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                         }
 205
 206                         if (accnosfile2 == "not found") { accnosfile2 = ""; }
 207
 208                         fastafile = validParameter.validFile(parameters, "fasta", true);
 209                         if (fastafile == "not open") { abort = true; }
 210                         else if (fastafile == "not found") {  fastafile = "";  }
 211
 212                         namefile = validParameter.validFile(parameters, "name", true);
 213                         if (namefile == "not open") { abort = true; }
 214                         else if (namefile == "not found") {  namefile = "";  }
 215
 216                         groupfile = validParameter.validFile(parameters, "group", true);
 217                         if (groupfile == "not open") { abort = true; }
 218                         else if (groupfile == "not found") {  groupfile = "";  }
 219
 220                         alignfile = validParameter.validFile(parameters, "alignreport", true);
 221                         if (alignfile == "not open") { abort = true; }
 222                         else if (alignfile == "not found") {  alignfile = "";  }
 223
 224                         listfile = validParameter.validFile(parameters, "list", true);
 225                         if (listfile == "not open") { abort = true; }
 226                         else if (listfile == "not found") {  listfile = "";  }
 227
 228                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 229                         if (taxfile == "not open") { abort = true; }
 230                         else if (taxfile == "not found") {  taxfile = "";  }
 231
 232                         qualfile = validParameter.validFile(parameters, "qfile", true);
 233                         if (qualfile == "not open") { abort = true; }
 234                         else if (qualfile == "not found") {  qualfile = "";  }
 235
 236                         accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
 237                         if (accnosfile2 == "not open") { abort = true; }
 238                         else if (accnosfile2 == "not found") {  accnosfile2 = "";  }
 239
 240
 241                         string usedDups = "true";
 242                         string temp = validParameter.validFile(parameters, "dups", false);      if (temp == "not found") { temp = "true"; usedDups = ""; }
 243                         dups = m->isTrue(temp);
 244
 245                         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; }
 246                 }
 247
 248         }
 249         catch(exception& e) {
 250                 m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
 251                 exit(1);
 252         }
 253 }
 254 //**********************************************************************************************************************
 255
 256 int GetSeqsCommand::execute(){
 257         try {
 258
 259                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 260
 261                 //get names you want to keep
 262                 readAccnos();
 263
 264                 if (m->control_pressed) { return 0; }
 265
 266                 //read through the correct file and output lines you want to keep
 267                 if (namefile != "")                     {               readName();                     }
 268                 if (fastafile != "")            {               readFasta();            }
 269                 if (groupfile != "")            {               readGroup();            }
 270                 if (alignfile != "")            {               readAlign();            }
 271                 if (listfile != "")                     {               readList();                     }
 272                 if (taxfile != "")                      {               readTax();                      }
 273                 if (qualfile != "")                     {               readQual();                     }
 274                 if (accnosfile2 != "")          {               compareAccnos();        }
 275
 276                 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str());  } return 0; }
 277
 278                 m->mothurOut("Selected " + toString(names.size()) + " sequences."); m->mothurOutEndLine();
 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                         itTypes = outputTypes.find("qfile");
 314                         if (itTypes != outputTypes.end()) {
 315                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 316                         }
 317
 318                 }
 319
 320                 return 0;
 321         }
 322
 323         catch(exception& e) {
 324                 m->errorOut(e, "GetSeqsCommand", "execute");
 325                 exit(1);
 326         }
 327 }
 328
 329 //**********************************************************************************************************************
 330 int GetSeqsCommand::readFasta(){
 331         try {
 332                 string thisOutputDir = outputDir;
 333                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 334                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" +  m->getExtension(fastafile);
 335                 ofstream out;
 336                 m->openOutputFile(outputFileName, out);
 337
 338
 339                 ifstream in;
 340                 m->openInputFile(fastafile, in);
 341                 string name;
 342
 343                 bool wroteSomething = false;
 344
 345                 while(!in.eof()){
 346
 347                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 348
 349                         Sequence currSeq(in);
 350                         name = currSeq.getName();
 351
 352                         if (name != "") {
 353                                 //if this name is in the accnos file
 354                                 if (names.count(name) != 0) {
 355                                         wroteSomething = true;
 356
 357                                         currSeq.printSequence(out);
 358                                 }
 359                         }
 360                         m->gobble(in);
 361                 }
 362                 in.close();
 363                 out.close();
 364
 365
 366                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 367                 outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);
 368
 369                 return 0;
 370
 371         }
 372         catch(exception& e) {
 373                 m->errorOut(e, "GetSeqsCommand", "readFasta");
 374                 exit(1);
 375         }
 376 }
 377 //**********************************************************************************************************************
 378 int GetSeqsCommand::readQual(){
 379         try {
 380                 string thisOutputDir = outputDir;
 381                 if (outputDir == "") {  thisOutputDir += m->hasPath(qualfile);  }
 382                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + "pick" +  m->getExtension(qualfile);
 383                 ofstream out;
 384                 m->openOutputFile(outputFileName, out);
 385
 386
 387                 ifstream in;
 388                 m->openInputFile(qualfile, in);
 389                 string name;
 390
 391                 bool wroteSomething = false;
 392
 393
 394                 while(!in.eof()){
 395                         string saveName = "";
 396                         string name = "";
 397                         string scores = "";
 398
 399                         in >> name;
 400
 401                         if (name.length() != 0) {
 402                                 saveName = name.substr(1);
 403                                 while (!in.eof())       {
 404                                         char c = in.get();
 405                                         if (c == 10 || c == 13){        break;  }
 406                                         else { name += c; }
 407                                 }
 408                                 m->gobble(in);
 409                         }
 410
 411                         while(in){
 412                                 char letter= in.get();
 413                                 if(letter == '>'){      in.putback(letter);     break;  }
 414                                 else{ scores += letter; }
 415                         }
 416
 417                         m->gobble(in);
 418
 419                         if (names.count(saveName) != 0) {
 420                                 wroteSomething = true;
 421
 422                                 out << name << endl << scores;
 423                         }
 424
 425                         m->gobble(in);
 426                 }
 427                 in.close();
 428                 out.close();
 429
 430
 431                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 432                 outputNames.push_back(outputFileName);  outputTypes["qfile"].push_back(outputFileName);
 433
 434                 return 0;
 435
 436         }
 437         catch(exception& e) {
 438                 m->errorOut(e, "GetSeqsCommand", "readQual");
 439                 exit(1);
 440         }
 441 }
 442 //**********************************************************************************************************************
 443 int GetSeqsCommand::readList(){
 444         try {
 445                 string thisOutputDir = outputDir;
 446                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 447                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 448                 ofstream out;
 449                 m->openOutputFile(outputFileName, out);
 450
 451                 ifstream in;
 452                 m->openInputFile(listfile, in);
 453
 454                 bool wroteSomething = false;
 455
 456                 while(!in.eof()){
 457
 458                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 459
 460                         //read in list vector
 461                         ListVector list(in);
 462
 463                         //make a new list vector
 464                         ListVector newList;
 465                         newList.setLabel(list.getLabel());
 466
 467                         //for each bin
 468                         for (int i = 0; i < list.getNumBins(); i++) {
 469
 470                                 //parse out names that are in accnos file
 471                                 string binnames = list.get(i);
 472
 473                                 string newNames = "";
 474                                 while (binnames.find_first_of(',') != -1) {
 475                                         string name = binnames.substr(0,binnames.find_first_of(','));
 476                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 477
 478                                         //if that name is in the .accnos file, add it
 479                                         if (names.count(name) != 0) {  newNames += name + ",";  }
 480                                 }
 481
 482                                 //get last name
 483                                 if (names.count(binnames) != 0) {  newNames += binnames + ",";  }
 484
 485                                 //if there are names in this bin add to new list
 486                                 if (newNames != "") {
 487                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 488                                         newList.push_back(newNames);
 489                                 }
 490                         }
 491
 492                         //print new listvector
 493                         if (newList.getNumBins() != 0) {
 494                                 wroteSomething = true;
 495                                 newList.print(out);
 496                         }
 497
 498                         m->gobble(in);
 499                 }
 500                 in.close();
 501                 out.close();
 502
 503                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 504                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 505
 506                 return 0;
 507
 508         }
 509         catch(exception& e) {
 510                 m->errorOut(e, "GetSeqsCommand", "readList");
 511                 exit(1);
 512         }
 513 }
 514 //**********************************************************************************************************************
 515 int GetSeqsCommand::readName(){
 516         try {
 517                 string thisOutputDir = outputDir;
 518                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 519                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" +  m->getExtension(namefile);
 520                 ofstream out;
 521                 m->openOutputFile(outputFileName, out);
 522
 523
 524                 ifstream in;
 525                 m->openInputFile(namefile, in);
 526                 string name, firstCol, secondCol;
 527
 528                 bool wroteSomething = false;
 529
 530
 531                 while(!in.eof()){
 532
 533                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 534
 535                         in >> firstCol;
 536                         in >> secondCol;
 537
 538                         string hold = "";
 539                         if (dups) { hold = secondCol; }
 540
 541                         vector<string> parsedNames;
 542                         m->splitAtComma(secondCol, parsedNames);
 543
 544                         vector<string> validSecond;
 545                         for (int i = 0; i < parsedNames.size(); i++) {
 546                                 if (names.count(parsedNames[i]) != 0) {
 547                                         validSecond.push_back(parsedNames[i]);
 548                                 }
 549                         }
 550
 551                         if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
 552                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 553                                 out << firstCol << '\t' << hold << endl;
 554                                 wroteSomething = true;
 555                         }else {
 556                                 //if the name in the first column is in the set then print it and any other names in second column also in set
 557                                 if (names.count(firstCol) != 0) {
 558
 559                                         wroteSomething = true;
 560
 561                                         out << firstCol << '\t';
 562
 563                                         //you know you have at least one valid second since first column is valid
 564                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 565                                         out << validSecond[validSecond.size()-1] << endl;
 566
 567
 568                                 //make first name in set you come to first column and then add the remaining names to second column
 569                                 }else {
 570                                         //you want part of this row
 571                                         if (validSecond.size() != 0) {
 572
 573                                                 wroteSomething = true;
 574
 575                                                 out << validSecond[0] << '\t';
 576
 577                                                 //you know you have at least one valid second since first column is valid
 578                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 579                                                 out << validSecond[validSecond.size()-1] << endl;
 580                                         }
 581                                 }
 582                         }
 583                         m->gobble(in);
 584                 }
 585                 in.close();
 586                 out.close();
 587
 588                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 589                 outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
 590
 591                 return 0;
 592
 593         }
 594         catch(exception& e) {
 595                 m->errorOut(e, "GetSeqsCommand", "readName");
 596                 exit(1);
 597         }
 598 }
 599
 600 //**********************************************************************************************************************
 601 int GetSeqsCommand::readGroup(){
 602         try {
 603                 string thisOutputDir = outputDir;
 604                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 605                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 606                 ofstream out;
 607                 m->openOutputFile(outputFileName, out);
 608
 609
 610                 ifstream in;
 611                 m->openInputFile(groupfile, in);
 612                 string name, group;
 613
 614                 bool wroteSomething = false;
 615
 616                 while(!in.eof()){
 617
 618                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 619
 620
 621                         in >> name;                             //read from first column
 622                         in >> group;                    //read from second column
 623
 624                         //if this name is in the accnos file
 625                         if (names.count(name) != 0) {
 626                                 wroteSomething = true;
 627
 628                                 out << name << '\t' << group << endl;
 629                         }
 630
 631                         m->gobble(in);
 632                 }
 633                 in.close();
 634                 out.close();
 635
 636                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 637                 outputNames.push_back(outputFileName);  outputTypes["group"].push_back(outputFileName);
 638
 639                 return 0;
 640
 641         }
 642         catch(exception& e) {
 643                 m->errorOut(e, "GetSeqsCommand", "readGroup");
 644                 exit(1);
 645         }
 646 }
 647 //**********************************************************************************************************************
 648 int GetSeqsCommand::readTax(){
 649         try {
 650                 string thisOutputDir = outputDir;
 651                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 652                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 653                 ofstream out;
 654                 m->openOutputFile(outputFileName, out);
 655
 656                 ifstream in;
 657                 m->openInputFile(taxfile, in);
 658                 string name, tax;
 659
 660                 bool wroteSomething = false;
 661
 662                 while(!in.eof()){
 663
 664                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 665
 666                         in >> name;                             //read from first column
 667                         in >> tax;                      //read from second column
 668
 669                         //if this name is in the accnos file
 670                         if (names.count(name) != 0) {
 671                                 wroteSomething = true;
 672
 673                                 out << name << '\t' << tax << endl;
 674                         }
 675
 676                         m->gobble(in);
 677                 }
 678                 in.close();
 679                 out.close();
 680
 681                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 682                 outputNames.push_back(outputFileName);  outputTypes["taxonomy"].push_back(outputFileName);
 683
 684                 return 0;
 685
 686         }
 687         catch(exception& e) {
 688                 m->errorOut(e, "GetSeqsCommand", "readTax");
 689                 exit(1);
 690         }
 691 }
 692 //**********************************************************************************************************************
 693 //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
 694 int GetSeqsCommand::readAlign(){
 695         try {
 696                 string thisOutputDir = outputDir;
 697                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 698                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
 699                 ofstream out;
 700                 m->openOutputFile(outputFileName, out);
 701
 702
 703                 ifstream in;
 704                 m->openInputFile(alignfile, in);
 705                 string name, junk;
 706
 707                 bool wroteSomething = false;
 708
 709                 //read column headers
 710                 for (int i = 0; i < 16; i++) {
 711                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 712                         else                    {       break;                  }
 713                 }
 714                 out << endl;
 715
 716                 while(!in.eof()){
 717
 718                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 719
 720
 721                         in >> name;                             //read from first column
 722
 723                         //if this name is in the accnos file
 724                         if (names.count(name) != 0) {
 725                                 wroteSomething = true;
 726
 727                                 out << name << '\t';
 728
 729                                 //read rest
 730                                 for (int i = 0; i < 15; i++) {
 731                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 732                                         else                    {       break;                  }
 733                                 }
 734                                 out << endl;
 735
 736                         }else {//still read just don't do anything with it
 737                                 //read rest
 738                                 for (int i = 0; i < 15; i++) {
 739                                         if (!in.eof())  {       in >> junk;             }
 740                                         else                    {       break;                  }
 741                                 }
 742                         }
 743
 744                         m->gobble(in);
 745                 }
 746                 in.close();
 747                 out.close();
 748
 749                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 750                 outputNames.push_back(outputFileName);  outputTypes["alignreport"].push_back(outputFileName);
 751
 752                 return 0;
 753
 754         }
 755         catch(exception& e) {
 756                 m->errorOut(e, "GetSeqsCommand", "readAlign");
 757                 exit(1);
 758         }
 759 }
 760 //**********************************************************************************************************************
 761
 762 int GetSeqsCommand::readAccnos(){
 763         try {
 764
 765                 ifstream in;
 766                 m->openInputFile(accnosfile, in);
 767                 string name;
 768
 769                 while(!in.eof()){
 770                         in >> name;
 771
 772                         names.insert(name);
 773
 774                         m->gobble(in);
 775                 }
 776                 in.close();
 777
 778                 return 0;
 779
 780         }
 781         catch(exception& e) {
 782                 m->errorOut(e, "GetSeqsCommand", "readAccnos");
 783                 exit(1);
 784         }
 785 }
 786 //**********************************************************************************************************************
 787
 788 int GetSeqsCommand::compareAccnos(){
 789         try {
 790
 791                 string thisOutputDir = outputDir;
 792                 if (outputDir == "") {  thisOutputDir += m->hasPath(accnosfile);  }
 793                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(accnosfile)) + "accnos.report";
 794                 ofstream out;
 795                 m->openOutputFile(outputFileName, out);
 796
 797                 ifstream in;
 798                 m->openInputFile(accnosfile2, in);
 799                 string name;
 800
 801                 set<string> namesAccnos2;
 802                 set<string> namesDups;
 803                 set<string> namesAccnos = names;
 804
 805                 map<string, int> nameCount;
 806
 807                 if (namefile != "") {
 808                         ifstream inName;
 809                         m->openInputFile(namefile, inName);
 810
 811
 812                         while(!inName.eof()){
 813
 814                                 if (m->control_pressed) { inName.close(); return 0; }
 815
 816                                 string thisname, repnames;
 817
 818                                 inName >> thisname;             m->gobble(inName);              //read from first column
 819                                 inName >> repnames;                     //read from second column
 820
 821                                 int num = m->getNumNames(repnames);
 822                                 nameCount[thisname] = num;
 823
 824                                 m->gobble(inName);
 825                         }
 826                         inName.close();
 827                 }
 828
 829                 while(!in.eof()){
 830                         in >> name;
 831
 832                         if (namesAccnos.count(name) == 0){ //name unique to accnos2
 833                                 int pos = name.find_last_of('_');
 834                                 string tempName = name;
 835                                 if (pos != string::npos) {  tempName = tempName.substr(pos+1); cout << tempName << endl; }
 836                                 if (namesAccnos.count(tempName) == 0){
 837                                         namesAccnos2.insert(name);
 838                                 }else { //you are in both so erase
 839                                         namesAccnos.erase(name);
 840                                         namesDups.insert(name);
 841                                 }
 842                         }else { //you are in both so erase
 843                                 namesAccnos.erase(name);
 844                                 namesDups.insert(name);
 845                         }
 846
 847                         m->gobble(in);
 848                 }
 849                 in.close();
 850
 851                 out << "Names in both files : " + toString(namesDups.size()) << endl;
 852                 m->mothurOut("Names in both files : " + toString(namesDups.size())); m->mothurOutEndLine();
 853
 854                 for (set<string>::iterator it = namesDups.begin(); it != namesDups.end(); it++) {
 855                         out << (*it);
 856                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
 857                         out << endl;
 858                 }
 859
 860                 out << "Names unique to " + accnosfile + " : " + toString(namesAccnos.size()) << endl;
 861                 m->mothurOut("Names unique to " + accnosfile + " : " + toString(namesAccnos.size())); m->mothurOutEndLine();
 862
 863                 for (set<string>::iterator it = namesAccnos.begin(); it != namesAccnos.end(); it++) {
 864                         out << (*it);
 865                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
 866                         out << endl;
 867                 }
 868
 869                 out << "Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size()) << endl;
 870                 m->mothurOut("Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size())); m->mothurOutEndLine();
 871
 872                 for (set<string>::iterator it = namesAccnos2.begin(); it != namesAccnos2.end(); it++) {
 873                         out << (*it);
 874                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
 875                         out << endl;
 876                 }
 877
 878                 out.close();
 879
 880                 outputNames.push_back(outputFileName);  outputTypes["accnosreport"].push_back(outputFileName);
 881
 882                 return 0;
 883
 884         }
 885         catch(exception& e) {
 886                 m->errorOut(e, "GetSeqsCommand", "readAccnos");
 887                 exit(1);
 888         }
 889 }
 890
 891
 892 //**********************************************************************************************************************
 893