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::getValidParameters(){
  16         try {
  17                 string Array[] =  {"fasta","name", "group", "qfile","alignreport", "accnos", "accnos2","dups", "list","taxonomy","outputdir","inputdir"};
  18                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  19                 return myArray;
  20         }
  21         catch(exception& e) {
  22                 m->errorOut(e, "GetSeqsCommand", "getValidParameters");
  23                 exit(1);
  24         }
  25 }
  26 //**********************************************************************************************************************
  27 GetSeqsCommand::GetSeqsCommand(){
  28         try {
  29                 abort = true;
  30                 //initialize outputTypes
  31                 vector<string> tempOutNames;
  32                 outputTypes["fasta"] = tempOutNames;
  33                 outputTypes["taxonomy"] = tempOutNames;
  34                 outputTypes["name"] = tempOutNames;
  35                 outputTypes["group"] = tempOutNames;
  36                 outputTypes["alignreport"] = tempOutNames;
  37                 outputTypes["list"] = tempOutNames;
  38                 outputTypes["qfile"] = tempOutNames;
  39                 outputTypes["accnosreport"] = tempOutNames;
  40         }
  41         catch(exception& e) {
  42                 m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
  43                 exit(1);
  44         }
  45 }
  46 //**********************************************************************************************************************
  47 vector<string> GetSeqsCommand::getRequiredParameters(){
  48         try {
  49                 string Array[] =  {"accnos"};
  50                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  51                 return myArray;
  52         }
  53         catch(exception& e) {
  54                 m->errorOut(e, "GetSeqsCommand", "getRequiredParameters");
  55                 exit(1);
  56         }
  57 }
  58 //**********************************************************************************************************************
  59 vector<string> GetSeqsCommand::getRequiredFiles(){
  60         try {
  61                 vector<string> myArray;
  62                 return myArray;
  63         }
  64         catch(exception& e) {
  65                 m->errorOut(e, "GetSeqsCommand", "getRequiredFiles");
  66                 exit(1);
  67         }
  68 }
  69 //**********************************************************************************************************************
  70 GetSeqsCommand::GetSeqsCommand(string option)  {
  71         try {
  72                 abort = false;
  73
  74                 //allow user to run help
  75                 if(option == "help") { help(); abort = true; }
  76
  77                 else {
  78                         //valid paramters for this command
  79                         string Array[] =  {"fasta","name", "group", "alignreport", "qfile", "accnos", "accnos2","dups", "list","taxonomy","outputdir","inputdir"};
  80                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  81
  82                         OptionParser parser(option);
  83                         map<string,string> parameters = parser.getParameters();
  84
  85                         ValidParameters validParameter;
  86                         map<string,string>::iterator it;
  87
  88                         //check to make sure all parameters are valid for command
  89                         for (it = parameters.begin(); it != parameters.end(); it++) {
  90                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  91                         }
  92
  93                         //initialize outputTypes
  94                         vector<string> tempOutNames;
  95                         outputTypes["fasta"] = tempOutNames;
  96                         outputTypes["taxonomy"] = tempOutNames;
  97                         outputTypes["name"] = tempOutNames;
  98                         outputTypes["group"] = tempOutNames;
  99                         outputTypes["alignreport"] = tempOutNames;
 100                         outputTypes["list"] = tempOutNames;
 101                         outputTypes["qfile"] = tempOutNames;
 102                         outputTypes["accnosreport"] = tempOutNames;
 103
 104                         //if the user changes the output directory command factory will send this info to us in the output parameter
 105                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 106
 107                         //if the user changes the input directory command factory will send this info to us in the output parameter
 108                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 109                         if (inputDir == "not found"){   inputDir = "";          }
 110                         else {
 111                                 string path;
 112                                 it = parameters.find("alignreport");
 113                                 //user has given a template file
 114                                 if(it != parameters.end()){
 115                                         path = m->hasPath(it->second);
 116                                         //if the user has not given a path then, add inputdir. else leave path alone.
 117                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
 118                                 }
 119
 120                                 it = parameters.find("fasta");
 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["fasta"] = inputDir + it->second;            }
 126                                 }
 127
 128                                 it = parameters.find("accnos");
 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["accnos"] = inputDir + it->second;           }
 134                                 }
 135
 136                                 it = parameters.find("accnos2");
 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["accnos2"] = inputDir + it->second;          }
 142                                 }
 143
 144                                 it = parameters.find("list");
 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["list"] = inputDir + it->second;             }
 150                                 }
 151
 152                                 it = parameters.find("name");
 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["name"] = inputDir + it->second;             }
 158                                 }
 159
 160                                 it = parameters.find("group");
 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["group"] = inputDir + it->second;            }
 166                                 }
 167
 168                                 it = parameters.find("taxonomy");
 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["taxonomy"] = inputDir + it->second;         }
 174                                 }
 175
 176                                 it = parameters.find("qfile");
 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["qfile"] = inputDir + it->second;            }
 182                                 }
 183                         }
 184
 185
 186                         //check for required parameters
 187                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 188                         if (accnosfile == "not open") { abort = true; }
 189                         else if (accnosfile == "not found") {  accnosfile = "";  m->mothurOut("You must provide an accnos file."); m->mothurOutEndLine(); abort = true; }
 190
 191                         accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
 192                         if (accnosfile2 == "not open") { abort = true; }
 193
 194                         fastafile = validParameter.validFile(parameters, "fasta", true);
 195                         if (fastafile == "not open") { abort = true; }
 196                         else if (fastafile == "not found") {  fastafile = "";  }
 197
 198                         namefile = validParameter.validFile(parameters, "name", true);
 199                         if (namefile == "not open") { abort = true; }
 200                         else if (namefile == "not found") {  namefile = "";  }
 201
 202                         groupfile = validParameter.validFile(parameters, "group", true);
 203                         if (groupfile == "not open") { abort = true; }
 204                         else if (groupfile == "not found") {  groupfile = "";  }
 205
 206                         alignfile = validParameter.validFile(parameters, "alignreport", true);
 207                         if (alignfile == "not open") { abort = true; }
 208                         else if (alignfile == "not found") {  alignfile = "";  }
 209
 210                         listfile = validParameter.validFile(parameters, "list", true);
 211                         if (listfile == "not open") { abort = true; }
 212                         else if (listfile == "not found") {  listfile = "";  }
 213
 214                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 215                         if (taxfile == "not open") { abort = true; }
 216                         else if (taxfile == "not found") {  taxfile = "";  }
 217
 218                         qualfile = validParameter.validFile(parameters, "qfile", true);
 219                         if (qualfile == "not open") { abort = true; }
 220                         else if (qualfile == "not found") {  qualfile = "";  }
 221
 222                         string usedDups = "true";
 223                         string temp = validParameter.validFile(parameters, "dups", false);      if (temp == "not found") { temp = "false"; usedDups = ""; }
 224                         dups = m->isTrue(temp);
 225
 226                         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; }
 227
 228                         if ((usedDups != "") && (namefile == "")) {  m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine();  abort = true; }
 229
 230                 }
 231
 232         }
 233         catch(exception& e) {
 234                 m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
 235                 exit(1);
 236         }
 237 }
 238 //**********************************************************************************************************************
 239
 240 void GetSeqsCommand::help(){
 241         try {
 242                 m->mothurOut("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");
 243                 m->mothurOut("It outputs a file containing only the sequences in the .accnos file.\n");
 244                 m->mothurOut("The get.seqs command parameters are accnos, fasta, name, group, list, taxonomy, qfile, alignreport and dups.  You must provide accnos and at least one of the other parameters.\n");
 245                 m->mothurOut("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");
 246                 m->mothurOut("The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
 247                 m->mothurOut("Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n");
 248                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 249         }
 250         catch(exception& e) {
 251                 m->errorOut(e, "GetSeqsCommand", "help");
 252                 exit(1);
 253         }
 254 }
 255
 256 //**********************************************************************************************************************
 257
 258 int GetSeqsCommand::execute(){
 259         try {
 260
 261                 if (abort == true) { return 0; }
 262
 263                 //get names you want to keep
 264                 readAccnos();
 265
 266                 if (m->control_pressed) { return 0; }
 267
 268                 //read through the correct file and output lines you want to keep
 269                 if (namefile != "")                     {               readName();                     }
 270                 if (fastafile != "")            {               readFasta();            }
 271                 if (groupfile != "")            {               readGroup();            }
 272                 if (alignfile != "")            {               readAlign();            }
 273                 if (listfile != "")                     {               readList();                     }
 274                 if (taxfile != "")                      {               readTax();                      }
 275                 if (qualfile != "")                     {               readQual();                     }
 276                 if (accnosfile2 != "")          {               compareAccnos();        }
 277
 278                 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str());  } return 0; }
 279
 280                 m->mothurOut("Selected " + toString(names.size()) + " sequences."); m->mothurOutEndLine();
 281
 282                 if (outputNames.size() != 0) {
 283                         m->mothurOutEndLine();
 284                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 285                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 286                         m->mothurOutEndLine();
 287                 }
 288
 289                 return 0;
 290         }
 291
 292         catch(exception& e) {
 293                 m->errorOut(e, "GetSeqsCommand", "execute");
 294                 exit(1);
 295         }
 296 }
 297
 298 //**********************************************************************************************************************
 299 int GetSeqsCommand::readFasta(){
 300         try {
 301                 string thisOutputDir = outputDir;
 302                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 303                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" +  m->getExtension(fastafile);
 304                 ofstream out;
 305                 m->openOutputFile(outputFileName, out);
 306
 307
 308                 ifstream in;
 309                 m->openInputFile(fastafile, in);
 310                 string name;
 311
 312                 bool wroteSomething = false;
 313
 314                 while(!in.eof()){
 315
 316                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 317
 318                         Sequence currSeq(in);
 319                         name = currSeq.getName();
 320
 321                         if (name != "") {
 322                                 //if this name is in the accnos file
 323                                 if (names.count(name) != 0) {
 324                                         wroteSomething = true;
 325
 326                                         currSeq.printSequence(out);
 327                                 }
 328                         }
 329                         m->gobble(in);
 330                 }
 331                 in.close();
 332                 out.close();
 333
 334
 335                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 336                 outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);
 337
 338                 return 0;
 339
 340         }
 341         catch(exception& e) {
 342                 m->errorOut(e, "GetSeqsCommand", "readFasta");
 343                 exit(1);
 344         }
 345 }
 346 //**********************************************************************************************************************
 347 int GetSeqsCommand::readQual(){
 348         try {
 349                 string thisOutputDir = outputDir;
 350                 if (outputDir == "") {  thisOutputDir += m->hasPath(qualfile);  }
 351                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + "pick" +  m->getExtension(qualfile);
 352                 ofstream out;
 353                 m->openOutputFile(outputFileName, out);
 354
 355
 356                 ifstream in;
 357                 m->openInputFile(qualfile, in);
 358                 string name;
 359
 360                 bool wroteSomething = false;
 361
 362
 363                 while(!in.eof()){
 364                         string saveName = "";
 365                         string name = "";
 366                         string scores = "";
 367
 368                         in >> name;
 369
 370                         if (name.length() != 0) {
 371                                 saveName = name.substr(1);
 372                                 while (!in.eof())       {
 373                                         char c = in.get();
 374                                         if (c == 10 || c == 13){        break;  }
 375                                         else { name += c; }
 376                                 }
 377                                 m->gobble(in);
 378                         }
 379
 380                         while(in){
 381                                 char letter= in.get();
 382                                 if(letter == '>'){      in.putback(letter);     break;  }
 383                                 else{ scores += letter; }
 384                         }
 385
 386                         m->gobble(in);
 387
 388                         if (names.count(saveName) != 0) {
 389                                 wroteSomething = true;
 390
 391                                 out << name << endl << scores;
 392                         }
 393
 394                         m->gobble(in);
 395                 }
 396                 in.close();
 397                 out.close();
 398
 399
 400                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 401                 outputNames.push_back(outputFileName);  outputTypes["qfile"].push_back(outputFileName);
 402
 403                 return 0;
 404
 405         }
 406         catch(exception& e) {
 407                 m->errorOut(e, "GetSeqsCommand", "readQual");
 408                 exit(1);
 409         }
 410 }
 411 //**********************************************************************************************************************
 412 int GetSeqsCommand::readList(){
 413         try {
 414                 string thisOutputDir = outputDir;
 415                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 416                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 417                 ofstream out;
 418                 m->openOutputFile(outputFileName, out);
 419
 420                 ifstream in;
 421                 m->openInputFile(listfile, in);
 422
 423                 bool wroteSomething = false;
 424
 425                 while(!in.eof()){
 426
 427                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 428
 429                         //read in list vector
 430                         ListVector list(in);
 431
 432                         //make a new list vector
 433                         ListVector newList;
 434                         newList.setLabel(list.getLabel());
 435
 436                         //for each bin
 437                         for (int i = 0; i < list.getNumBins(); i++) {
 438
 439                                 //parse out names that are in accnos file
 440                                 string binnames = list.get(i);
 441
 442                                 string newNames = "";
 443                                 while (binnames.find_first_of(',') != -1) {
 444                                         string name = binnames.substr(0,binnames.find_first_of(','));
 445                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 446
 447                                         //if that name is in the .accnos file, add it
 448                                         if (names.count(name) != 0) {  newNames += name + ",";  }
 449                                 }
 450
 451                                 //get last name
 452                                 if (names.count(binnames) != 0) {  newNames += binnames + ",";  }
 453
 454                                 //if there are names in this bin add to new list
 455                                 if (newNames != "") {
 456                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 457                                         newList.push_back(newNames);
 458                                 }
 459                         }
 460
 461                         //print new listvector
 462                         if (newList.getNumBins() != 0) {
 463                                 wroteSomething = true;
 464                                 newList.print(out);
 465                         }
 466
 467                         m->gobble(in);
 468                 }
 469                 in.close();
 470                 out.close();
 471
 472                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 473                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 474
 475                 return 0;
 476
 477         }
 478         catch(exception& e) {
 479                 m->errorOut(e, "GetSeqsCommand", "readList");
 480                 exit(1);
 481         }
 482 }
 483 //**********************************************************************************************************************
 484 int GetSeqsCommand::readName(){
 485         try {
 486                 string thisOutputDir = outputDir;
 487                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 488                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" +  m->getExtension(namefile);
 489                 ofstream out;
 490                 m->openOutputFile(outputFileName, out);
 491
 492
 493                 ifstream in;
 494                 m->openInputFile(namefile, in);
 495                 string name, firstCol, secondCol;
 496
 497                 bool wroteSomething = false;
 498
 499
 500                 while(!in.eof()){
 501
 502                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 503
 504                         in >> firstCol;
 505                         in >> secondCol;
 506
 507                         string hold = "";
 508                         if (dups) { hold = secondCol; }
 509
 510                         vector<string> parsedNames;
 511                         //parse second column saving each name
 512                         while (secondCol.find_first_of(',') != -1) {
 513                                 name = secondCol.substr(0,secondCol.find_first_of(','));
 514                                 secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
 515                                 parsedNames.push_back(name);
 516                         }
 517
 518                         //get name after last ,
 519                         parsedNames.push_back(secondCol);
 520
 521                         vector<string> validSecond;
 522                         for (int i = 0; i < parsedNames.size(); i++) {
 523                                 if (names.count(parsedNames[i]) != 0) {
 524                                         validSecond.push_back(parsedNames[i]);
 525                                 }
 526                         }
 527
 528                         if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
 529                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 530                                 out << firstCol << '\t' << hold << endl;
 531                                 wroteSomething = true;
 532                         }else {
 533                                 //if the name in the first column is in the set then print it and any other names in second column also in set
 534                                 if (names.count(firstCol) != 0) {
 535
 536                                         wroteSomething = true;
 537
 538                                         out << firstCol << '\t';
 539
 540                                         //you know you have at least one valid second since first column is valid
 541                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 542                                         out << validSecond[validSecond.size()-1] << endl;
 543
 544
 545                                 //make first name in set you come to first column and then add the remaining names to second column
 546                                 }else {
 547                                         //you want part of this row
 548                                         if (validSecond.size() != 0) {
 549
 550                                                 wroteSomething = true;
 551
 552                                                 out << validSecond[0] << '\t';
 553
 554                                                 //you know you have at least one valid second since first column is valid
 555                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 556                                                 out << validSecond[validSecond.size()-1] << endl;
 557                                         }
 558                                 }
 559                         }
 560                         m->gobble(in);
 561                 }
 562                 in.close();
 563                 out.close();
 564
 565                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 566                 outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
 567
 568                 return 0;
 569
 570         }
 571         catch(exception& e) {
 572                 m->errorOut(e, "GetSeqsCommand", "readName");
 573                 exit(1);
 574         }
 575 }
 576
 577 //**********************************************************************************************************************
 578 int GetSeqsCommand::readGroup(){
 579         try {
 580                 string thisOutputDir = outputDir;
 581                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 582                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 583                 ofstream out;
 584                 m->openOutputFile(outputFileName, out);
 585
 586
 587                 ifstream in;
 588                 m->openInputFile(groupfile, in);
 589                 string name, group;
 590
 591                 bool wroteSomething = false;
 592
 593                 while(!in.eof()){
 594
 595                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 596
 597
 598                         in >> name;                             //read from first column
 599                         in >> group;                    //read from second column
 600
 601                         //if this name is in the accnos file
 602                         if (names.count(name) != 0) {
 603                                 wroteSomething = true;
 604
 605                                 out << name << '\t' << group << endl;
 606                         }
 607
 608                         m->gobble(in);
 609                 }
 610                 in.close();
 611                 out.close();
 612
 613                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 614                 outputNames.push_back(outputFileName);  outputTypes["group"].push_back(outputFileName);
 615
 616                 return 0;
 617
 618         }
 619         catch(exception& e) {
 620                 m->errorOut(e, "GetSeqsCommand", "readGroup");
 621                 exit(1);
 622         }
 623 }
 624 //**********************************************************************************************************************
 625 int GetSeqsCommand::readTax(){
 626         try {
 627                 string thisOutputDir = outputDir;
 628                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 629                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 630                 ofstream out;
 631                 m->openOutputFile(outputFileName, out);
 632
 633                 ifstream in;
 634                 m->openInputFile(taxfile, in);
 635                 string name, tax;
 636
 637                 bool wroteSomething = false;
 638
 639                 while(!in.eof()){
 640
 641                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 642
 643                         in >> name;                             //read from first column
 644                         in >> tax;                      //read from second column
 645
 646                         //if this name is in the accnos file
 647                         if (names.count(name) != 0) {
 648                                 wroteSomething = true;
 649
 650                                 out << name << '\t' << tax << endl;
 651                         }
 652
 653                         m->gobble(in);
 654                 }
 655                 in.close();
 656                 out.close();
 657
 658                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 659                 outputNames.push_back(outputFileName);  outputTypes["taxonomy"].push_back(outputFileName);
 660
 661                 return 0;
 662
 663         }
 664         catch(exception& e) {
 665                 m->errorOut(e, "GetSeqsCommand", "readTax");
 666                 exit(1);
 667         }
 668 }
 669 //**********************************************************************************************************************
 670 //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
 671 int GetSeqsCommand::readAlign(){
 672         try {
 673                 string thisOutputDir = outputDir;
 674                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 675                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
 676                 ofstream out;
 677                 m->openOutputFile(outputFileName, out);
 678
 679
 680                 ifstream in;
 681                 m->openInputFile(alignfile, in);
 682                 string name, junk;
 683
 684                 bool wroteSomething = false;
 685
 686                 //read column headers
 687                 for (int i = 0; i < 16; i++) {
 688                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 689                         else                    {       break;                  }
 690                 }
 691                 out << endl;
 692
 693                 while(!in.eof()){
 694
 695                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 696
 697
 698                         in >> name;                             //read from first column
 699
 700                         //if this name is in the accnos file
 701                         if (names.count(name) != 0) {
 702                                 wroteSomething = true;
 703
 704                                 out << name << '\t';
 705
 706                                 //read rest
 707                                 for (int i = 0; i < 15; i++) {
 708                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 709                                         else                    {       break;                  }
 710                                 }
 711                                 out << endl;
 712
 713                         }else {//still read just don't do anything with it
 714                                 //read rest
 715                                 for (int i = 0; i < 15; i++) {
 716                                         if (!in.eof())  {       in >> junk;             }
 717                                         else                    {       break;                  }
 718                                 }
 719                         }
 720
 721                         m->gobble(in);
 722                 }
 723                 in.close();
 724                 out.close();
 725
 726                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 727                 outputNames.push_back(outputFileName);  outputTypes["alignreport"].push_back(outputFileName);
 728
 729                 return 0;
 730
 731         }
 732         catch(exception& e) {
 733                 m->errorOut(e, "GetSeqsCommand", "readAlign");
 734                 exit(1);
 735         }
 736 }
 737 //**********************************************************************************************************************
 738
 739 int GetSeqsCommand::readAccnos(){
 740         try {
 741
 742                 ifstream in;
 743                 m->openInputFile(accnosfile, in);
 744                 string name;
 745
 746                 while(!in.eof()){
 747                         in >> name;
 748
 749                         names.insert(name);
 750
 751                         m->gobble(in);
 752                 }
 753                 in.close();
 754
 755                 return 0;
 756
 757         }
 758         catch(exception& e) {
 759                 m->errorOut(e, "GetSeqsCommand", "readAccnos");
 760                 exit(1);
 761         }
 762 }
 763 //**********************************************************************************************************************
 764
 765 int GetSeqsCommand::compareAccnos(){
 766         try {
 767
 768                 string thisOutputDir = outputDir;
 769                 if (outputDir == "") {  thisOutputDir += m->hasPath(accnosfile);  }
 770                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(accnosfile)) + "accnos.report";
 771                 ofstream out;
 772                 m->openOutputFile(outputFileName, out);
 773
 774                 ifstream in;
 775                 m->openInputFile(accnosfile2, in);
 776                 string name;
 777
 778                 set<string> namesAccnos2;
 779                 set<string> namesDups;
 780                 set<string> namesAccnos = names;
 781
 782                 while(!in.eof()){
 783                         in >> name;
 784
 785                         if (namesAccnos.count(name) == 0){ //name unique to accnos2
 786                                 namesAccnos2.insert(name);
 787                         }else { //you are in both so erase
 788                                 namesAccnos.erase(name);
 789                                 namesDups.insert(name);
 790                         }
 791
 792                         m->gobble(in);
 793                 }
 794                 in.close();
 795
 796                 out << "Names in both files : " + toString(namesDups.size()) << endl;
 797                 m->mothurOut("Names in both files : " + toString(namesDups.size())); m->mothurOutEndLine();
 798
 799                 for (set<string>::iterator it = namesDups.begin(); it != namesDups.end(); it++) {
 800                         out << (*it) << endl;
 801                 }
 802
 803                 out << "Names unique to " + accnosfile + " : " + toString(namesAccnos.size()) << endl;
 804                 m->mothurOut("Names unique to " + accnosfile + " : " + toString(namesAccnos.size())); m->mothurOutEndLine();
 805
 806                 for (set<string>::iterator it = namesAccnos.begin(); it != namesAccnos.end(); it++) {
 807                         out << (*it) << endl;
 808                 }
 809
 810                 out << "Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size()) << endl;
 811                 m->mothurOut("Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size())); m->mothurOutEndLine();
 812
 813                 for (set<string>::iterator it = namesAccnos2.begin(); it != namesAccnos2.end(); it++) {
 814                         out << (*it) << endl;
 815                 }
 816
 817                 out.close();
 818
 819                 outputNames.push_back(outputFileName);  outputTypes["accnosreport"].push_back(outputFileName);
 820
 821                 return 0;
 822
 823         }
 824         catch(exception& e) {
 825                 m->errorOut(e, "GetSeqsCommand", "readAccnos");
 826                 exit(1);
 827         }
 828 }
 829
 830
 831 //**********************************************************************************************************************
 832