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", "", "", "NameCount", "FNGLT", "none",false,false); parameters.push_back(pname);
  19         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "FNGLT", "none",false,false); parameters.push_back(pcount);
  20                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "FNGLT", "none",false,false); parameters.push_back(pgroup);
  21                 CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
  22                 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
  23                 CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);
  24                 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pqfile);
  25                 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos);
  26                 CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
  27                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  28                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  29                 CommandParameter paccnos2("accnos2", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paccnos2);
  30
  31                 vector<string> myArray;
  32                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  33                 return myArray;
  34         }
  35         catch(exception& e) {
  36                 m->errorOut(e, "GetSeqsCommand", "setParameters");
  37                 exit(1);
  38         }
  39 }
  40 //**********************************************************************************************************************
  41 string GetSeqsCommand::getHelpString(){
  42         try {
  43                 string helpString = "";
  44                 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";
  45                 helpString += "It outputs a file containing only the sequences in the .accnos file.\n";
  46                 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";
  47                 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";
  48                 helpString += "The get.seqs command should be in the following format: get.seqs(accnos=yourAccnos, fasta=yourFasta).\n";
  49                 helpString += "Example get.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n";
  50                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  51                 return helpString;
  52         }
  53         catch(exception& e) {
  54                 m->errorOut(e, "GetSeqsCommand", "getHelpString");
  55                 exit(1);
  56         }
  57 }
  58
  59 //**********************************************************************************************************************
  60 GetSeqsCommand::GetSeqsCommand(){
  61         try {
  62                 abort = true; calledHelp = true;
  63                 setParameters();
  64                 vector<string> tempOutNames;
  65                 outputTypes["fasta"] = tempOutNames;
  66                 outputTypes["taxonomy"] = tempOutNames;
  67                 outputTypes["name"] = tempOutNames;
  68                 outputTypes["group"] = tempOutNames;
  69                 outputTypes["alignreport"] = tempOutNames;
  70                 outputTypes["list"] = tempOutNames;
  71                 outputTypes["qfile"] = tempOutNames;
  72         outputTypes["count"] = tempOutNames;
  73                 outputTypes["accnosreport"] = tempOutNames;
  74         }
  75         catch(exception& e) {
  76                 m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
  77                 exit(1);
  78         }
  79 }
  80 //**********************************************************************************************************************
  81 string GetSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
  82         try {
  83         string outputFileName = "";
  84                 map<string, vector<string> >::iterator it;
  85
  86         //is this a type this command creates
  87         it = outputTypes.find(type);
  88         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  89         else {
  90             if (type == "fasta")            {   outputFileName =  "pick" + m->getExtension(inputName);   }
  91             else if (type == "taxonomy")    {   outputFileName =  "pick" + m->getExtension(inputName);   }
  92             else if (type == "name")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
  93             else if (type == "count")       {   outputFileName =  "pick.count.table";   }
  94             else if (type == "group")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
  95             else if (type == "list")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
  96             else if (type == "qfile")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
  97             else if (type == "accnosreport"){   outputFileName =  "accnos.report";                       }
  98             else if (type == "alignreport") {   outputFileName =  "pick.align.report";                   }
  99             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
 100         }
 101         return outputFileName;
 102         }
 103         catch(exception& e) {
 104                 m->errorOut(e, "GetSeqsCommand", "getOutputFileNameTag");
 105                 exit(1);
 106         }
 107 }
 108 //**********************************************************************************************************************
 109 GetSeqsCommand::GetSeqsCommand(string option)  {
 110         try {
 111                 abort = false; calledHelp = false;
 112
 113                 //allow user to run help
 114                 if(option == "help") { help(); abort = true; calledHelp = true; }
 115                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 116
 117                 else {
 118                         vector<string> myArray = setParameters();
 119
 120                         OptionParser parser(option);
 121                         map<string,string> parameters = parser.getParameters();
 122
 123                         ValidParameters validParameter;
 124                         map<string,string>::iterator it;
 125
 126                         //check to make sure all parameters are valid for command
 127                         for (it = parameters.begin(); it != parameters.end(); it++) {
 128                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 129                         }
 130
 131                         //initialize outputTypes
 132                         vector<string> tempOutNames;
 133                         outputTypes["fasta"] = tempOutNames;
 134                         outputTypes["taxonomy"] = tempOutNames;
 135                         outputTypes["name"] = tempOutNames;
 136                         outputTypes["group"] = tempOutNames;
 137                         outputTypes["alignreport"] = tempOutNames;
 138                         outputTypes["list"] = tempOutNames;
 139                         outputTypes["qfile"] = tempOutNames;
 140                         outputTypes["accnosreport"] = tempOutNames;
 141             outputTypes["count"] = tempOutNames;
 142
 143                         //if the user changes the output directory command factory will send this info to us in the output parameter
 144                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 145
 146                         //if the user changes the input directory command factory will send this info to us in the output parameter
 147                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 148                         if (inputDir == "not found"){   inputDir = "";          }
 149                         else {
 150                                 string path;
 151                                 it = parameters.find("alignreport");
 152                                 //user has given a template file
 153                                 if(it != parameters.end()){
 154                                         path = m->hasPath(it->second);
 155                                         //if the user has not given a path then, add inputdir. else leave path alone.
 156                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
 157                                 }
 158
 159                                 it = parameters.find("fasta");
 160                                 //user has given a template file
 161                                 if(it != parameters.end()){
 162                                         path = m->hasPath(it->second);
 163                                         //if the user has not given a path then, add inputdir. else leave path alone.
 164                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 165                                 }
 166
 167                                 it = parameters.find("accnos");
 168                                 //user has given a template file
 169                                 if(it != parameters.end()){
 170                                         path = m->hasPath(it->second);
 171                                         //if the user has not given a path then, add inputdir. else leave path alone.
 172                                         if (path == "") {       parameters["accnos"] = inputDir + it->second;           }
 173                                 }
 174
 175                                 it = parameters.find("accnos2");
 176                                 //user has given a template file
 177                                 if(it != parameters.end()){
 178                                         path = m->hasPath(it->second);
 179                                         //if the user has not given a path then, add inputdir. else leave path alone.
 180                                         if (path == "") {       parameters["accnos2"] = inputDir + it->second;          }
 181                                 }
 182
 183                                 it = parameters.find("list");
 184                                 //user has given a template file
 185                                 if(it != parameters.end()){
 186                                         path = m->hasPath(it->second);
 187                                         //if the user has not given a path then, add inputdir. else leave path alone.
 188                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 189                                 }
 190
 191                                 it = parameters.find("name");
 192                                 //user has given a template file
 193                                 if(it != parameters.end()){
 194                                         path = m->hasPath(it->second);
 195                                         //if the user has not given a path then, add inputdir. else leave path alone.
 196                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 197                                 }
 198
 199                                 it = parameters.find("group");
 200                                 //user has given a template file
 201                                 if(it != parameters.end()){
 202                                         path = m->hasPath(it->second);
 203                                         //if the user has not given a path then, add inputdir. else leave path alone.
 204                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 205                                 }
 206
 207                                 it = parameters.find("taxonomy");
 208                                 //user has given a template file
 209                                 if(it != parameters.end()){
 210                                         path = m->hasPath(it->second);
 211                                         //if the user has not given a path then, add inputdir. else leave path alone.
 212                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 213                                 }
 214
 215                                 it = parameters.find("qfile");
 216                                 //user has given a template file
 217                                 if(it != parameters.end()){
 218                                         path = m->hasPath(it->second);
 219                                         //if the user has not given a path then, add inputdir. else leave path alone.
 220                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 221                                 }
 222
 223                 it = parameters.find("count");
 224                                 //user has given a template file
 225                                 if(it != parameters.end()){
 226                                         path = m->hasPath(it->second);
 227                                         //if the user has not given a path then, add inputdir. else leave path alone.
 228                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 229                                 }
 230                         }
 231
 232
 233                         //check for required parameters
 234                         accnosfile = validParameter.validFile(parameters, "accnos", true);
 235                         if (accnosfile == "not open") { abort = true; }
 236                         else if (accnosfile == "not found") {
 237                                 accnosfile = m->getAccnosFile();
 238                                 if (accnosfile != "") {  m->mothurOut("Using " + accnosfile + " as input file for the accnos parameter."); m->mothurOutEndLine(); }
 239                                 else {
 240                                         m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine();
 241                                         abort = true;
 242                                 }
 243                         }else { m->setAccnosFile(accnosfile); }
 244
 245                         if (accnosfile2 == "not found") { accnosfile2 = ""; }
 246
 247                         fastafile = validParameter.validFile(parameters, "fasta", true);
 248                         if (fastafile == "not open") { fastafile = ""; abort = true; }
 249                         else if (fastafile == "not found") {  fastafile = "";  }
 250                         else { m->setFastaFile(fastafile); }
 251
 252                         namefile = validParameter.validFile(parameters, "name", true);
 253                         if (namefile == "not open") { namefile = ""; abort = true; }
 254                         else if (namefile == "not found") {  namefile = "";  }
 255                         else { m->setNameFile(namefile); }
 256
 257                         groupfile = validParameter.validFile(parameters, "group", true);
 258                         if (groupfile == "not open") { abort = true; }
 259                         else if (groupfile == "not found") {  groupfile = "";  }
 260                         else { m->setGroupFile(groupfile); }
 261
 262                         alignfile = validParameter.validFile(parameters, "alignreport", true);
 263                         if (alignfile == "not open") { abort = true; }
 264                         else if (alignfile == "not found") {  alignfile = "";  }
 265
 266                         listfile = validParameter.validFile(parameters, "list", true);
 267                         if (listfile == "not open") { abort = true; }
 268                         else if (listfile == "not found") {  listfile = "";  }
 269                         else { m->setListFile(listfile); }
 270
 271                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 272                         if (taxfile == "not open") { taxfile = ""; abort = true; }
 273                         else if (taxfile == "not found") {  taxfile = "";  }
 274                         else { m->setTaxonomyFile(taxfile); }
 275
 276                         qualfile = validParameter.validFile(parameters, "qfile", true);
 277                         if (qualfile == "not open") { abort = true; }
 278                         else if (qualfile == "not found") {  qualfile = "";  }
 279                         else { m->setQualFile(qualfile); }
 280
 281                         accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
 282                         if (accnosfile2 == "not open") { abort = true; }
 283                         else if (accnosfile2 == "not found") {  accnosfile2 = "";  }
 284
 285             countfile = validParameter.validFile(parameters, "count", true);
 286             if (countfile == "not open") { countfile = ""; abort = true; }
 287             else if (countfile == "not found") { countfile = "";  }
 288             else { m->setCountTableFile(countfile); }
 289
 290             if ((namefile != "") && (countfile != "")) {
 291                 m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
 292             }
 293
 294             if ((groupfile != "") && (countfile != "")) {
 295                 m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
 296             }
 297
 298
 299                         string usedDups = "true";
 300                         string temp = validParameter.validFile(parameters, "dups", false);      if (temp == "not found") { temp = "true"; usedDups = ""; }
 301                         dups = m->isTrue(temp);
 302
 303                         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; }
 304
 305             if (countfile == "") {
 306                 if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
 307                     vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
 308                     parser.getNameFile(files);
 309                 }
 310             }
 311                 }
 312
 313         }
 314         catch(exception& e) {
 315                 m->errorOut(e, "GetSeqsCommand", "GetSeqsCommand");
 316                 exit(1);
 317         }
 318 }
 319 //**********************************************************************************************************************
 320
 321 int GetSeqsCommand::execute(){
 322         try {
 323
 324                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 325
 326                 //get names you want to keep
 327                 names = m->readAccnos(accnosfile);
 328
 329                 if (m->control_pressed) { return 0; }
 330
 331         if (countfile != "") {
 332             if ((fastafile != "") || (listfile != "") || (taxfile != "")) {
 333                 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");
 334             }
 335         }
 336
 337                 //read through the correct file and output lines you want to keep
 338                 if (namefile != "")                     {               readName();                     }
 339                 if (fastafile != "")            {               readFasta();            }
 340                 if (groupfile != "")            {               readGroup();            }
 341         if (countfile != "")            {               readCount();            }
 342                 if (alignfile != "")            {               readAlign();            }
 343                 if (listfile != "")                     {               readList();                     }
 344                 if (taxfile != "")                      {               readTax();                      }
 345                 if (qualfile != "")                     {               readQual();                     }
 346                 if (accnosfile2 != "")          {               compareAccnos();        }
 347
 348         if (m->debug) { runSanityCheck(); }
 349
 350                 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);  } return 0; }
 351
 352
 353                 if (outputNames.size() != 0) {
 354                         m->mothurOutEndLine();
 355                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 356                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 357                         m->mothurOutEndLine();
 358
 359                         //set fasta file as new current fastafile
 360                         string current = "";
 361                         itTypes = outputTypes.find("fasta");
 362                         if (itTypes != outputTypes.end()) {
 363                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 364                         }
 365
 366                         itTypes = outputTypes.find("name");
 367                         if (itTypes != outputTypes.end()) {
 368                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 369                         }
 370
 371                         itTypes = outputTypes.find("group");
 372                         if (itTypes != outputTypes.end()) {
 373                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 374                         }
 375
 376                         itTypes = outputTypes.find("list");
 377                         if (itTypes != outputTypes.end()) {
 378                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
 379                         }
 380
 381                         itTypes = outputTypes.find("taxonomy");
 382                         if (itTypes != outputTypes.end()) {
 383                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 384                         }
 385
 386                         itTypes = outputTypes.find("qfile");
 387                         if (itTypes != outputTypes.end()) {
 388                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 389                         }
 390
 391             itTypes = outputTypes.find("count");
 392                         if (itTypes != outputTypes.end()) {
 393                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 394                         }
 395                 }
 396
 397                 return 0;
 398         }
 399
 400         catch(exception& e) {
 401                 m->errorOut(e, "GetSeqsCommand", "execute");
 402                 exit(1);
 403         }
 404 }
 405
 406 //**********************************************************************************************************************
 407 int GetSeqsCommand::readFasta(){
 408         try {
 409                 string thisOutputDir = outputDir;
 410                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 411                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
 412                 ofstream out;
 413                 m->openOutputFile(outputFileName, out);
 414
 415
 416                 ifstream in;
 417                 m->openInputFile(fastafile, in);
 418                 string name;
 419
 420                 bool wroteSomething = false;
 421                 int selectedCount = 0;
 422
 423         if (m->debug) { set<string> temp; sanity["fasta"] = temp; }
 424
 425                 while(!in.eof()){
 426
 427                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 428
 429                         Sequence currSeq(in);
 430                         name = currSeq.getName();
 431
 432                         if (name != "") {
 433                                 //if this name is in the accnos file
 434                                 if (names.count(name) != 0) {
 435                                         wroteSomething = true;
 436
 437                                         currSeq.printSequence(out);
 438                                         selectedCount++;
 439
 440                     if (m->debug) { sanity["fasta"].insert(name); }
 441                                 }
 442                         }
 443                         m->gobble(in);
 444                 }
 445                 in.close();
 446                 out.close();
 447
 448
 449                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 450                 outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);
 451
 452                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
 453
 454                 return 0;
 455
 456         }
 457         catch(exception& e) {
 458                 m->errorOut(e, "GetSeqsCommand", "readFasta");
 459                 exit(1);
 460         }
 461 }
 462 //**********************************************************************************************************************
 463 int GetSeqsCommand::readQual(){
 464         try {
 465                 string thisOutputDir = outputDir;
 466                 if (outputDir == "") {  thisOutputDir += m->hasPath(qualfile);  }
 467                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("qfile", qualfile);
 468                 ofstream out;
 469                 m->openOutputFile(outputFileName, out);
 470
 471
 472                 ifstream in;
 473                 m->openInputFile(qualfile, in);
 474                 string name;
 475
 476                 bool wroteSomething = false;
 477                 int selectedCount = 0;
 478
 479         if (m->debug) { set<string> temp; sanity["qual"] = temp; }
 480
 481                 while(!in.eof()){
 482                         string saveName = "";
 483                         string name = "";
 484                         string scores = "";
 485
 486                         in >> name;
 487
 488                         if (name.length() != 0) {
 489                                 saveName = name.substr(1);
 490                                 while (!in.eof())       {
 491                                         char c = in.get();
 492                                         if (c == 10 || c == 13){        break;  }
 493                                         else { name += c; }
 494                                 }
 495                                 m->gobble(in);
 496                         }
 497
 498                         while(in){
 499                                 char letter= in.get();
 500                                 if(letter == '>'){      in.putback(letter);     break;  }
 501                                 else{ scores += letter; }
 502                         }
 503
 504                         m->gobble(in);
 505
 506                         if (names.count(saveName) != 0) {
 507                                 wroteSomething = true;
 508
 509                                 out << name << endl << scores;
 510                                 selectedCount++;
 511                 if (m->debug) { sanity["qual"].insert(name); }
 512                         }
 513
 514                         m->gobble(in);
 515                 }
 516                 in.close();
 517                 out.close();
 518
 519
 520                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 521                 outputNames.push_back(outputFileName);  outputTypes["qfile"].push_back(outputFileName);
 522
 523                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your quality file."); m->mothurOutEndLine();
 524
 525
 526                 return 0;
 527
 528         }
 529         catch(exception& e) {
 530                 m->errorOut(e, "GetSeqsCommand", "readQual");
 531                 exit(1);
 532         }
 533 }
 534 //**********************************************************************************************************************
 535 int GetSeqsCommand::readCount(){
 536         try {
 537                 string thisOutputDir = outputDir;
 538                 if (outputDir == "") {  thisOutputDir += m->hasPath(countfile);  }
 539                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
 540
 541                 ofstream out;
 542                 m->openOutputFile(outputFileName, out);
 543
 544                 ifstream in;
 545                 m->openInputFile(countfile, in);
 546
 547                 bool wroteSomething = false;
 548                 int selectedCount = 0;
 549
 550         string headers = m->getline(in); m->gobble(in);
 551         out << headers << endl;
 552
 553         string name, rest; int thisTotal;
 554         while (!in.eof()) {
 555
 556             if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 557
 558             in >> name; m->gobble(in);
 559             in >> thisTotal; m->gobble(in);
 560             rest = m->getline(in); m->gobble(in);
 561             if (m->debug) { m->mothurOut("[DEBUG]: " + name + '\t' + rest + "\n"); }
 562
 563             if (names.count(name) != 0) {
 564                 out << name << '\t' << thisTotal << '\t' << rest << endl;
 565                 wroteSomething = true;
 566                 selectedCount+= thisTotal;
 567             }
 568         }
 569         in.close();
 570                 out.close();
 571
 572                 if (wroteSomething == false) {  m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 573                 outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
 574
 575                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your count file."); m->mothurOutEndLine();
 576
 577                 return 0;
 578         }
 579         catch(exception& e) {
 580                 m->errorOut(e, "GetSeqsCommand", "readCount");
 581                 exit(1);
 582         }
 583 }
 584
 585 //**********************************************************************************************************************
 586 int GetSeqsCommand::readList(){
 587         try {
 588                 string thisOutputDir = outputDir;
 589                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 590                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
 591                 ofstream out;
 592                 m->openOutputFile(outputFileName, out);
 593
 594                 ifstream in;
 595                 m->openInputFile(listfile, in);
 596
 597                 bool wroteSomething = false;
 598                 int selectedCount = 0;
 599
 600         if (m->debug) { set<string> temp; sanity["list"] = temp; }
 601
 602                 while(!in.eof()){
 603
 604                         selectedCount = 0;
 605
 606                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 607
 608                         //read in list vector
 609                         ListVector list(in);
 610
 611                         //make a new list vector
 612                         ListVector newList;
 613                         newList.setLabel(list.getLabel());
 614
 615                         //for each bin
 616                         for (int i = 0; i < list.getNumBins(); i++) {
 617
 618                                 //parse out names that are in accnos file
 619                                 string binnames = list.get(i);
 620
 621                                 string newNames = "";
 622                                 while (binnames.find_first_of(',') != -1) {
 623                                         string name = binnames.substr(0,binnames.find_first_of(','));
 624                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 625
 626                                         //if that name is in the .accnos file, add it
 627                                         if (names.count(name) != 0) {  newNames += name + ",";  selectedCount++; if (m->debug) { sanity["list"].insert(name); } }
 628                                 }
 629
 630                                 //get last name
 631                                 if (names.count(binnames) != 0) {  newNames += binnames + ",";  selectedCount++;  if (m->debug) { sanity["list"].insert(binnames); } }
 632
 633                                 //if there are names in this bin add to new list
 634                                 if (newNames != "") {
 635                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 636                                         newList.push_back(newNames);
 637                                 }
 638                         }
 639
 640                         //print new listvector
 641                         if (newList.getNumBins() != 0) {
 642                                 wroteSomething = true;
 643                                 newList.print(out);
 644                         }
 645
 646                         m->gobble(in);
 647                 }
 648                 in.close();
 649                 out.close();
 650
 651                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 652                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 653
 654                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine();
 655
 656                 return 0;
 657
 658         }
 659         catch(exception& e) {
 660                 m->errorOut(e, "GetSeqsCommand", "readList");
 661                 exit(1);
 662         }
 663 }
 664 //**********************************************************************************************************************
 665 int GetSeqsCommand::readName(){
 666         try {
 667                 string thisOutputDir = outputDir;
 668                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 669                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
 670                 ofstream out;
 671                 m->openOutputFile(outputFileName, out);
 672
 673
 674                 ifstream in;
 675                 m->openInputFile(namefile, in);
 676                 string name, firstCol, secondCol;
 677
 678                 bool wroteSomething = false;
 679                 int selectedCount = 0;
 680
 681         if (m->debug) { set<string> temp; sanity["name"] = temp; }
 682         if (m->debug) { set<string> temp; sanity["dupname"] = temp; }
 683
 684                 while(!in.eof()){
 685
 686                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 687
 688                         in >> firstCol;
 689                         in >> secondCol;
 690
 691                         string hold = "";
 692                         if (dups) { hold = secondCol; }
 693
 694                         vector<string> parsedNames;
 695                         m->splitAtComma(secondCol, parsedNames);
 696
 697                         vector<string> validSecond;
 698                         for (int i = 0; i < parsedNames.size(); i++) {
 699                                 if (names.count(parsedNames[i]) != 0) {
 700                                         validSecond.push_back(parsedNames[i]);
 701                     if (m->debug) { sanity["dupname"].insert(parsedNames[i]); }
 702                                 }
 703                         }
 704
 705                         if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
 706                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]); if (m->debug) { sanity["dupname"].insert(parsedNames[i]); } }
 707                                 out << firstCol << '\t' << hold << endl;
 708                                 wroteSomething = true;
 709                                 selectedCount += parsedNames.size();
 710                 if (m->debug) { sanity["name"].insert(firstCol); }
 711                         }else {
 712                                 selectedCount += validSecond.size();
 713
 714                                 //if the name in the first column is in the set then print it and any other names in second column also in set
 715                                 if (names.count(firstCol) != 0) {
 716
 717                                         wroteSomething = true;
 718
 719                                         out << firstCol << '\t';
 720
 721                                         //you know you have at least one valid second since first column is valid
 722                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 723                                         out << validSecond[validSecond.size()-1] << endl;
 724
 725                     if (m->debug) { sanity["name"].insert(firstCol); }
 726
 727
 728                                 //make first name in set you come to first column and then add the remaining names to second column
 729                                 }else {
 730                                         //you want part of this row
 731                                         if (validSecond.size() != 0) {
 732
 733                                                 wroteSomething = true;
 734
 735                                                 out << validSecond[0] << '\t';
 736
 737                                                 //you know you have at least one valid second since first column is valid
 738                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 739                                                 out << validSecond[validSecond.size()-1] << endl;
 740
 741                         if (m->debug) { sanity["name"].insert(validSecond[0]); }
 742                                         }
 743                                 }
 744                         }
 745                         m->gobble(in);
 746                 }
 747                 in.close();
 748                 out.close();
 749
 750                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 751                 outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
 752
 753                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your name file."); m->mothurOutEndLine();
 754
 755                 return 0;
 756
 757         }
 758         catch(exception& e) {
 759                 m->errorOut(e, "GetSeqsCommand", "readName");
 760                 exit(1);
 761         }
 762 }
 763
 764 //**********************************************************************************************************************
 765 int GetSeqsCommand::readGroup(){
 766         try {
 767                 string thisOutputDir = outputDir;
 768                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 769                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
 770                 ofstream out;
 771                 m->openOutputFile(outputFileName, out);
 772
 773
 774                 ifstream in;
 775                 m->openInputFile(groupfile, in);
 776                 string name, group;
 777
 778                 bool wroteSomething = false;
 779                 int selectedCount = 0;
 780
 781         if (m->debug) { set<string> temp; sanity["group"] = temp; }
 782
 783                 while(!in.eof()){
 784
 785                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 786
 787
 788                         in >> name;                             //read from first column
 789                         in >> group;                    //read from second column
 790
 791                         //if this name is in the accnos file
 792                         if (names.count(name) != 0) {
 793                                 wroteSomething = true;
 794
 795                                 out << name << '\t' << group << endl;
 796                                 selectedCount++;
 797
 798                 if (m->debug) {  sanity["group"].insert(name); }
 799                         }
 800
 801                         m->gobble(in);
 802                 }
 803                 in.close();
 804                 out.close();
 805
 806                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 807                 outputNames.push_back(outputFileName);  outputTypes["group"].push_back(outputFileName);
 808
 809                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your group file."); m->mothurOutEndLine();
 810
 811
 812                 return 0;
 813
 814         }
 815         catch(exception& e) {
 816                 m->errorOut(e, "GetSeqsCommand", "readGroup");
 817                 exit(1);
 818         }
 819 }
 820 //**********************************************************************************************************************
 821 int GetSeqsCommand::readTax(){
 822         try {
 823                 string thisOutputDir = outputDir;
 824                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 825                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
 826                 ofstream out;
 827                 m->openOutputFile(outputFileName, out);
 828
 829                 ifstream in;
 830                 m->openInputFile(taxfile, in);
 831                 string name, tax;
 832
 833                 bool wroteSomething = false;
 834                 int selectedCount = 0;
 835
 836         if (m->debug) { set<string> temp; sanity["tax"] = temp; }
 837
 838                 while(!in.eof()){
 839
 840                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 841
 842                         in >> name;                             //read from first column
 843                         in >> tax;                      //read from second column
 844
 845                         //if this name is in the accnos file
 846                         if (names.count(name) != 0) {
 847                                 wroteSomething = true;
 848
 849                                 out << name << '\t' << tax << endl;
 850                                 selectedCount++;
 851
 852                 if (m->debug) { sanity["tax"].insert(name); }
 853                         }
 854
 855                         m->gobble(in);
 856                 }
 857                 in.close();
 858                 out.close();
 859
 860                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 861                 outputNames.push_back(outputFileName);  outputTypes["taxonomy"].push_back(outputFileName);
 862
 863                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine();
 864
 865                 return 0;
 866
 867         }
 868         catch(exception& e) {
 869                 m->errorOut(e, "GetSeqsCommand", "readTax");
 870                 exit(1);
 871         }
 872 }
 873 //**********************************************************************************************************************
 874 //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
 875 int GetSeqsCommand::readAlign(){
 876         try {
 877                 string thisOutputDir = outputDir;
 878                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 879                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + getOutputFileNameTag("alignreport");
 880                 ofstream out;
 881                 m->openOutputFile(outputFileName, out);
 882
 883
 884                 ifstream in;
 885                 m->openInputFile(alignfile, in);
 886                 string name, junk;
 887
 888                 bool wroteSomething = false;
 889                 int selectedCount = 0;
 890
 891                 //read column headers
 892                 for (int i = 0; i < 16; i++) {
 893                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 894                         else                    {       break;                  }
 895                 }
 896                 out << endl;
 897
 898                 while(!in.eof()){
 899
 900                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 901
 902
 903                         in >> name;                             //read from first column
 904
 905                         //if this name is in the accnos file
 906                         if (names.count(name) != 0) {
 907                                 wroteSomething = true;
 908                                 selectedCount++;
 909
 910                                 out << name << '\t';
 911
 912                                 //read rest
 913                                 for (int i = 0; i < 15; i++) {
 914                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 915                                         else                    {       break;                  }
 916                                 }
 917                                 out << endl;
 918
 919                         }else {//still read just don't do anything with it
 920                                 //read rest
 921                                 for (int i = 0; i < 15; i++) {
 922                                         if (!in.eof())  {       in >> junk;             }
 923                                         else                    {       break;                  }
 924                                 }
 925                         }
 926
 927                         m->gobble(in);
 928                 }
 929                 in.close();
 930                 out.close();
 931
 932                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 933                 outputNames.push_back(outputFileName);  outputTypes["alignreport"].push_back(outputFileName);
 934
 935                 m->mothurOut("Selected " + toString(selectedCount) + " sequences from your alignreport file."); m->mothurOutEndLine();
 936
 937                 return 0;
 938
 939         }
 940         catch(exception& e) {
 941                 m->errorOut(e, "GetSeqsCommand", "readAlign");
 942                 exit(1);
 943         }
 944 }
 945 //**********************************************************************************************************************
 946 //just looking at common mistakes.
 947 int GetSeqsCommand::runSanityCheck(){
 948         try {
 949         string thisOutputDir = outputDir;
 950         if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 951         string filename = outputDir + "get.seqs.debug.report";
 952
 953         ofstream out;
 954                 m->openOutputFile(filename, out);
 955
 956
 957         //compare fasta, name, qual and taxonomy if given to make sure they contain the same seqs
 958         if (fastafile != "") {
 959             if (namefile != "") { //compare with fasta
 960                 if (sanity["fasta"] != sanity["name"]) { //create mismatch file
 961                     createMisMatchFile(out, fastafile, namefile, sanity["fasta"], sanity["name"]);
 962                 }
 963             }
 964             if (qualfile != "") {
 965                 if (sanity["fasta"] != sanity["qual"]) { //create mismatch file
 966                     createMisMatchFile(out, fastafile, qualfile, sanity["fasta"], sanity["qual"]);
 967                 }
 968             }
 969             if (taxfile != "") {
 970                 if (sanity["fasta"] != sanity["tax"]) { //create mismatch file
 971                     createMisMatchFile(out, fastafile, taxfile, sanity["fasta"], sanity["tax"]);
 972                 }
 973             }
 974         }
 975
 976         //compare dupnames, groups and list if given to make sure they match
 977         if (namefile != "") {
 978             if (groupfile != "") {
 979                 if (sanity["dupname"] != sanity["group"]) { //create mismatch file
 980                     createMisMatchFile(out, namefile, groupfile, sanity["dupname"], sanity["group"]);
 981                 }
 982             }
 983             if (listfile != "") {
 984                 if (sanity["dupname"] != sanity["list"]) { //create mismatch file
 985                     createMisMatchFile(out, namefile, listfile, sanity["dupname"], sanity["list"]);
 986                 }
 987             }
 988         }else{
 989
 990             if ((groupfile != "") && (fastafile != "")) {
 991                 if (sanity["fasta"] != sanity["group"]) { //create mismatch file
 992                     createMisMatchFile(out, fastafile, groupfile, sanity["fasta"], sanity["group"]);
 993                 }
 994             }
 995         }
 996
 997         out.close();
 998
 999         if (m->isBlank(filename)) { m->mothurRemove(filename); }
1000         else { m->mothurOut("\n[DEBUG]: " + filename + " contains the file mismatches.\n");outputNames.push_back(filename); outputTypes["debug"].push_back(filename); }
1001
1002         return 0;
1003     }
1004         catch(exception& e) {
1005                 m->errorOut(e, "GetSeqsCommand", "runSanityCheck");
1006                 exit(1);
1007         }
1008 }
1009 //**********************************************************************************************************************
1010 //just looking at common mistakes.
1011 int GetSeqsCommand::createMisMatchFile(ofstream& out, string filename1, string filename2, set<string> set1, set<string> set2){
1012         try {
1013         out << "****************************************" << endl << endl;
1014         out << "Names unique to " << filename1 << ":\n";
1015
1016         //remove names in set1 that are also in set2
1017         for (set<string>::iterator it = set1.begin(); it != set1.end();) {
1018             string name = *it;
1019
1020             if (set2.count(name) == 0)  { out << name << endl;  } //name unique to set1
1021             else                        { set2.erase(name);     } //you are in both so erase
1022             set1.erase(it++);
1023         }
1024
1025         out << "\nNames unique to " << filename2 << ":\n";
1026         //output results
1027         for (set<string>::iterator it = set2.begin(); it != set2.end(); it++) {  out << *it << endl;  }
1028
1029         out << "****************************************" << endl << endl;
1030
1031         return 0;
1032     }
1033         catch(exception& e) {
1034                 m->errorOut(e, "GetSeqsCommand", "runSanityCheck");
1035                 exit(1);
1036         }
1037 }
1038 //**********************************************************************************************************************
1039
1040 int GetSeqsCommand::compareAccnos(){
1041         try {
1042
1043                 string thisOutputDir = outputDir;
1044                 if (outputDir == "") {  thisOutputDir += m->hasPath(accnosfile);  }
1045                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(accnosfile)) + getOutputFileNameTag("accnosreport");
1046                 ofstream out;
1047                 m->openOutputFile(outputFileName, out);
1048
1049                 ifstream in;
1050                 m->openInputFile(accnosfile2, in);
1051                 string name;
1052
1053                 set<string> namesAccnos2;
1054                 set<string> namesDups;
1055                 set<string> namesAccnos = names;
1056
1057                 map<string, int> nameCount;
1058
1059                 if (namefile != "") {
1060                         ifstream inName;
1061                         m->openInputFile(namefile, inName);
1062
1063
1064                         while(!inName.eof()){
1065
1066                                 if (m->control_pressed) { inName.close(); return 0; }
1067
1068                                 string thisname, repnames;
1069
1070                                 inName >> thisname;             m->gobble(inName);              //read from first column
1071                                 inName >> repnames;                     //read from second column
1072
1073                                 int num = m->getNumNames(repnames);
1074                                 nameCount[thisname] = num;
1075
1076                                 m->gobble(inName);
1077                         }
1078                         inName.close();
1079                 }
1080
1081                 while(!in.eof()){
1082                         in >> name;
1083
1084                         if (namesAccnos.count(name) == 0){ //name unique to accnos2
1085                                 int pos = name.find_last_of('_');
1086                                 string tempName = name;
1087                                 if (pos != string::npos) {  tempName = tempName.substr(pos+1); cout << tempName << endl; }
1088                                 if (namesAccnos.count(tempName) == 0){
1089                                         namesAccnos2.insert(name);
1090                                 }else { //you are in both so erase
1091                                         namesAccnos.erase(name);
1092                                         namesDups.insert(name);
1093                                 }
1094                         }else { //you are in both so erase
1095                                 namesAccnos.erase(name);
1096                                 namesDups.insert(name);
1097                         }
1098
1099                         m->gobble(in);
1100                 }
1101                 in.close();
1102
1103                 out << "Names in both files : " + toString(namesDups.size()) << endl;
1104                 m->mothurOut("Names in both files : " + toString(namesDups.size())); m->mothurOutEndLine();
1105
1106                 for (set<string>::iterator it = namesDups.begin(); it != namesDups.end(); it++) {
1107                         out << (*it);
1108                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
1109                         out << endl;
1110                 }
1111
1112                 out << "Names unique to " + accnosfile + " : " + toString(namesAccnos.size()) << endl;
1113                 m->mothurOut("Names unique to " + accnosfile + " : " + toString(namesAccnos.size())); m->mothurOutEndLine();
1114
1115                 for (set<string>::iterator it = namesAccnos.begin(); it != namesAccnos.end(); it++) {
1116                         out << (*it);
1117                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
1118                         out << endl;
1119                 }
1120
1121                 out << "Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size()) << endl;
1122                 m->mothurOut("Names unique to " + accnosfile2 + " : " + toString(namesAccnos2.size())); m->mothurOutEndLine();
1123
1124                 for (set<string>::iterator it = namesAccnos2.begin(); it != namesAccnos2.end(); it++) {
1125                         out << (*it);
1126                         if (namefile != "") { out << '\t' << nameCount[(*it)]; }
1127                         out << endl;
1128                 }
1129
1130                 out.close();
1131
1132                 outputNames.push_back(outputFileName);  outputTypes["accnosreport"].push_back(outputFileName);
1133
1134                 return 0;
1135
1136         }
1137         catch(exception& e) {
1138                 m->errorOut(e, "GetSeqsCommand", "compareAccnos");
1139                 exit(1);
1140         }
1141 }
1142
1143
1144 //**********************************************************************************************************************
1145