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 #include "counttable.h"
  14
  15 //**********************************************************************************************************************
  16 vector<string> GetSeqsCommand::setParameters(){
  17         try {
  18                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
  19         CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none",false,false); parameters.push_back(pname);
  20         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none",false,false); parameters.push_back(pcount);
  21                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none",false,false); parameters.push_back(pgroup);
  22                 CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
  23                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
  24                 CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);
  25                 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pqfile);
  26                 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos);
  27                 CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
  28                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  29                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  30                 CommandParameter paccnos2("accnos2", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos2);
  31
  32                 vector<string> myArray;
  33                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  34                 return myArray;
  35         }
  36         catch(exception& e) {
  37                 m->errorOut(e, "GetSeqsCommand", "setParameters");
  38                 exit(1);
  39         }
  40 }
  41 //**********************************************************************************************************************
  42 string GetSeqsCommand::getHelpString(){
  43         try {
  44                 string helpString = "";
  45                 helpString += "The get.seqs command reads an .accnos file and any of the following file types: fasta, name, group, count, list, taxonomy, quality or alignreport file.\n";
  46                 helpString += "It outputs a file containing only the sequences in the .accnos file.\n";
  47                 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";
  48                 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";
  49                 helpString += "The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n";
  50                 helpString += "Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n";
  51                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  52                 return helpString;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "GetSeqsCommand", "getHelpString");
  56                 exit(1);
  57         }
  58 }
  59
  60 //**********************************************************************************************************************
  61 GetSeqsCommand::GetSeqsCommand(){
  62         try {
  63                 abort = true; calledHelp = true;
  64                 setParameters();
  65                 vector<string> tempOutNames;
  66                 outputTypes["fasta"] = tempOutNames;
  67                 outputTypes["taxonomy"] = tempOutNames;
  68                 outputTypes["name"] = tempOutNames;
  69                 outputTypes["group"] = tempOutNames;
  70                 outputTypes["alignreport"] = tempOutNames;
  71                 outputTypes["list"] = tempOutNames;
  72                 outputTypes["qfile"] = tempOutNames;
  73         outputTypes["count"] = tempOutNames;
  74                 outputTypes["accnosreport"] = tempOutNames;
  75         }
  76         catch(exception& e) {
  77                 m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
  78                 exit(1);
  79         }
  80 }
  81 //**********************************************************************************************************************
  82 string GetSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
  83         try {
  84         string outputFileName = "";
  85                 map<string, vector<string> >::iterator it;
  86
  87         //is this a type this command creates
  88         it = outputTypes.find(type);
  89         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  90         else {
  91             if (type == "fasta")            {   outputFileName =  "pick" + m->getExtension(inputName);   }
  92             else if (type == "taxonomy")    {   outputFileName =  "pick" + m->getExtension(inputName);   }
  93             else if (type == "name")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
  94             else if (type == "count")       {   outputFileName =  "pick.count_table";   }
  95             else if (type == "group")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
  96             else if (type == "list")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
  97             else if (type == "qfile")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
  98             else if (type == "accnosreport"){   outputFileName =  "accnos.report";                       }
  99             else if (type == "alignreport") {   outputFileName =  "pick.align.report";                   }
 100             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
 101         }
 102         return outputFileName;
 103         }
 104         catch(exception& e) {
 105                 m->errorOut(e, "GetSeqsCommand", "getOutputFileNameTag");
 106                 exit(1);
 107         }
 108 }
 109 //**********************************************************************************************************************
 110 GetSeqsCommand::GetSeqsCommand(string option)  {
 111         try {
 112                 abort = false; calledHelp = false;
 113
 114                 //allow user to run help
 115                 if(option == "help") { help(); abort = true; calledHelp = true; }
 116                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 117
 118                 else {
 119                         vector<string> myArray = setParameters();
 120
 121                         OptionParser parser(option);
 122                         map<string,string> parameters = parser.getParameters();
 123
 124                         ValidParameters validParameter;
 125                         map<string,string>::iterator it;
 126
 127                         //check to make sure all parameters are valid for command
 128                         for (it = parameters.begin(); it != parameters.end(); it++) {
 129                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 130                         }
 131
 132                         //initialize outputTypes
 133                         vector<string> tempOutNames;
 134                         outputTypes["fasta"] = tempOutNames;
 135                         outputTypes["taxonomy"] = tempOutNames;
 136                         outputTypes["name"] = tempOutNames;
 137                         outputTypes["group"] = tempOutNames;
 138                         outputTypes["alignreport"] = tempOutNames;
 139                         outputTypes["list"] = tempOutNames;
 140                         outputTypes["qfile"] = tempOutNames;
 141                         outputTypes["accnosreport"] = tempOutNames;
 142             outputTypes["count"] = tempOutNames;
 143
 144                         //if the user changes the output directory command factory will send this info to us in the output parameter
 145                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 146
 147                         //if the user changes the input directory command factory will send this info to us in the output parameter
 148                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 149                         if (inputDir == "not found"){   inputDir = "";          }
 150                         else {
 151                                 string path;
 152                                 it = parameters.find("alignreport");
 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["alignreport"] = inputDir + it->second;              }
 158                                 }
 159
 160                                 it = parameters.find("fasta");
 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["fasta"] = inputDir + it->second;            }
 166                                 }
 167
 168                                 it = parameters.find("accnos");
 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["accnos"] = inputDir + it->second;           }
 174                                 }
 175
 176                                 it = parameters.find("accnos2");
 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["accnos2"] = inputDir + it->second;          }
 182                                 }
 183
 184                                 it = parameters.find("list");
 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["list"] = inputDir + it->second;             }
 190                                 }
 191
 192                                 it = parameters.find("name");
 193                                 //user has given a template file
 194                                 if(it != parameters.end()){
 195                                         path = m->hasPath(it->second);
 196                                         //if the user has not given a path then, add inputdir. else leave path alone.
 197                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 198                                 }
 199
 200                                 it = parameters.find("group");
 201                                 //user has given a template file
 202                                 if(it != parameters.end()){
 203                                         path = m->hasPath(it->second);
 204                                         //if the user has not given a path then, add inputdir. else leave path alone.
 205                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 206                                 }
 207
 208                                 it = parameters.find("taxonomy");
 209                                 //user has given a template file
 210                                 if(it != parameters.end()){
 211                                         path = m->hasPath(it->second);
 212                                         //if the user has not given a path then, add inputdir. else leave path alone.
 213                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 214                                 }
 215
 216                                 it = parameters.find("qfile");
 217                                 //user has given a template file
 218                                 if(it != parameters.end()){
 219                                         path = m->hasPath(it->second);
 220                                         //if the user has not given a path then, add inputdir. else leave path alone.
 221                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 222                                 }
 223
 224                 it = parameters.find("count");
 225                                 //user has given a template file
 226                                 if(it != parameters.end()){
 227                                         path = m->hasPath(it->second);
 228                                         //if the user has not given a path then, add inputdir. else leave path alone.
 229                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 230                                 }
 231                         }
 232
 233
 234                         //check for required parameters
 235                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 236                         if (accnosfile == "not open") { abort = true; }
 237                         else if (accnosfile == "not found") {
 238                                 accnosfile = m->getAccnosFile();
 239                                 if (accnosfile != "") {  m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); }
 240                                 else {
 241                                         m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine();
 242                                         abort = true;
 243                                 }
 244                         }else { m->setAccnosFile(accnosfile); }
 245
 246                         if (accnosfile2 == "not found") { accnosfile2 = ""; }
 247
 248                         fastafile = validParameter.validFile(parameters, "fasta", true);
 249                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 250                         else if (fastafile == "not found") {  fastafile = "";  }
 251                         else { m->setFastaFile(fastafile); }
 252
 253                         namefile = validParameter.validFile(parameters, "name", true);
 254                         if (namefile == "not open") { namefile = ""; abort = true; }
 255                         else if (namefile == "not found") {  namefile = "";  }
 256                         else { m->setNameFile(namefile); }
 257
 258                         groupfile = validParameter.validFile(parameters, "group", true);
 259                         if (groupfile == "not open") { abort = true; }
 260                         else if (groupfile == "not found") {  groupfile = "";  }
 261                         else { m->setGroupFile(groupfile); }
 262
 263                         alignfile = validParameter.validFile(parameters, "alignreport", true);
 264                         if (alignfile == "not open") { abort = true; }
 265                         else if (alignfile == "not found") {  alignfile = "";  }
 266
 267                         listfile = validParameter.validFile(parameters, "list", true);
 268                         if (listfile == "not open") { abort = true; }
 269                         else if (listfile == "not found") {  listfile = "";  }
 270                         else { m->setListFile(listfile); }
 271
 272                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 273                         if (taxfile == "not open") { taxfile = ""; abort = true; }
 274                         else if (taxfile == "not found") {  taxfile = "";  }
 275                         else { m->setTaxonomyFile(taxfile); }
 276
 277                         qualfile = validParameter.validFile(parameters, "qfile", true);
 278                         if (qualfile == "not open") { abort = true; }
 279                         else if (qualfile == "not found") {  qualfile = "";  }
 280                         else { m->setQualFile(qualfile); }
 281
 282                         accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
 283                         if (accnosfile2 == "not open") { abort = true; }
 284                         else if (accnosfile2 == "not found") {  accnosfile2 = "";  }
 285
 286             countfile = validParameter.validFile(parameters, "count", true);
 287             if (countfile == "not open") { countfile = ""; abort = true; }
 288             else if (countfile == "not found") { countfile = "";  }
 289             else { m->setCountTableFile(countfile); }
 290
 291             if ((namefile != "") && (countfile != "")) {
 292                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 293             }
 294
 295             if ((groupfile != "") && (countfile != "")) {
 296                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 297             }
 298
 299
 300                         string usedDups = "true";
 301                         string temp = validParameter.validFile(parameters, "dups", false);      if (temp == "not found") { temp = "true"; usedDups = ""; }
 302                         dups = m->isTrue(temp);
 303
 304                         if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == "") && (accnosfile2 == "") && (countfile == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, count, alignreport, taxonomy, quality or listfile."); m->mothurOutEndLine(); abort = true; }
 305
 306             if (countfile == "") {
 307                 if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
 308                     vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
 309                     parser.getNameFile(files);
 310                 }
 311             }
 312                 }
 313
 314         }
 315         catch(exception& e) {
 316                 m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
 317                 exit(1);
 318         }
 319 }
 320 //**********************************************************************************************************************
 321
 322 int GetSeqsCommand::execute(){
 323         try {
 324
 325                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 326
 327                 //get names you want to keep
 328                 names = m->readAccnos(accnosfile);
 329
 330                 if (m->control_pressed) { return 0; }
 331
 332         if (countfile != "") {
 333             if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
 334                 m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
 335             }
 336         }
 337
 338                 //read through the correct file and output lines you want to keep
 339                 if (namefile != "")                     {               readName();                     }
 340                 if (fastafile != "")            {               readFasta();            }
 341                 if (groupfile != "")            {               readGroup();            }
 342         if (countfile != "")            {               readCount();            }
 343                 if (alignfile != "")            {               readAlign();            }
 344                 if (listfile != "")                     {               readList();                     }
 345                 if (taxfile != "")                      {               readTax();                      }
 346                 if (qualfile != "")                     {               readQual();                     }
 347                 if (accnosfile2 != "")          {               compareAccnos();        }
 348
 349         if (m->debug) { runSanityCheck(); }
 350
 351                 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);  } return 0; }
 352
 353
 354                 if (outputNames.size() != 0) {
 355                         m->mothurOutEndLine();
 356                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 357                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 358                         m->mothurOutEndLine();
 359
 360                         //set fasta file as new current fastafile
 361                         string current = "";
 362                         itTypes = outputTypes.find("fasta");
 363                         if (itTypes != outputTypes.end()) {
 364                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 365                         }
 366
 367                         itTypes = outputTypes.find("name");
 368                         if (itTypes != outputTypes.end()) {
 369                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 370                         }
 371
 372                         itTypes = outputTypes.find("group");
 373                         if (itTypes != outputTypes.end()) {
 374                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 375                         }
 376
 377                         itTypes = outputTypes.find("list");
 378                         if (itTypes != outputTypes.end()) {
 379                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 380                         }
 381
 382                         itTypes = outputTypes.find("taxonomy");
 383                         if (itTypes != outputTypes.end()) {
 384                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 385                         }
 386
 387                         itTypes = outputTypes.find("qfile");
 388                         if (itTypes != outputTypes.end()) {
 389                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 390                         }
 391
 392             itTypes = outputTypes.find("count");
 393                         if (itTypes != outputTypes.end()) {
 394                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 395                         }
 396                 }
 397
 398                 return 0;
 399         }
 400
 401         catch(exception& e) {
 402                 m->errorOut(e, "GetSeqsCommand", "execute");
 403                 exit(1);
 404         }
 405 }
 406
 407 //**********************************************************************************************************************
 408 int GetSeqsCommand::readFasta(){
 409         try {
 410                 string thisOutputDir = outputDir;
 411                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 412                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
 413                 ofstream out;
 414                 m->openOutputFile(outputFileName, out);
 415
 416
 417                 ifstream in;
 418                 m->openInputFile(fastafile, in);
 419                 string name;
 420
 421                 bool wroteSomething = false;
 422                 int selectedCount = 0;
 423
 424         if (m->debug) { set<string> temp; sanity["fasta"] = temp; }
 425
 426                 while(!in.eof()){
 427
 428                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 429
 430                         Sequence currSeq(in);
 431                         name = currSeq.getName();
 432
 433                         if (name != "") {
 434                                 //if this name is in the accnos file
 435                                 if (names.count(name) != 0) {
 436                                         wroteSomething = true;
 437
 438                                         currSeq.printSequence(out);
 439                                         selectedCount++;
 440
 441                     if (m->debug) { sanity["fasta"].insert(name); }
 442                                 }
 443                         }
 444                         m->gobble(in);
 445                 }
 446                 in.close();
 447                 out.close();
 448
 449
 450                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 451                 outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);
 452
 453                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
 454
 455                 return 0;
 456
 457         }
 458         catch(exception& e) {
 459                 m->errorOut(e, "GetSeqsCommand", "readFasta");
 460                 exit(1);
 461         }
 462 }
 463 //**********************************************************************************************************************
 464 int GetSeqsCommand::readQual(){
 465         try {
 466                 string thisOutputDir = outputDir;
 467                 if (outputDir == "") {  thisOutputDir += m->hasPath(qualfile);  }
 468                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("qfile", qualfile);
 469                 ofstream out;
 470                 m->openOutputFile(outputFileName, out);
 471
 472
 473                 ifstream in;
 474                 m->openInputFile(qualfile, in);
 475                 string name;
 476
 477                 bool wroteSomething = false;
 478                 int selectedCount = 0;
 479
 480         if (m->debug) { set<string> temp; sanity["qual"] = temp; }
 481
 482                 while(!in.eof()){
 483                         string saveName = "";
 484                         string name = "";
 485                         string scores = "";
 486
 487                         in >> name;
 488
 489                         if (name.length() != 0) {
 490                                 saveName = name.substr(1);
 491                                 while (!in.eof())       {
 492                                         char c = in.get();
 493                                         if (c == 10 || c == 13){        break;  }
 494                                         else { name += c; }
 495                                 }
 496                                 m->gobble(in);
 497                         }
 498
 499                         while(in){
 500                                 char letter= in.get();
 501                                 if(letter == '>'){      in.putback(letter);     break;  }
 502                                 else{ scores += letter; }
 503                         }
 504
 505                         m->gobble(in);
 506
 507                         if (names.count(saveName) != 0) {
 508                                 wroteSomething = true;
 509
 510                                 out << name << endl << scores;
 511                                 selectedCount++;
 512                 if (m->debug) { sanity["qual"].insert(name); }
 513                         }
 514
 515                         m->gobble(in);
 516                 }
 517                 in.close();
 518                 out.close();
 519
 520
 521                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 522                 outputNames.push_back(outputFileName);  outputTypes["qfile"].push_back(outputFileName);
 523
 524                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your quality file."); m->mothurOutEndLine();
 525
 526
 527                 return 0;
 528
 529         }
 530         catch(exception& e) {
 531                 m->errorOut(e, "GetSeqsCommand", "readQual");
 532                 exit(1);
 533         }
 534 }
 535 //**********************************************************************************************************************
 536 int GetSeqsCommand::readCount(){
 537         try {
 538                 string thisOutputDir = outputDir;
 539                 if (outputDir == "") {  thisOutputDir += m->hasPath(countfile);  }
 540                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
 541
 542                 ofstream out;
 543                 m->openOutputFile(outputFileName, out);
 544
 545                 ifstream in;
 546                 m->openInputFile(countfile, in);
 547
 548                 bool wroteSomething = false;
 549                 int selectedCount = 0;
 550
 551         string headers = m->getline(in); m->gobble(in);
 552         out << headers << endl;
 553
 554         string name, rest; int thisTotal;
 555         while (!in.eof()) {
 556
 557             if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 558
 559             in >> name; m->gobble(in);
 560             in >> thisTotal; m->gobble(in);
 561             rest = m->getline(in); m->gobble(in);
 562             if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + rest + "\n"); }
 563
 564             if (names.count(name) != 0) {
 565                 out << name << '\t' << thisTotal << '\t' << rest << endl;
 566                 wroteSomething = true;
 567                 selectedCount+= thisTotal;
 568             }
 569         }
 570         in.close();
 571                 out.close();
 572
 573         //check for groups that have been eliminated
 574         CountTable ct;
 575         if (ct.testGroups(outputFileName)) {
 576             ct.readTable(outputFileName);
 577             ct.printTable(outputFileName);
 578         }
 579
 580                 if (wroteSomething == false) {  m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 581                 outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
 582
 583                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your count file."); m->mothurOutEndLine();
 584
 585                 return 0;
 586         }
 587         catch(exception& e) {
 588                 m->errorOut(e, "GetSeqsCommand", "readCount");
 589                 exit(1);
 590         }
 591 }
 592
 593 //**********************************************************************************************************************
 594 int GetSeqsCommand::readList(){
 595         try {
 596                 string thisOutputDir = outputDir;
 597                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 598                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
 599                 ofstream out;
 600                 m->openOutputFile(outputFileName, out);
 601
 602                 ifstream in;
 603                 m->openInputFile(listfile, in);
 604
 605                 bool wroteSomething = false;
 606                 int selectedCount = 0;
 607
 608         if (m->debug) { set<string> temp; sanity["list"] = temp; }
 609
 610                 while(!in.eof()){
 611
 612                         selectedCount = 0;
 613
 614                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 615
 616                         //read in list vector
 617                         ListVector list(in);
 618
 619                         //make a new list vector
 620                         ListVector newList;
 621                         newList.setLabel(list.getLabel());
 622
 623                         //for each bin
 624                         for (int i = 0; i < list.getNumBins(); i++) {
 625
 626                                 //parse out names that are in accnos file
 627                                 string binnames = list.get(i);
 628                 vector<string> bnames;
 629                 m->splitAtComma(binnames, bnames);
 630
 631                                 string newNames = "";
 632                 for (int i = 0; i < bnames.size(); i++) {
 633                                         string name = bnames[i];
 634                                         //if that name is in the .accnos file, add it
 635                                         if (names.count(name) != 0) {  newNames += name + ",";  selectedCount++; if (m->debug) { sanity["list"].insert(name); } }
 636                                 }
 637
 638                                 //if there are names in this bin add to new list
 639                                 if (newNames != "") {
 640                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 641                                         newList.push_back(newNames);
 642                                 }
 643                         }
 644
 645                         //print new listvector
 646                         if (newList.getNumBins() != 0) {
 647                                 wroteSomething = true;
 648                                 newList.print(out);
 649                         }
 650
 651                         m->gobble(in);
 652                 }
 653                 in.close();
 654                 out.close();
 655
 656                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 657                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 658
 659                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine();
 660
 661                 return 0;
 662
 663         }
 664         catch(exception& e) {
 665                 m->errorOut(e, "GetSeqsCommand", "readList");
 666                 exit(1);
 667         }
 668 }
 669 //**********************************************************************************************************************
 670 int GetSeqsCommand::readName(){
 671         try {
 672                 string thisOutputDir = outputDir;
 673                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 674                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
 675                 ofstream out;
 676                 m->openOutputFile(outputFileName, out);
 677
 678
 679                 ifstream in;
 680                 m->openInputFile(namefile, in);
 681                 string name, firstCol, secondCol;
 682
 683                 bool wroteSomething = false;
 684                 int selectedCount = 0;
 685
 686         if (m->debug) { set<string> temp; sanity["name"] = temp; }
 687         if (m->debug) { set<string> temp; sanity["dupname"] = temp; }
 688
 689                 while(!in.eof()){
 690
 691                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 692
 693                         in >> firstCol;
 694                         in >> secondCol;
 695
 696                         string hold = "";
 697                         if (dups) { hold = secondCol; }
 698
 699                         vector<string> parsedNames;
 700                         m->splitAtComma(secondCol, parsedNames);
 701
 702                         vector<string> validSecond;
 703                         for (int i = 0; i < parsedNames.size(); i++) {
 704                                 if (names.count(parsedNames[i]) != 0) {
 705                                         validSecond.push_back(parsedNames[i]);
 706                     if (m->debug) { sanity["dupname"].insert(parsedNames[i]); }
 707                                 }
 708                         }
 709
 710                         if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
 711                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]); if (m->debug) { sanity["dupname"].insert(parsedNames[i]); } }
 712                                 out << firstCol << '\t' << hold << endl;
 713                                 wroteSomething = true;
 714                                 selectedCount += parsedNames.size();
 715                 if (m->debug) { sanity["name"].insert(firstCol); }
 716                         }else {
 717                                 selectedCount += validSecond.size();
 718
 719                                 //if the name in the first column is in the set then print it and any other names in second column also in set
 720                                 if (names.count(firstCol) != 0) {
 721
 722                                         wroteSomething = true;
 723
 724                                         out << firstCol << '\t';
 725
 726                                         //you know you have at least one valid second since first column is valid
 727                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 728                                         out << validSecond[validSecond.size()-1] << endl;
 729
 730                     if (m->debug) { sanity["name"].insert(firstCol); }
 731
 732
 733                                 //make first name in set you come to first column and then add the remaining names to second column
 734                                 }else {
 735                                         //you want part of this row
 736                                         if (validSecond.size() != 0) {
 737
 738                                                 wroteSomething = true;
 739
 740                                                 out << validSecond[0] << '\t';
 741
 742                                                 //you know you have at least one valid second since first column is valid
 743                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 744                                                 out << validSecond[validSecond.size()-1] << endl;
 745
 746                         if (m->debug) { sanity["name"].insert(validSecond[0]); }
 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["name"].push_back(outputFileName);
 757
 758                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your name file."); m->mothurOutEndLine();
 759
 760                 return 0;
 761
 762         }
 763         catch(exception& e) {
 764                 m->errorOut(e, "GetSeqsCommand", "readName");
 765                 exit(1);
 766         }
 767 }
 768
 769 //**********************************************************************************************************************
 770 int GetSeqsCommand::readGroup(){
 771         try {
 772                 string thisOutputDir = outputDir;
 773                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 774                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
 775                 ofstream out;
 776                 m->openOutputFile(outputFileName, out);
 777
 778
 779                 ifstream in;
 780                 m->openInputFile(groupfile, in);
 781                 string name, group;
 782
 783                 bool wroteSomething = false;
 784                 int selectedCount = 0;
 785
 786         if (m->debug) { set<string> temp; sanity["group"] = temp; }
 787
 788                 while(!in.eof()){
 789
 790                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 791
 792
 793                         in >> name;                             //read from first column
 794                         in >> group;                    //read from second column
 795
 796                         //if this name is in the accnos file
 797                         if (names.count(name) != 0) {
 798                                 wroteSomething = true;
 799
 800                                 out << name << '\t' << group << endl;
 801                                 selectedCount++;
 802
 803                 if (m->debug) {  sanity["group"].insert(name); }
 804                         }
 805
 806                         m->gobble(in);
 807                 }
 808                 in.close();
 809                 out.close();
 810
 811                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 812                 outputNames.push_back(outputFileName);  outputTypes["group"].push_back(outputFileName);
 813
 814                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your group file."); m->mothurOutEndLine();
 815
 816
 817                 return 0;
 818
 819         }
 820         catch(exception& e) {
 821                 m->errorOut(e, "GetSeqsCommand", "readGroup");
 822                 exit(1);
 823         }
 824 }
 825 //**********************************************************************************************************************
 826 int GetSeqsCommand::readTax(){
 827         try {
 828                 string thisOutputDir = outputDir;
 829                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 830                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
 831                 ofstream out;
 832                 m->openOutputFile(outputFileName, out);
 833
 834                 ifstream in;
 835                 m->openInputFile(taxfile, in);
 836                 string name, tax;
 837
 838                 bool wroteSomething = false;
 839                 int selectedCount = 0;
 840
 841         if (m->debug) { set<string> temp; sanity["tax"] = temp; }
 842
 843                 while(!in.eof()){
 844
 845                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 846
 847                         in >> name;                             //read from first column
 848                         in >> tax;                      //read from second column
 849
 850                         //if this name is in the accnos file
 851                         if (names.count(name) != 0) {
 852                                 wroteSomething = true;
 853
 854                                 out << name << '\t' << tax << endl;
 855                                 selectedCount++;
 856
 857                 if (m->debug) { sanity["tax"].insert(name); }
 858                         }
 859
 860                         m->gobble(in);
 861                 }
 862                 in.close();
 863                 out.close();
 864
 865                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 866                 outputNames.push_back(outputFileName);  outputTypes["taxonomy"].push_back(outputFileName);
 867
 868                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine();
 869
 870                 return 0;
 871
 872         }
 873         catch(exception& e) {
 874                 m->errorOut(e, "GetSeqsCommand", "readTax");
 875                 exit(1);
 876         }
 877 }
 878 //**********************************************************************************************************************
 879 //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
 880 int GetSeqsCommand::readAlign(){
 881         try {
 882                 string thisOutputDir = outputDir;
 883                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 884                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + getOutputFileNameTag("alignreport");
 885                 ofstream out;
 886                 m->openOutputFile(outputFileName, out);
 887
 888
 889                 ifstream in;
 890                 m->openInputFile(alignfile, in);
 891                 string name, junk;
 892
 893                 bool wroteSomething = false;
 894                 int selectedCount = 0;
 895
 896                 //read column headers
 897                 for (int i = 0; i < 16; i++) {
 898                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 899                         else                    {       break;                  }
 900                 }
 901                 out << endl;
 902
 903                 while(!in.eof()){
 904
 905                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 906
 907
 908                         in >> name;                             //read from first column
 909
 910                         //if this name is in the accnos file
 911                         if (names.count(name) != 0) {
 912                                 wroteSomething = true;
 913                                 selectedCount++;
 914
 915                                 out << name << '\t';
 916
 917                                 //read rest
 918                                 for (int i = 0; i < 15; i++) {
 919                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 920                                         else                    {       break;                  }
 921                                 }
 922                                 out << endl;
 923
 924                         }else {//still read just don't do anything with it
 925                                 //read rest
 926                                 for (int i = 0; i < 15; i++) {
 927                                         if (!in.eof())  {       in >> junk;             }
 928                                         else                    {       break;                  }
 929                                 }
 930                         }
 931
 932                         m->gobble(in);
 933                 }
 934                 in.close();
 935                 out.close();
 936
 937                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 938                 outputNames.push_back(outputFileName);  outputTypes["alignreport"].push_back(outputFileName);
 939
 940                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your alignreport file."); m->mothurOutEndLine();
 941
 942                 return 0;
 943
 944         }
 945         catch(exception& e) {
 946                 m->errorOut(e, "GetSeqsCommand", "readAlign");
 947                 exit(1);
 948         }
 949 }
 950 //**********************************************************************************************************************
 951 //just looking at common mistakes.
 952 int GetSeqsCommand::runSanityCheck(){
 953         try {
 954         string thisOutputDir = outputDir;
 955         if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 956         string filename = outputDir + "get.seqs.debug.report";
 957
 958         ofstream out;
 959                 m->openOutputFile(filename, out);
 960
 961
 962         //compare fasta, name, qual and taxonomy if given to make sure they contain the same seqs
 963         if (fastafile != "") {
 964             if (namefile != "") { //compare with fasta
 965                 if (sanity["fasta"] != sanity["name"]) { //create mismatch file
 966                     createMisMatchFile(out, fastafile, namefile, sanity["fasta"], sanity["name"]);
 967                 }
 968             }
 969             if (qualfile != "") {
 970                 if (sanity["fasta"] != sanity["qual"]) { //create mismatch file
 971                     createMisMatchFile(out, fastafile, qualfile, sanity["fasta"], sanity["qual"]);
 972                 }
 973             }
 974             if (taxfile != "") {
 975                 if (sanity["fasta"] != sanity["tax"]) { //create mismatch file
 976                     createMisMatchFile(out, fastafile, taxfile, sanity["fasta"], sanity["tax"]);
 977                 }
 978             }
 979         }
 980
 981         //compare dupnames, groups and list if given to make sure they match
 982         if (namefile != "") {
 983             if (groupfile != "") {
 984                 if (sanity["dupname"] != sanity["group"]) { //create mismatch file
 985                     createMisMatchFile(out, namefile, groupfile, sanity["dupname"], sanity["group"]);
 986                 }
 987             }
 988             if (listfile != "") {
 989                 if (sanity["dupname"] != sanity["list"]) { //create mismatch file
 990                     createMisMatchFile(out, namefile, listfile, sanity["dupname"], sanity["list"]);
 991                 }
 992             }
 993         }else{
 994
 995             if ((groupfile != "") && (fastafile != "")) {
 996                 if (sanity["fasta"] != sanity["group"]) { //create mismatch file
 997                     createMisMatchFile(out, fastafile, groupfile, sanity["fasta"], sanity["group"]);
 998                 }
 999             }
1000         }
1001
1002         out.close();
1003
1004         if (m->isBlank(filename)) { m->mothurRemove(filename); }
1005         else { m->mothurOut("\n[DEBUG]: " + filename + " contains the file mismatches.\n");outputNames.push_back(filename); outputTypes["debug"].push_back(filename); }
1006
1007         return 0;
1008     }
1009         catch(exception& e) {
1010                 m->errorOut(e, "GetSeqsCommand", "runSanityCheck");
1011                 exit(1);
1012         }
1013 }
1014 //**********************************************************************************************************************
1015 //just looking at common mistakes.
1016 int GetSeqsCommand::createMisMatchFile(ofstream& out, string filename1, string filename2, set<string> set1, set<string> set2){
1017         try {
1018         out << "****************************************" << endl << endl;
1019         out << "Names unique to " << filename1 << ":\n";
1020
1021         //remove names in set1 that are also in set2
1022         for (set<string>::iterator it = set1.begin(); it != set1.end();) {
1023             string name = *it;
1024
1025             if (set2.count(name) == 0)  { out << name << endl;  } //name unique to set1
1026             else                        { set2.erase(name);     } //you are in both so erase
1027             set1.erase(it++);
1028         }
1029
1030         out << "\nNames unique to " << filename2 << ":\n";
1031         //output results
1032         for (set<string>::iterator it = set2.begin(); it != set2.end(); it++) {  out << *it << endl;  }
1033
1034         out << "****************************************" << endl << endl;
1035
1036         return 0;
1037     }
1038         catch(exception& e) {
1039                 m->errorOut(e, "GetSeqsCommand", "runSanityCheck");
1040                 exit(1);
1041         }
1042 }
1043 //**********************************************************************************************************************
1044
1045 int GetSeqsCommand::compareAccnos(){
1046         try {
1047
1048                 string thisOutputDir = outputDir;
1049                 if (outputDir == "") {  thisOutputDir += m->hasPath(accnosfile);  }
1050                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(accnosfile)) + getOutputFileNameTag("accnosreport");
1051                 ofstream out;
1052                 m->openOutputFile(outputFileName, out);
1053
1054                 ifstream in;
1055                 m->openInputFile(accnosfile2, in);
1056                 string name;
1057
1058                 set<string> namesAccnos2;
1059                 set<string> namesDups;
1060                 set<string> namesAccnos = names;
1061
1062                 map<string, int> nameCount;
1063
1064                 if (namefile != "") {
1065                         ifstream inName;
1066                         m->openInputFile(namefile, inName);
1067
1068
1069                         while(!inName.eof()){
1070
1071                                 if (m->control_pressed) { inName.close(); return 0; }
1072
1073                                 string thisname, repnames;
1074
1075                                 inName >> thisname;             m->gobble(inName);              //read from first column
1076                                 inName >> repnames;                     //read from second column
1077
1078                                 int num = m->getNumNames(repnames);
1079                                 nameCount[thisname] = num;
1080
1081                                 m->gobble(inName);
1082                         }
1083                         inName.close();
1084                 }
1085
1086                 while(!in.eof()){
1087                         in >> name;
1088
1089                         if (namesAccnos.count(name) == 0){ //name unique to accnos2
1090                                 int pos = name.find_last_of('_');
1091                                 string tempName = name;
1092                                 if (pos != string::npos) {  tempName = tempName.substr(pos+1); cout << tempName << endl; }
1093                                 if (namesAccnos.count(tempName) == 0){
1094                                         namesAccnos2.insert(name);
1095                                 }else { //you are in both so erase
1096                                         namesAccnos.erase(name);
1097                                         namesDups.insert(name);
1098                                 }
1099                         }else { //you are in both so erase
1100                                 namesAccnos.erase(name);
1101                                 namesDups.insert(name);
1102                         }
1103
1104                         m->gobble(in);
1105                 }
1106                 in.close();
1107
1108                 out << "Names in both files : " + toString(namesDups.size()) << endl;
1109                 m->mothurOut("Names in both files : " + toString(namesDups.size())); m->mothurOutEndLine();
1110
1111                 for (set<string>::iterator it = namesDups.begin(); it != namesDups.end(); it++) {
1112                         out << (*it);
1113                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
1114                         out << endl;
1115                 }
1116
1117                 out << "Names unique to " + accnosfile + " : " + toString(namesAccnos.size()) << endl;
1118                 m->mothurOut("Names unique to " + accnosfile + " : " + toString(namesAccnos.size())); m->mothurOutEndLine();
1119
1120                 for (set<string>::iterator it = namesAccnos.begin(); it != namesAccnos.end(); it++) {
1121                         out << (*it);
1122                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
1123                         out << endl;
1124                 }
1125
1126                 out << "Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size()) << endl;
1127                 m->mothurOut("Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size())); m->mothurOutEndLine();
1128
1129                 for (set<string>::iterator it = namesAccnos2.begin(); it != namesAccnos2.end(); it++) {
1130                         out << (*it);
1131                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
1132                         out << endl;
1133                 }
1134
1135                 out.close();
1136
1137                 outputNames.push_back(outputFileName);  outputTypes["accnosreport"].push_back(outputFileName);
1138
1139                 return 0;
1140
1141         }
1142         catch(exception& e) {
1143                 m->errorOut(e, "GetSeqsCommand", "compareAccnos");
1144                 exit(1);
1145         }
1146 }
1147
1148
1149 //**********************************************************************************************************************
1150