != outputTypes.end()) {
 307                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 308                         }
 309
 310                         itTypes = outputTypes.find("group");
 311                         if (itTypes != outputTypes.end()) {
 312                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 313                         }
 314
 315                         itTypes = outputTypes.find("list");
 316                         if (itTypes != outputTypes.end()) {
 317                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 318                         }
 319
 320                         itTypes = outputTypes.find("taxonomy");
 321                         if (itTypes != outputTypes.end()) {
 322                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 323                         }
 324
 325                         itTypes = outputTypes.find("qfile");
 326                         if (itTypes != outputTypes.end()) {
 327                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 328                         }
 329
 330                 }
 331
 332                 return 0;
 333         }
 334
 335         catch(exception& e) {
 336                 m->errorOut(e, "GetSeqsCommand", "execute");
 337                 exit(1);
 338         }
 339 }
 340
 341 //**********************************************************************************************************************
 342 int GetSeqsCommand::readFasta(){
 343         try {
 344                 string thisOutputDir = outputDir;
 345                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 346                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" +  m->getExtension(fastafile);
 347                 ofstream out;
 348                 m->openOutputFile(outputFileName, out);
 349
 350
 351                 ifstream in;
 352                 m->openInputFile(fastafile, in);
 353                 string name;
 354
 355                 bool wroteSomething = false;
 356                 int selectedCount = 0;
 357
 358         if (m->debug) { set<string> temp; sanity["fasta"] = temp; }
 359
 360                 while(!in.eof()){
 361
 362                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 363
 364                         Sequence currSeq(in);
 365                         name = currSeq.getName();
 366
 367                         if (name != "") {
 368                                 //if this name is in the accnos file
 369                                 if (names.count(name) != 0) {
 370                                         wroteSomething = true;
 371
 372                                         currSeq.printSequence(out);
 373                                         selectedCount++;
 374
 375                     if (m->debug) { sanity["fasta"].insert(name); }
 376                                 }
 377                         }
 378                         m->gobble(in);
 379                 }
 380                 in.close();
 381                 out.close();
 382
 383
 384                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 385                 outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);
 386
 387                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
 388
 389                 return 0;
 390
 391         }
 392         catch(exception& e) {
 393                 m->errorOut(e, "GetSeqsCommand", "readFasta");
 394                 exit(1);
 395         }
 396 }
 397 //**********************************************************************************************************************
 398 int GetSeqsCommand::readQual(){
 399         try {
 400                 string thisOutputDir = outputDir;
 401                 if (outputDir == "") {  thisOutputDir += m->hasPath(qualfile);  }
 402                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + "pick" +  m->getExtension(qualfile);
 403                 ofstream out;
 404                 m->openOutputFile(outputFileName, out);
 405
 406
 407                 ifstream in;
 408                 m->openInputFile(qualfile, in);
 409                 string name;
 410
 411                 bool wroteSomething = false;
 412                 int selectedCount = 0;
 413
 414         if (m->debug) { set<string> temp; sanity["qual"] = temp; }
 415
 416                 while(!in.eof()){
 417                         string saveName = "";
 418                         string name = "";
 419                         string scores = "";
 420
 421                         in >> name;
 422
 423                         if (name.length() != 0) {
 424                                 saveName = name.substr(1);
 425                                 while (!in.eof())       {
 426                                         char c = in.get();
 427                                         if (c == 10 || c == 13){        break;  }
 428                                         else { name += c; }
 429                                 }
 430                                 m->gobble(in);
 431                         }
 432
 433                         while(in){
 434                                 char letter= in.get();
 435                                 if(letter == '>'){      in.putback(letter);     break;  }
 436                                 else{ scores += letter; }
 437                         }
 438
 439                         m->gobble(in);
 440
 441                         if (names.count(saveName) != 0) {
 442                                 wroteSomething = true;
 443
 444                                 out << name << endl << scores;
 445                                 selectedCount++;
 446                 if (m->debug) { sanity["qual"].insert(name); }
 447                         }
 448
 449                         m->gobble(in);
 450                 }
 451                 in.close();
 452                 out.close();
 453
 454
 455                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 456                 outputNames.push_back(outputFileName);  outputTypes["qfile"].push_back(outputFileName);
 457
 458                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your quality file."); m->mothurOutEndLine();
 459
 460
 461                 return 0;
 462
 463         }
 464         catch(exception& e) {
 465                 m->errorOut(e, "GetSeqsCommand", "readQual");
 466                 exit(1);
 467         }
 468 }
 469 //**********************************************************************************************************************
 470 int GetSeqsCommand::readList(){
 471         try {
 472                 string thisOutputDir = outputDir;
 473                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 474                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 475                 ofstream out;
 476                 m->openOutputFile(outputFileName, out);
 477
 478                 ifstream in;
 479                 m->openInputFile(listfile, in);
 480
 481                 bool wroteSomething = false;
 482                 int selectedCount = 0;
 483
 484         if (m->debug) { set<string> temp; sanity["list"] = temp; }
 485
 486                 while(!in.eof()){
 487
 488                         selectedCount = 0;
 489
 490                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 491
 492                         //read in list vector
 493                         ListVector list(in);
 494
 495                         //make a new list vector
 496                         ListVector newList;
 497                         newList.setLabel(list.getLabel());
 498
 499                         //for each bin
 500                         for (int i = 0; i < list.getNumBins(); i++) {
 501
 502                                 //parse out names that are in accnos file
 503                                 string binnames = list.get(i);
 504
 505                                 string newNames = "";
 506                                 while (binnames.find_first_of(',') != -1) {
 507                                         string name = binnames.substr(0,binnames.find_first_of(','));
 508                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 509
 510                                         //if that name is in the .accnos file, add it
 511                                         if (names.count(name) != 0) {  newNames += name + ",";  selectedCount++; if (m->debug) { sanity["list"].insert(name); } }
 512                                 }
 513
 514                                 //get last name
 515                                 if (names.count(binnames) != 0) {  newNames += binnames + ",";  selectedCount++;  if (m->debug) { sanity["list"].insert(binnames); } }
 516
 517                                 //if there are names in this bin add to new list
 518                                 if (newNames != "") {
 519                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 520                                         newList.push_back(newNames);
 521                                 }
 522                         }
 523
 524                         //print new listvector
 525                         if (newList.getNumBins() != 0) {
 526                                 wroteSomething = true;
 527                                 newList.print(out);
 528                         }
 529
 530                         m->gobble(in);
 531                 }
 532                 in.close();
 533                 out.close();
 534
 535                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 536                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 537
 538                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine();
 539
 540                 return 0;
 541
 542         }
 543         catch(exception& e) {
 544                 m->errorOut(e, "GetSeqsCommand", "readList");
 545                 exit(1);
 546         }
 547 }
 548 //**********************************************************************************************************************
 549 int GetSeqsCommand::readName(){
 550         try {
 551                 string thisOutputDir = outputDir;
 552                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 553                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" +  m->getExtension(namefile);
 554                 ofstream out;
 555                 m->openOutputFile(outputFileName, out);
 556
 557
 558                 ifstream in;
 559                 m->openInputFile(namefile, in);
 560                 string name, firstCol, secondCol;
 561
 562                 bool wroteSomething = false;
 563                 int selectedCount = 0;
 564
 565         if (m->debug) { set<string> temp; sanity["name"] = temp; }
 566         if (m->debug) { set<string> temp; sanity["dupname"] = temp; }
 567
 568                 while(!in.eof()){
 569
 570                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 571
 572                         in >> firstCol;
 573                         in >> secondCol;
 574
 575                         string hold = "";
 576                         if (dups) { hold = secondCol; }
 577
 578                         vector<string> parsedNames;
 579                         m->splitAtComma(secondCol, parsedNames);
 580
 581                         vector<string> validSecond;
 582                         for (int i = 0; i < parsedNames.size(); i++) {
 583                                 if (names.count(parsedNames[i]) != 0) {
 584                                         validSecond.push_back(parsedNames[i]);
 585                     if (m->debug) { sanity["dupname"].insert(parsedNames[i]); }
 586                                 }
 587                         }
 588
 589                         if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
 590                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]); if (m->debug) { sanity["dupname"].insert(parsedNames[i]); } }
 591                                 out << firstCol << '\t' << hold << endl;
 592                                 wroteSomething = true;
 593                                 selectedCount += parsedNames.size();
 594                 if (m->debug) { sanity["name"].insert(firstCol); }
 595                         }else {
 596                                 selectedCount += validSecond.size();
 597
 598                                 //if the name in the first column is in the set then print it and any other names in second column also in set
 599                                 if (names.count(firstCol) != 0) {
 600
 601                                         wroteSomething = true;
 602
 603                                         out << firstCol << '\t';
 604
 605                                         //you know you have at least one valid second since first column is valid
 606                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 607                                         out << validSecond[validSecond.size()-1] << endl;
 608
 609                     if (m->debug) { sanity["name"].insert(firstCol); }
 610
 611
 612                                 //make first name in set you come to first column and then add the remaining names to second column
 613                                 }else {
 614                                         //you want part of this row
 615                                         if (validSecond.size() != 0) {
 616
 617                                                 wroteSomething = true;
 618
 619                                                 out << validSecond[0] << '\t';
 620
 621                                                 //you know you have at least one valid second since first column is valid
 622                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 623                                                 out << validSecond[validSecond.size()-1] << endl;
 624
 625                         if (m->debug) { sanity["name"].insert(validSecond[0]); }
 626                                         }
 627                                 }
 628                         }
 629                         m->gobble(in);
 630                 }
 631                 in.close();
 632                 out.close();
 633
 634                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 635                 outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
 636
 637                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your name file."); m->mothurOutEndLine();
 638
 639                 return 0;
 640
 641         }
 642         catch(exception& e) {
 643                 m->errorOut(e, "GetSeqsCommand", "readName");
 644                 exit(1);
 645         }
 646 }
 647
 648 //**********************************************************************************************************************
 649 int GetSeqsCommand::readGroup(){
 650         try {
 651                 string thisOutputDir = outputDir;
 652                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 653                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 654                 ofstream out;
 655                 m->openOutputFile(outputFileName, out);
 656
 657
 658                 ifstream in;
 659                 m->openInputFile(groupfile, in);
 660                 string name, group;
 661
 662                 bool wroteSomething = false;
 663                 int selectedCount = 0;
 664
 665         if (m->debug) { set<string> temp; sanity["group"] = temp; }
 666
 667                 while(!in.eof()){
 668
 669                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 670
 671
 672                         in >> name;                             //read from first column
 673                         in >> group;                    //read from second column
 674
 675                         //if this name is in the accnos file
 676                         if (names.count(name) != 0) {
 677                                 wroteSomething = true;
 678
 679                                 out << name << '\t' << group << endl;
 680                                 selectedCount++;
 681
 682                 if (m->debug) {  sanity["group"].insert(name); }
 683                         }
 684
 685                         m->gobble(in);
 686                 }
 687                 in.close();
 688                 out.close();
 689
 690                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 691                 outputNames.push_back(outputFileName);  outputTypes["group"].push_back(outputFileName);
 692
 693                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your group file."); m->mothurOutEndLine();
 694
 695
 696                 return 0;
 697
 698         }
 699         catch(exception& e) {
 700                 m->errorOut(e, "GetSeqsCommand", "readGroup");
 701                 exit(1);
 702         }
 703 }
 704 //**********************************************************************************************************************
 705 int GetSeqsCommand::readTax(){
 706         try {
 707                 string thisOutputDir = outputDir;
 708                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 709                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 710                 ofstream out;
 711                 m->openOutputFile(outputFileName, out);
 712
 713                 ifstream in;
 714                 m->openInputFile(taxfile, in);
 715                 string name, tax;
 716
 717                 bool wroteSomething = false;
 718                 int selectedCount = 0;
 719
 720         if (m->debug) { set<string> temp; sanity["tax"] = temp; }
 721
 722                 while(!in.eof()){
 723
 724                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 725
 726                         in >> name;                             //read from first column
 727                         in >> tax;                      //read from second column
 728
 729                         //if this name is in the accnos file
 730                         if (names.count(name) != 0) {
 731                                 wroteSomething = true;
 732
 733                                 out << name << '\t' << tax << endl;
 734                                 selectedCount++;
 735
 736                 if (m->debug) { sanity["tax"].insert(name); }
 737                         }
 738
 739                         m->gobble(in);
 740                 }
 741                 in.close();
 742                 out.close();
 743
 744                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 745                 outputNames.push_back(outputFileName);  outputTypes["taxonomy"].push_back(outputFileName);
 746
 747                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine();
 748
 749                 return 0;
 750
 751         }
 752         catch(exception& e) {
 753                 m->errorOut(e, "GetSeqsCommand", "readTax");
 754                 exit(1);
 755         }
 756 }
 757 //**********************************************************************************************************************
 758 //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
 759 int GetSeqsCommand::readAlign(){
 760         try {
 761                 string thisOutputDir = outputDir;
 762                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 763                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
 764                 ofstream out;
 765                 m->openOutputFile(outputFileName, out);
 766
 767
 768                 ifstream in;
 769                 m->openInputFile(alignfile, in);
 770                 string name, junk;
 771
 772                 bool wroteSomething = false;
 773                 int selectedCount = 0;
 774
 775                 //read column headers
 776                 for (int i = 0; i < 16; i++) {
 777                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 778                         else                    {       break;                  }
 779                 }
 780                 out << endl;
 781
 782                 while(!in.eof()){
 783
 784                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 785
 786
 787                         in >> name;                             //read from first column
 788
 789                         //if this name is in the accnos file
 790                         if (names.count(name) != 0) {
 791                                 wroteSomething = true;
 792                                 selectedCount++;
 793
 794                                 out << name << '\t';
 795
 796                                 //read rest
 797                                 for (int i = 0; i < 15; i++) {
 798                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 799                                         else                    {       break;                  }
 800                                 }
 801                                 out << endl;
 802
 803                         }else {//still read just don't do anything with it
 804                                 //read rest
 805                                 for (int i = 0; i < 15; i++) {
 806                                         if (!in.eof())  {       in >> junk;             }
 807                                         else                    {       break;                  }
 808                                 }
 809                         }
 810
 811                         m->gobble(in);
 812                 }
 813                 in.close();
 814                 out.close();
 815
 816                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 817                 outputNames.push_back(outputFileName);  outputTypes["alignreport"].push_back(outputFileName);
 818
 819                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your alignreport file."); m->mothurOutEndLine();
 820
 821                 return 0;
 822
 823         }
 824         catch(exception& e) {
 825                 m->errorOut(e, "GetSeqsCommand", "readAlign");
 826                 exit(1);
 827         }
 828 }
 829 //**********************************************************************************************************************
 830
 831 int GetSeqsCommand::readAccnos(){
 832         try {
 833
 834                 ifstream in;
 835                 m->openInputFile(accnosfile, in);
 836                 string name;
 837
 838                 while(!in.eof()){
 839                         in >> name;
 840
 841                         names.insert(name);
 842
 843                         m->gobble(in);
 844                 }
 845                 in.close();
 846
 847                 return 0;
 848
 849         }
 850         catch(exception& e) {
 851                 m->errorOut(e, "GetSeqsCommand", "readAccnos");
 852                 exit(1);
 853         }
 854 }
 855 //**********************************************************************************************************************
 856 //just looking at common mistakes.
 857 int GetSeqsCommand::runSanityCheck(){
 858         try {
 859         string thisOutputDir = outputDir;
 860         if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 861         string filename = outputDir + "get.seqs.debug.report";
 862
 863         ofstream out;
 864                 m->openOutputFile(filename, out);
 865
 866
 867         //compare fasta, name, qual and taxonomy if given to make sure they contain the same seqs
 868         if (fastafile != "") {
 869             if (namefile != "") { //compare with fasta
 870                 if (sanity["fasta"] != sanity["name"]) { //create mismatch file
 871                     createMisMatchFile(out, fastafile, namefile, sanity["fasta"], sanity["name"]);
 872                 }
 873             }
 874             if (qualfile != "") {
 875                 if (sanity["fasta"] != sanity["qual"]) { //create mismatch file
 876                     createMisMatchFile(out, fastafile, qualfile, sanity["fasta"], sanity["qual"]);
 877                 }
 878             }
 879             if (taxfile != "") {
 880                 if (sanity["fasta"] != sanity["tax"]) { //create mismatch file
 881                     createMisMatchFile(out, fastafile, taxfile, sanity["fasta"], sanity["tax"]);
 882                 }
 883             }
 884         }
 885
 886         //compare dupnames, groups and list if given to make sure they match
 887         if (namefile != "") {
 888             if (groupfile != "") {
 889                 if (sanity["dupname"] != sanity["group"]) { //create mismatch file
 890                     createMisMatchFile(out, namefile, groupfile, sanity["dupname"], sanity["group"]);
 891                 }
 892             }
 893             if (listfile != "") {
 894                 if (sanity["dupname"] != sanity["list"]) { //create mismatch file
 895                     createMisMatchFile(out, namefile, listfile, sanity["dupname"], sanity["list"]);
 896                 }
 897             }
 898         }else{
 899
 900             if ((groupfile != "") && (fastafile != "")) {
 901                 if (sanity["fasta"] != sanity["group"]) { //create mismatch file
 902                     createMisMatchFile(out, fastafile, groupfile, sanity["fasta"], sanity["group"]);
 903                 }
 904             }
 905         }
 906
 907         out.close();
 908
 909         if (m->isBlank(filename)) { m->mothurRemove(filename); }
 910         else { m->mothurOut("\n[DEBUG]: " + filename + " contains the file mismatches.\n");outputNames.push_back(filename); outputTypes["debug"].push_back(filename); }
 911
 912         return 0;
 913     }
 914         catch(exception& e) {
 915                 m->errorOut(e, "GetSeqsCommand", "runSanityCheck");
 916                 exit(1);
 917         }
 918 }
 919 //**********************************************************************************************************************
 920 //just looking at common mistakes.
 921 int GetSeqsCommand::createMisMatchFile(ofstream& out, string filename1, string filename2, set<string> set1, set<string> set2){
 922         try {
 923         out << "****************************************" << endl << endl;
 924         out << "Names unique to " << filename1 << ":\n";
 925
 926         //remove names in set1 that are also in set2
 927         for (set<string>::iterator it = set1.begin(); it != set1.end();) {
 928             string name = *it;
 929
 930             if (set2.count(name) == 0)  { out << name << endl;  } //name unique to set1
 931             else                        { set2.erase(name);     } //you are in both so erase
 932             set1.erase(it++);
 933         }
 934
 935         out << "\nNames unique to " << filename2 << ":\n";
 936         //output results
 937         for (set<string>::iterator it = set2.begin(); it != set2.end(); it++) {  out << *it << endl;  }
 938
 939         out << "****************************************" << endl << endl;
 940
 941         return 0;
 942     }
 943         catch(exception& e) {
 944                 m->errorOut(e, "GetSeqsCommand", "runSanityCheck");
 945                 exit(1);
 946         }
 947 }
 948 //**********************************************************************************************************************
 949
 950 int GetSeqsCommand::compareAccnos(){
 951         try {
 952
 953                 string thisOutputDir = outputDir;
 954                 if (outputDir == "") {  thisOutputDir += m->hasPath(accnosfile);  }
 955                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(accnosfile)) + "accnos.report";
 956                 ofstream out;
 957                 m->openOutputFile(outputFileName, out);
 958
 959                 ifstream in;
 960                 m->openInputFile(accnosfile2, in);
 961                 string name;
 962
 963                 set<string> namesAccnos2;
 964                 set<string> namesDups;
 965                 set<string> namesAccnos = names;
 966
 967                 map<string, int> nameCount;
 968
 969                 if (namefile != "") {
 970                         ifstream inName;
 971                         m->openInputFile(namefile, inName);
 972
 973
 974                         while(!inName.eof()){
 975
 976                                 if (m->control_pressed) { inName.close(); return 0; }
 977
 978                                 string thisname, repnames;
 979
 980                                 inName >> thisname;             m->gobble(inName);              //read from first column
 981                                 inName >> repnames;                     //read from second column
 982
 983                                 int num = m->getNumNames(repnames);
 984                                 nameCount[thisname] = num;
 985
 986                                 m->gobble(inName);
 987                         }
 988                         inName.close();
 989                 }
 990
 991                 while(!in.eof()){
 992                         in >> name;
 993
 994                         if (namesAccnos.count(name) == 0){ //name unique to accnos2
 995                                 int pos = name.find_last_of('_');
 996                                 string tempName = name;
 997                                 if (pos != string::npos) {  tempName = tempName.substr(pos+1); cout << tempName << endl; }
 998                                 if (namesAccnos.count(tempName) == 0){
 999                                         namesAccnos2.insert(name);
1000                                 }else { //you are in both so erase
1001                                         namesAccnos.erase(name);
1002                                         namesDups.insert(name);
1003                                 }
1004                         }else { //you are in both so erase
1005                                 namesAccnos.erase(name);
1006                                 namesDups.insert(name);
1007                         }
1008
1009                         m->gobble(in);
1010                 }
1011                 in.close();
1012
1013                 out << "Names in both files : " + toString(namesDups.size()) << endl;
1014                 m->mothurOut("Names in both files : " + toString(namesDups.size())); m->mothurOutEndLine();
1015
1016                 for (set<string>::iterator it = namesDups.begin(); it != namesDups.end(); it++) {
1017                         out << (*it);
1018                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
1019                         out << endl;
1020                 }
1021
1022                 out << "Names unique to " + accnosfile + " : " + toString(namesAccnos.size()) << endl;
1023                 m->mothurOut("Names unique to " + accnosfile + " : " + toString(namesAccnos.size())); m->mothurOutEndLine();
1024
1025                 for (set<string>::iterator it = namesAccnos.begin(); it != namesAccnos.end(); it++) {
1026                         out << (*it);
1027                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
1028                         out << endl;
1029                 }
1030
1031                 out << "Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size()) << endl;
1032                 m->mothurOut("Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size())); m->mothurOutEndLine();
1033
1034                 for (set<string>::iterator it = namesAccnos2.begin(); it != namesAccnos2.end(); it++) {
1035                         out << (*it);
1036                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
1037                         out << endl;
1038                 }
1039
1040                 out.close();
1041
1042                 outputNames.push_back(outputFileName);  outputTypes["accnosreport"].push_back(outputFileName);
1043
1044                 return 0;
1045
1046         }
1047         catch(exception& e) {
1048                 m->errorOut(e, "GetSeqsCommand", "readAccnos");
1049                 exit(1);
1050         }
1051 }
1052
1053
1054 //**********************************************************************************************************************
1055