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") { 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") { 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") { 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
 254         }
 255         catch(exception& e) {
 256                 m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
 257                 exit(1);
 258         }
 259 }
 260 //**********************************************************************************************************************
 261
 262 int GetSeqsCommand::execute(){
 263         try {
 264
 265                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 266
 267                 //get names you want to keep
 268                 readAccnos();
 269
 270                 if (m->control_pressed) { return 0; }
 271
 272                 //read through the correct file and output lines you want to keep
 273                 if (namefile != "")                     {               readName();                     }
 274                 if (fastafile != "")            {               readFasta();            }
 275                 if (groupfile != "")            {               readGroup();            }
 276                 if (alignfile != "")            {               readAlign();            }
 277                 if (listfile != "")                     {               readList();                     }
 278                 if (taxfile != "")                      {               readTax();                      }
 279                 if (qualfile != "")                     {               readQual();                     }
 280                 if (accnosfile2 != "")          {               compareAccnos();        }
 281
 282                 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str());  } return 0; }
 283
 284                 m->mothurOut("Selected " + toString(names.size()) + " sequences."); m->mothurOutEndLine();
 285
 286                 if (outputNames.size() != 0) {
 287                         m->mothurOutEndLine();
 288                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 289                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 290                         m->mothurOutEndLine();
 291
 292                         //set fasta file as new current fastafile
 293                         string current = "";
 294                         itTypes = outputTypes.find("fasta");
 295                         if (itTypes != outputTypes.end()) {
 296                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 297                         }
 298
 299                         itTypes = outputTypes.find("name");
 300                         if (itTypes != outputTypes.end()) {
 301                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 302                         }
 303
 304                         itTypes = outputTypes.find("group");
 305                         if (itTypes != outputTypes.end()) {
 306                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 307                         }
 308
 309                         itTypes = outputTypes.find("list");
 310                         if (itTypes != outputTypes.end()) {
 311                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 312                         }
 313
 314                         itTypes = outputTypes.find("taxonomy");
 315                         if (itTypes != outputTypes.end()) {
 316                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 317                         }
 318
 319                         itTypes = outputTypes.find("qfile");
 320                         if (itTypes != outputTypes.end()) {
 321                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 322                         }
 323
 324                 }
 325
 326                 return 0;
 327         }
 328
 329         catch(exception& e) {
 330                 m->errorOut(e, "GetSeqsCommand", "execute");
 331                 exit(1);
 332         }
 333 }
 334
 335 //**********************************************************************************************************************
 336 int GetSeqsCommand::readFasta(){
 337         try {
 338                 string thisOutputDir = outputDir;
 339                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 340                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" +  m->getExtension(fastafile);
 341                 ofstream out;
 342                 m->openOutputFile(outputFileName, out);
 343
 344
 345                 ifstream in;
 346                 m->openInputFile(fastafile, in);
 347                 string name;
 348
 349                 bool wroteSomething = false;
 350
 351                 while(!in.eof()){
 352
 353                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 354
 355                         Sequence currSeq(in);
 356                         name = currSeq.getName();
 357
 358                         if (name != "") {
 359                                 //if this name is in the accnos file
 360                                 if (names.count(name) != 0) {
 361                                         wroteSomething = true;
 362
 363                                         currSeq.printSequence(out);
 364                                 }
 365                         }
 366                         m->gobble(in);
 367                 }
 368                 in.close();
 369                 out.close();
 370
 371
 372                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 373                 outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);
 374
 375                 return 0;
 376
 377         }
 378         catch(exception& e) {
 379                 m->errorOut(e, "GetSeqsCommand", "readFasta");
 380                 exit(1);
 381         }
 382 }
 383 //**********************************************************************************************************************
 384 int GetSeqsCommand::readQual(){
 385         try {
 386                 string thisOutputDir = outputDir;
 387                 if (outputDir == "") {  thisOutputDir += m->hasPath(qualfile);  }
 388                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + "pick" +  m->getExtension(qualfile);
 389                 ofstream out;
 390                 m->openOutputFile(outputFileName, out);
 391
 392
 393                 ifstream in;
 394                 m->openInputFile(qualfile, in);
 395                 string name;
 396
 397                 bool wroteSomething = false;
 398
 399
 400                 while(!in.eof()){
 401                         string saveName = "";
 402                         string name = "";
 403                         string scores = "";
 404
 405                         in >> name;
 406
 407                         if (name.length() != 0) {
 408                                 saveName = name.substr(1);
 409                                 while (!in.eof())       {
 410                                         char c = in.get();
 411                                         if (c == 10 || c == 13){        break;  }
 412                                         else { name += c; }
 413                                 }
 414                                 m->gobble(in);
 415                         }
 416
 417                         while(in){
 418                                 char letter= in.get();
 419                                 if(letter == '>'){      in.putback(letter);     break;  }
 420                                 else{ scores += letter; }
 421                         }
 422
 423                         m->gobble(in);
 424
 425                         if (names.count(saveName) != 0) {
 426                                 wroteSomething = true;
 427
 428                                 out << name << endl << scores;
 429                         }
 430
 431                         m->gobble(in);
 432                 }
 433                 in.close();
 434                 out.close();
 435
 436
 437                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 438                 outputNames.push_back(outputFileName);  outputTypes["qfile"].push_back(outputFileName);
 439
 440                 return 0;
 441
 442         }
 443         catch(exception& e) {
 444                 m->errorOut(e, "GetSeqsCommand", "readQual");
 445                 exit(1);
 446         }
 447 }
 448 //**********************************************************************************************************************
 449 int GetSeqsCommand::readList(){
 450         try {
 451                 string thisOutputDir = outputDir;
 452                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 453                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 454                 ofstream out;
 455                 m->openOutputFile(outputFileName, out);
 456
 457                 ifstream in;
 458                 m->openInputFile(listfile, in);
 459
 460                 bool wroteSomething = false;
 461
 462                 while(!in.eof()){
 463
 464                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 465
 466                         //read in list vector
 467                         ListVector list(in);
 468
 469                         //make a new list vector
 470                         ListVector newList;
 471                         newList.setLabel(list.getLabel());
 472
 473                         //for each bin
 474                         for (int i = 0; i < list.getNumBins(); i++) {
 475
 476                                 //parse out names that are in accnos file
 477                                 string binnames = list.get(i);
 478
 479                                 string newNames = "";
 480                                 while (binnames.find_first_of(',') != -1) {
 481                                         string name = binnames.substr(0,binnames.find_first_of(','));
 482                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 483
 484                                         //if that name is in the .accnos file, add it
 485                                         if (names.count(name) != 0) {  newNames += name + ",";  }
 486                                 }
 487
 488                                 //get last name
 489                                 if (names.count(binnames) != 0) {  newNames += binnames + ",";  }
 490
 491                                 //if there are names in this bin add to new list
 492                                 if (newNames != "") {
 493                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 494                                         newList.push_back(newNames);
 495                                 }
 496                         }
 497
 498                         //print new listvector
 499                         if (newList.getNumBins() != 0) {
 500                                 wroteSomething = true;
 501                                 newList.print(out);
 502                         }
 503
 504                         m->gobble(in);
 505                 }
 506                 in.close();
 507                 out.close();
 508
 509                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 510                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 511
 512                 return 0;
 513
 514         }
 515         catch(exception& e) {
 516                 m->errorOut(e, "GetSeqsCommand", "readList");
 517                 exit(1);
 518         }
 519 }
 520 //**********************************************************************************************************************
 521 int GetSeqsCommand::readName(){
 522         try {
 523                 string thisOutputDir = outputDir;
 524                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 525                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" +  m->getExtension(namefile);
 526                 ofstream out;
 527                 m->openOutputFile(outputFileName, out);
 528
 529
 530                 ifstream in;
 531                 m->openInputFile(namefile, in);
 532                 string name, firstCol, secondCol;
 533
 534                 bool wroteSomething = false;
 535
 536
 537                 while(!in.eof()){
 538
 539                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 540
 541                         in >> firstCol;
 542                         in >> secondCol;
 543
 544                         string hold = "";
 545                         if (dups) { hold = secondCol; }
 546
 547                         vector<string> parsedNames;
 548                         m->splitAtComma(secondCol, parsedNames);
 549
 550                         vector<string> validSecond;
 551                         for (int i = 0; i < parsedNames.size(); i++) {
 552                                 if (names.count(parsedNames[i]) != 0) {
 553                                         validSecond.push_back(parsedNames[i]);
 554                                 }
 555                         }
 556
 557                         if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
 558                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 559                                 out << firstCol << '\t' << hold << endl;
 560                                 wroteSomething = true;
 561                         }else {
 562                                 //if the name in the first column is in the set then print it and any other names in second column also in set
 563                                 if (names.count(firstCol) != 0) {
 564
 565                                         wroteSomething = true;
 566
 567                                         out << firstCol << '\t';
 568
 569                                         //you know you have at least one valid second since first column is valid
 570                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 571                                         out << validSecond[validSecond.size()-1] << endl;
 572
 573
 574                                 //make first name in set you come to first column and then add the remaining names to second column
 575                                 }else {
 576                                         //you want part of this row
 577                                         if (validSecond.size() != 0) {
 578
 579                                                 wroteSomething = true;
 580
 581                                                 out << validSecond[0] << '\t';
 582
 583                                                 //you know you have at least one valid second since first column is valid
 584                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 585                                                 out << validSecond[validSecond.size()-1] << endl;
 586                                         }
 587                                 }
 588                         }
 589                         m->gobble(in);
 590                 }
 591                 in.close();
 592                 out.close();
 593
 594                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 595                 outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
 596
 597                 return 0;
 598
 599         }
 600         catch(exception& e) {
 601                 m->errorOut(e, "GetSeqsCommand", "readName");
 602                 exit(1);
 603         }
 604 }
 605
 606 //**********************************************************************************************************************
 607 int GetSeqsCommand::readGroup(){
 608         try {
 609                 string thisOutputDir = outputDir;
 610                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 611                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 612                 ofstream out;
 613                 m->openOutputFile(outputFileName, out);
 614
 615
 616                 ifstream in;
 617                 m->openInputFile(groupfile, in);
 618                 string name, group;
 619
 620                 bool wroteSomething = false;
 621
 622                 while(!in.eof()){
 623
 624                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 625
 626
 627                         in >> name;                             //read from first column
 628                         in >> group;                    //read from second column
 629
 630                         //if this name is in the accnos file
 631                         if (names.count(name) != 0) {
 632                                 wroteSomething = true;
 633
 634                                 out << name << '\t' << group << endl;
 635                         }
 636
 637                         m->gobble(in);
 638                 }
 639                 in.close();
 640                 out.close();
 641
 642                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 643                 outputNames.push_back(outputFileName);  outputTypes["group"].push_back(outputFileName);
 644
 645                 return 0;
 646
 647         }
 648         catch(exception& e) {
 649                 m->errorOut(e, "GetSeqsCommand", "readGroup");
 650                 exit(1);
 651         }
 652 }
 653 //**********************************************************************************************************************
 654 int GetSeqsCommand::readTax(){
 655         try {
 656                 string thisOutputDir = outputDir;
 657                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 658                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 659                 ofstream out;
 660                 m->openOutputFile(outputFileName, out);
 661
 662                 ifstream in;
 663                 m->openInputFile(taxfile, in);
 664                 string name, tax;
 665
 666                 bool wroteSomething = false;
 667
 668                 while(!in.eof()){
 669
 670                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 671
 672                         in >> name;                             //read from first column
 673                         in >> tax;                      //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' << tax << endl;
 680                         }
 681
 682                         m->gobble(in);
 683                 }
 684                 in.close();
 685                 out.close();
 686
 687                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 688                 outputNames.push_back(outputFileName);  outputTypes["taxonomy"].push_back(outputFileName);
 689
 690                 return 0;
 691
 692         }
 693         catch(exception& e) {
 694                 m->errorOut(e, "GetSeqsCommand", "readTax");
 695                 exit(1);
 696         }
 697 }
 698 //**********************************************************************************************************************
 699 //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
 700 int GetSeqsCommand::readAlign(){
 701         try {
 702                 string thisOutputDir = outputDir;
 703                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 704                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
 705                 ofstream out;
 706                 m->openOutputFile(outputFileName, out);
 707
 708
 709                 ifstream in;
 710                 m->openInputFile(alignfile, in);
 711                 string name, junk;
 712
 713                 bool wroteSomething = false;
 714
 715                 //read column headers
 716                 for (int i = 0; i < 16; i++) {
 717                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 718                         else                    {       break;                  }
 719                 }
 720                 out << endl;
 721
 722                 while(!in.eof()){
 723
 724                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 725
 726
 727                         in >> name;                             //read from first 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';
 734
 735                                 //read rest
 736                                 for (int i = 0; i < 15; i++) {
 737                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 738                                         else                    {       break;                  }
 739                                 }
 740                                 out << endl;
 741
 742                         }else {//still read just don't do anything with it
 743                                 //read rest
 744                                 for (int i = 0; i < 15; i++) {
 745                                         if (!in.eof())  {       in >> junk;             }
 746                                         else                    {       break;                  }
 747                                 }
 748                         }
 749
 750                         m->gobble(in);
 751                 }
 752                 in.close();
 753                 out.close();
 754
 755                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 756                 outputNames.push_back(outputFileName);  outputTypes["alignreport"].push_back(outputFileName);
 757
 758                 return 0;
 759
 760         }
 761         catch(exception& e) {
 762                 m->errorOut(e, "GetSeqsCommand", "readAlign");
 763                 exit(1);
 764         }
 765 }
 766 //**********************************************************************************************************************
 767
 768 int GetSeqsCommand::readAccnos(){
 769         try {
 770
 771                 ifstream in;
 772                 m->openInputFile(accnosfile, in);
 773                 string name;
 774
 775                 while(!in.eof()){
 776                         in >> name;
 777
 778                         names.insert(name);
 779
 780                         m->gobble(in);
 781                 }
 782                 in.close();
 783
 784                 return 0;
 785
 786         }
 787         catch(exception& e) {
 788                 m->errorOut(e, "GetSeqsCommand", "readAccnos");
 789                 exit(1);
 790         }
 791 }
 792 //**********************************************************************************************************************
 793
 794 int GetSeqsCommand::compareAccnos(){
 795         try {
 796
 797                 string thisOutputDir = outputDir;
 798                 if (outputDir == "") {  thisOutputDir += m->hasPath(accnosfile);  }
 799                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(accnosfile)) + "accnos.report";
 800                 ofstream out;
 801                 m->openOutputFile(outputFileName, out);
 802
 803                 ifstream in;
 804                 m->openInputFile(accnosfile2, in);
 805                 string name;
 806
 807                 set<string> namesAccnos2;
 808                 set<string> namesDups;
 809                 set<string> namesAccnos = names;
 810
 811                 map<string, int> nameCount;
 812
 813                 if (namefile != "") {
 814                         ifstream inName;
 815                         m->openInputFile(namefile, inName);
 816
 817
 818                         while(!inName.eof()){
 819
 820                                 if (m->control_pressed) { inName.close(); return 0; }
 821
 822                                 string thisname, repnames;
 823
 824                                 inName >> thisname;             m->gobble(inName);              //read from first column
 825                                 inName >> repnames;                     //read from second column
 826
 827                                 int num = m->getNumNames(repnames);
 828                                 nameCount[thisname] = num;
 829
 830                                 m->gobble(inName);
 831                         }
 832                         inName.close();
 833                 }
 834
 835                 while(!in.eof()){
 836                         in >> name;
 837
 838                         if (namesAccnos.count(name) == 0){ //name unique to accnos2
 839                                 int pos = name.find_last_of('_');
 840                                 string tempName = name;
 841                                 if (pos != string::npos) {  tempName = tempName.substr(pos+1); cout << tempName << endl; }
 842                                 if (namesAccnos.count(tempName) == 0){
 843                                         namesAccnos2.insert(name);
 844                                 }else { //you are in both so erase
 845                                         namesAccnos.erase(name);
 846                                         namesDups.insert(name);
 847                                 }
 848                         }else { //you are in both so erase
 849                                 namesAccnos.erase(name);
 850                                 namesDups.insert(name);
 851                         }
 852
 853                         m->gobble(in);
 854                 }
 855                 in.close();
 856
 857                 out << "Names in both files : " + toString(namesDups.size()) << endl;
 858                 m->mothurOut("Names in both files : " + toString(namesDups.size())); m->mothurOutEndLine();
 859
 860                 for (set<string>::iterator it = namesDups.begin(); it != namesDups.end(); it++) {
 861                         out << (*it);
 862                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
 863                         out << endl;
 864                 }
 865
 866                 out << "Names unique to " + accnosfile + " : " + toString(namesAccnos.size()) << endl;
 867                 m->mothurOut("Names unique to " + accnosfile + " : " + toString(namesAccnos.size())); m->mothurOutEndLine();
 868
 869                 for (set<string>::iterator it = namesAccnos.begin(); it != namesAccnos.end(); it++) {
 870                         out << (*it);
 871                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
 872                         out << endl;
 873                 }
 874
 875                 out << "Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size()) << endl;
 876                 m->mothurOut("Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size())); m->mothurOutEndLine();
 877
 878                 for (set<string>::iterator it = namesAccnos2.begin(); it != namesAccnos2.end(); it++) {
 879                         out << (*it);
 880                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
 881                         out << endl;
 882                 }
 883
 884                 out.close();
 885
 886                 outputNames.push_back(outputFileName);  outputTypes["accnosreport"].push_back(outputFileName);
 887
 888                 return 0;
 889
 890         }
 891         catch(exception& e) {
 892                 m->errorOut(e, "GetSeqsCommand", "readAccnos");
 893                 exit(1);
 894         }
 895 }
 896
 897
 898 //**********************************************************************************************************************
 899