getlineagecommand.cpp

   1 /*
   2  *  getlineagecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 9/24/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "getlineagecommand.h"
  11 #include "sequence.hpp"
  12 #include "listvector.hpp"
  13
  14
  15 //**********************************************************************************************************************
  16 vector<string> GetLineageCommand::getValidParameters(){
  17         try {
  18                 string Array[] =  {"fasta","name", "group", "alignreport", "taxon", "dups", "list","taxonomy","outputdir","inputdir"};
  19                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  20                 return myArray;
  21         }
  22         catch(exception& e) {
  23                 m->errorOut(e, "GetLineageCommand", "getValidParameters");
  24                 exit(1);
  25         }
  26 }
  27 //**********************************************************************************************************************
  28 GetLineageCommand::GetLineageCommand(){
  29         try {
  30                 abort = true;
  31                 //initialize outputTypes
  32                 vector<string> tempOutNames;
  33                 outputTypes["fasta"] = tempOutNames;
  34                 outputTypes["taxonomy"] = tempOutNames;
  35                 outputTypes["name"] = tempOutNames;
  36                 outputTypes["group"] = tempOutNames;
  37                 outputTypes["alignreport"] = tempOutNames;
  38                 outputTypes["list"] = tempOutNames;
  39         }
  40         catch(exception& e) {
  41                 m->errorOut(e, "GetLineageCommand", "GetLineageCommand");
  42                 exit(1);
  43         }
  44 }
  45 //**********************************************************************************************************************
  46 vector<string> GetLineageCommand::getRequiredParameters(){
  47         try {
  48                 string Array[] =  {"taxonomy","taxon"};
  49                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  50                 return myArray;
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "GetLineageCommand", "getRequiredParameters");
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58 vector<string> GetLineageCommand::getRequiredFiles(){
  59         try {
  60                 vector<string> myArray;
  61                 return myArray;
  62         }
  63         catch(exception& e) {
  64                 m->errorOut(e, "GetLineageCommand", "getRequiredFiles");
  65                 exit(1);
  66         }
  67 }
  68 //**********************************************************************************************************************
  69 GetLineageCommand::GetLineageCommand(string option)  {
  70         try {
  71                 abort = false;
  72
  73                 //allow user to run help
  74                 if(option == "help") { help(); abort = true; }
  75
  76                 else {
  77                         //valid paramters for this command
  78                         string Array[] =  {"fasta","name", "group", "alignreport", "taxon", "dups", "list","taxonomy","outputdir","inputdir"};
  79                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  80
  81                         OptionParser parser(option);
  82                         map<string,string> parameters = parser.getParameters();
  83
  84                         ValidParameters validParameter;
  85                         map<string,string>::iterator it;
  86
  87                         //check to make sure all parameters are valid for command
  88                         for (it = parameters.begin(); it != parameters.end(); it++) {
  89                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  90                         }
  91
  92                         //initialize outputTypes
  93                         vector<string> tempOutNames;
  94                         outputTypes["fasta"] = tempOutNames;
  95                         outputTypes["taxonomy"] = tempOutNames;
  96                         outputTypes["name"] = tempOutNames;
  97                         outputTypes["group"] = tempOutNames;
  98                         outputTypes["alignreport"] = tempOutNames;
  99                         outputTypes["list"] = tempOutNames;
 100
 101                         //if the user changes the output directory command factory will send this info to us in the output parameter
 102                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 103
 104                         //if the user changes the input directory command factory will send this info to us in the output parameter
 105                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 106                         if (inputDir == "not found"){   inputDir = "";          }
 107                         else {
 108                                 string path;
 109                                 it = parameters.find("alignreport");
 110                                 //user has given a template file
 111                                 if(it != parameters.end()){
 112                                         path = m->hasPath(it->second);
 113                                         //if the user has not given a path then, add inputdir. else leave path alone.
 114                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
 115                                 }
 116
 117                                 it = parameters.find("fasta");
 118                                 //user has given a template file
 119                                 if(it != parameters.end()){
 120                                         path = m->hasPath(it->second);
 121                                         //if the user has not given a path then, add inputdir. else leave path alone.
 122                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 123                                 }
 124
 125                                 it = parameters.find("list");
 126                                 //user has given a template file
 127                                 if(it != parameters.end()){
 128                                         path = m->hasPath(it->second);
 129                                         //if the user has not given a path then, add inputdir. else leave path alone.
 130                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 131                                 }
 132
 133                                 it = parameters.find("name");
 134                                 //user has given a template file
 135                                 if(it != parameters.end()){
 136                                         path = m->hasPath(it->second);
 137                                         //if the user has not given a path then, add inputdir. else leave path alone.
 138                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 139                                 }
 140
 141                                 it = parameters.find("group");
 142                                 //user has given a template file
 143                                 if(it != parameters.end()){
 144                                         path = m->hasPath(it->second);
 145                                         //if the user has not given a path then, add inputdir. else leave path alone.
 146                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 147                                 }
 148
 149                                 it = parameters.find("taxonomy");
 150                                 //user has given a template file
 151                                 if(it != parameters.end()){
 152                                         path = m->hasPath(it->second);
 153                                         //if the user has not given a path then, add inputdir. else leave path alone.
 154                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 155                                 }
 156                         }
 157
 158
 159                         //check for required parameters
 160                         fastafile = validParameter.validFile(parameters, "fasta", true);
 161                         if (fastafile == "not open") { abort = true; }
 162                         else if (fastafile == "not found") {  fastafile = "";  }
 163
 164                         namefile = validParameter.validFile(parameters, "name", true);
 165                         if (namefile == "not open") { abort = true; }
 166                         else if (namefile == "not found") {  namefile = "";  }
 167
 168                         groupfile = validParameter.validFile(parameters, "group", true);
 169                         if (groupfile == "not open") { abort = true; }
 170                         else if (groupfile == "not found") {  groupfile = "";  }
 171
 172                         alignfile = validParameter.validFile(parameters, "alignreport", true);
 173                         if (alignfile == "not open") { abort = true; }
 174                         else if (alignfile == "not found") {  alignfile = "";  }
 175
 176                         listfile = validParameter.validFile(parameters, "list", true);
 177                         if (listfile == "not open") { abort = true; }
 178                         else if (listfile == "not found") {  listfile = "";  }
 179
 180                         taxfile = validParameter.validFile(parameters, "taxonomy", true);
 181                         if (taxfile == "not open") { abort = true; }
 182                         else if (taxfile == "not found") {  taxfile = ""; m->mothurOut("The taxonomy parameter is required for the get.lineage command."); m->mothurOutEndLine();  abort = true; }
 183
 184                         string usedDups = "true";
 185                         string temp = validParameter.validFile(parameters, "dups", false);
 186                         if (temp == "not found") {
 187                                 if (namefile != "") {  temp = "true";                                   }
 188                                 else                            {  temp = "false"; usedDups = "";       }
 189                         }
 190                         dups = m->isTrue(temp);
 191
 192                         taxons = validParameter.validFile(parameters, "taxon", false);
 193                         if (taxons == "not found") { taxons = "";  m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine();  abort = true;  }
 194                         else {
 195                                 //rip off quotes
 196                                 if (taxons[0] == '\'') {  taxons = taxons.substr(1); }
 197                                 if (taxons[(taxons.length()-1)] == '\'') {  taxons = taxons.substr(0, (taxons.length()-1)); }
 198                         }
 199
 200
 201                         if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; }
 202
 203                         if ((usedDups != "") && (namefile == "")) {  m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine();  abort = true; }
 204
 205                 }
 206
 207         }
 208         catch(exception& e) {
 209                 m->errorOut(e, "GetLineageCommand", "GetLineageCommand");
 210                 exit(1);
 211         }
 212 }
 213 //**********************************************************************************************************************
 214
 215 void GetLineageCommand::help(){
 216         try {
 217                 m->mothurOut("The get.lineage command reads a taxonomy file and any of the following file types: fasta, name, group, list or alignreport file.\n");
 218                 m->mothurOut("It outputs a file containing only the sequences from the taxonomy file that are from the taxon requested.\n");
 219                 m->mothurOut("The get.lineage command parameters are taxon, fasta, name, group, list, taxonomy, alignreport and dups.  You must provide taxonomy and taxon.\n");
 220                 m->mothurOut("The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n");
 221                 m->mothurOut("The taxon parameter allows you to select the taxons you would like to get.\n");
 222                 m->mothurOut("The get.lineage command should be in the following format: get.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n");
 223                 m->mothurOut("Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n");
 224                 m->mothurOut("Note: If you are running mothur in script mode you must wrap the taxon in ' characters so mothur will ignore the ; in the taxon.\n");
 225                 m->mothurOut("Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n");
 226                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 227         }
 228         catch(exception& e) {
 229                 m->errorOut(e, "GetLineageCommand", "help");
 230                 exit(1);
 231         }
 232 }
 233
 234 //**********************************************************************************************************************
 235
 236 int GetLineageCommand::execute(){
 237         try {
 238
 239                 if (abort == true) { return 0; }
 240
 241                 if (m->control_pressed) { return 0; }
 242
 243                 //read through the correct file and output lines you want to keep
 244                 if (taxfile != "")                      {               readTax();              }  //fills the set of names to get
 245                 if (namefile != "")                     {               readName();             }
 246                 if (fastafile != "")            {               readFasta();    }
 247                 if (groupfile != "")            {               readGroup();    }
 248                 if (alignfile != "")            {               readAlign();    }
 249                 if (listfile != "")                     {               readList();             }
 250
 251
 252                 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str());  } return 0; }
 253
 254                 if (outputNames.size() != 0) {
 255                         m->mothurOutEndLine();
 256                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 257                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 258                         m->mothurOutEndLine();
 259                 }
 260
 261                 return 0;
 262         }
 263
 264         catch(exception& e) {
 265                 m->errorOut(e, "GetLineageCommand", "execute");
 266                 exit(1);
 267         }
 268 }
 269
 270 //**********************************************************************************************************************
 271 int GetLineageCommand::readFasta(){
 272         try {
 273                 string thisOutputDir = outputDir;
 274                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 275                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" +  m->getExtension(fastafile);
 276                 ofstream out;
 277                 m->openOutputFile(outputFileName, out);
 278
 279
 280                 ifstream in;
 281                 m->openInputFile(fastafile, in);
 282                 string name;
 283
 284                 bool wroteSomething = false;
 285
 286                 while(!in.eof()){
 287
 288                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 289
 290                         Sequence currSeq(in);
 291                         name = currSeq.getName();
 292
 293                         if (name != "") {
 294                                 //if this name is in the accnos file
 295                                 if (names.count(name) != 0) {
 296                                         wroteSomething = true;
 297
 298                                         currSeq.printSequence(out);
 299                                 }
 300                         }
 301                         m->gobble(in);
 302                 }
 303                 in.close();
 304                 out.close();
 305
 306                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 307                 outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);
 308
 309                 return 0;
 310
 311         }
 312         catch(exception& e) {
 313                 m->errorOut(e, "GetLineageCommand", "readFasta");
 314                 exit(1);
 315         }
 316 }
 317 //**********************************************************************************************************************
 318 int GetLineageCommand::readList(){
 319         try {
 320                 string thisOutputDir = outputDir;
 321                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 322                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 323                 ofstream out;
 324                 m->openOutputFile(outputFileName, out);
 325
 326                 ifstream in;
 327                 m->openInputFile(listfile, in);
 328
 329                 bool wroteSomething = false;
 330
 331                 while(!in.eof()){
 332
 333                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 334
 335                         //read in list vector
 336                         ListVector list(in);
 337
 338                         //make a new list vector
 339                         ListVector newList;
 340                         newList.setLabel(list.getLabel());
 341
 342                         //for each bin
 343                         for (int i = 0; i < list.getNumBins(); i++) {
 344
 345                                 //parse out names that are in accnos file
 346                                 string binnames = list.get(i);
 347
 348                                 string newNames = "";
 349                                 while (binnames.find_first_of(',') != -1) {
 350                                         string name = binnames.substr(0,binnames.find_first_of(','));
 351                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 352
 353                                         //if that name is in the .accnos file, add it
 354                                         if (names.count(name) != 0) {  newNames += name + ",";  }
 355                                 }
 356
 357                                 //get last name
 358                                 if (names.count(binnames) != 0) {  newNames += binnames + ",";  }
 359
 360                                 //if there are names in this bin add to new list
 361                                 if (newNames != "") {
 362                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 363                                         newList.push_back(newNames);
 364                                 }
 365                         }
 366
 367                         //print new listvector
 368                         if (newList.getNumBins() != 0) {
 369                                 wroteSomething = true;
 370                                 newList.print(out);
 371                         }
 372
 373                         m->gobble(in);
 374                 }
 375                 in.close();
 376                 out.close();
 377
 378                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 379                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 380
 381                 return 0;
 382
 383         }
 384         catch(exception& e) {
 385                 m->errorOut(e, "GetLineageCommand", "readList");
 386                 exit(1);
 387         }
 388 }
 389 //**********************************************************************************************************************
 390 int GetLineageCommand::readName(){
 391         try {
 392                 string thisOutputDir = outputDir;
 393                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 394                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" +  m->getExtension(namefile);
 395                 ofstream out;
 396                 m->openOutputFile(outputFileName, out);
 397
 398
 399                 ifstream in;
 400                 m->openInputFile(namefile, in);
 401                 string name, firstCol, secondCol;
 402
 403                 bool wroteSomething = false;
 404
 405
 406                 while(!in.eof()){
 407
 408                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 409
 410                         in >> firstCol;
 411                         in >> secondCol;
 412
 413                         string hold = "";
 414                         if (dups) { hold = secondCol; }
 415
 416                         vector<string> parsedNames;
 417                         //parse second column saving each name
 418                         while (secondCol.find_first_of(',') != -1) {
 419                                 name = secondCol.substr(0,secondCol.find_first_of(','));
 420                                 secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
 421                                 parsedNames.push_back(name);
 422                         }
 423
 424                         //get name after last ,
 425                         parsedNames.push_back(secondCol);
 426
 427                         vector<string> validSecond;
 428                         for (int i = 0; i < parsedNames.size(); i++) {
 429                                 if (names.count(parsedNames[i]) != 0) {
 430                                         validSecond.push_back(parsedNames[i]);
 431                                 }
 432                         }
 433
 434                         if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
 435                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 436                                 out << firstCol << '\t' << hold << endl;
 437                                 wroteSomething = true;
 438                         }else {
 439                                 //if the name in the first column is in the set then print it and any other names in second column also in set
 440                                 if (names.count(firstCol) != 0) {
 441
 442                                         wroteSomething = true;
 443
 444                                         out << firstCol << '\t';
 445
 446                                         //you know you have at least one valid second since first column is valid
 447                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 448                                         out << validSecond[validSecond.size()-1] << endl;
 449
 450
 451                                 //make first name in set you come to first column and then add the remaining names to second column
 452                                 }else {
 453                                         //you want part of this row
 454                                         if (validSecond.size() != 0) {
 455
 456                                                 wroteSomething = true;
 457
 458                                                 out << validSecond[0] << '\t';
 459
 460                                                 //you know you have at least one valid second since first column is valid
 461                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 462                                                 out << validSecond[validSecond.size()-1] << endl;
 463                                         }
 464                                 }
 465                         }
 466                         m->gobble(in);
 467                 }
 468                 in.close();
 469                 out.close();
 470
 471                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 472                 outputNames.push_back(outputFileName);  outputTypes["name"].push_back(outputFileName);
 473
 474                 return 0;
 475
 476         }
 477         catch(exception& e) {
 478                 m->errorOut(e, "GetLineageCommand", "readName");
 479                 exit(1);
 480         }
 481 }
 482
 483 //**********************************************************************************************************************
 484 int GetLineageCommand::readGroup(){
 485         try {
 486                 string thisOutputDir = outputDir;
 487                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 488                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 489                 ofstream out;
 490                 m->openOutputFile(outputFileName, out);
 491
 492
 493                 ifstream in;
 494                 m->openInputFile(groupfile, in);
 495                 string name, group;
 496
 497                 bool wroteSomething = false;
 498
 499                 while(!in.eof()){
 500
 501                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 502
 503
 504                         in >> name;                             //read from first column
 505                         in >> group;                    //read from second column
 506
 507                         //if this name is in the accnos file
 508                         if (names.count(name) != 0) {
 509                                 wroteSomething = true;
 510
 511                                 out << name << '\t' << group << endl;
 512                         }
 513
 514                         m->gobble(in);
 515                 }
 516                 in.close();
 517                 out.close();
 518
 519                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 520                 outputNames.push_back(outputFileName);  outputTypes["group"].push_back(outputFileName);
 521
 522                 return 0;
 523
 524         }
 525         catch(exception& e) {
 526                 m->errorOut(e, "GetLineageCommand", "readGroup");
 527                 exit(1);
 528         }
 529 }
 530 //**********************************************************************************************************************
 531 int GetLineageCommand::readTax(){
 532         try {
 533                 string thisOutputDir = outputDir;
 534                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 535                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 536                 ofstream out;
 537                 m->openOutputFile(outputFileName, out);
 538
 539                 ifstream in;
 540                 m->openInputFile(taxfile, in);
 541                 string name, tax;
 542
 543                 bool wroteSomething = false;
 544
 545                 while(!in.eof()){
 546
 547                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 548
 549                         in >> name;                             //read from first column
 550                         in >> tax;                      //read from second column
 551
 552                         string newtax = tax;
 553
 554                         //if the users file contains confidence scores we want to ignore them when searching for the taxons
 555                         int hasConfidences = tax.find_first_of('(');
 556                         if (hasConfidences != string::npos) {
 557                                 newtax = removeConfidences(tax);
 558                         }
 559
 560                         int pos = newtax.find(taxons);
 561
 562                         if (pos != string::npos) { //this sequence contains the taxon the user wants
 563                                 names.insert(name);
 564                                 out << name << '\t' << tax << endl;
 565                         }
 566
 567                         m->gobble(in);
 568                 }
 569                 in.close();
 570                 out.close();
 571
 572                 if (names.size() == 0) { m->mothurOut("Your taxonomy file does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 573                 outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
 574
 575                 return 0;
 576
 577         }
 578         catch(exception& e) {
 579                 m->errorOut(e, "GetLineageCommand", "readTax");
 580                 exit(1);
 581         }
 582 }
 583 /**************************************************************************************************/
 584 string GetLineageCommand::removeConfidences(string tax) {
 585         try {
 586
 587                 string taxon = "";
 588                 int taxLength = tax.length();
 589                 for(int i=0;i<taxLength;i++){
 590                         if(tax[i] == ';'){
 591                                 taxon = taxon.substr(0, taxon.find_first_of('(')); //rip off confidence
 592                                 taxon += ";";
 593                         }
 594                         else{
 595                                 taxon += tax[i];
 596                         }
 597                 }
 598
 599                 return taxon;
 600         }
 601         catch(exception& e) {
 602                 m->errorOut(e, "GetLineageCommand", "removeConfidences");
 603                 exit(1);
 604         }
 605 }
 606 //**********************************************************************************************************************
 607 //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
 608 int GetLineageCommand::readAlign(){
 609         try {
 610                 string thisOutputDir = outputDir;
 611                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 612                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
 613                 ofstream out;
 614                 m->openOutputFile(outputFileName, out);
 615
 616
 617                 ifstream in;
 618                 m->openInputFile(alignfile, in);
 619                 string name, junk;
 620
 621                 bool wroteSomething = false;
 622
 623                 //read column headers
 624                 for (int i = 0; i < 16; i++) {
 625                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 626                         else                    {       break;                  }
 627                 }
 628                 out << endl;
 629
 630                 while(!in.eof()){
 631
 632                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 633
 634
 635                         in >> name;                             //read from first column
 636
 637                         //if this name is in the accnos file
 638                         if (names.count(name) != 0) {
 639                                 wroteSomething = true;
 640
 641                                 out << name << '\t';
 642
 643                                 //read rest
 644                                 for (int i = 0; i < 15; i++) {
 645                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 646                                         else                    {       break;                  }
 647                                 }
 648                                 out << endl;
 649
 650                         }else {//still read just don't do anything with it
 651                                 //read rest
 652                                 for (int i = 0; i < 15; i++) {
 653                                         if (!in.eof())  {       in >> junk;             }
 654                                         else                    {       break;                  }
 655                                 }
 656                         }
 657
 658                         m->gobble(in);
 659                 }
 660                 in.close();
 661                 out.close();
 662
 663                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 664                 outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
 665
 666                 return 0;
 667
 668         }
 669         catch(exception& e) {
 670                 m->errorOut(e, "GetLineageCommand", "readAlign");
 671                 exit(1);
 672         }
 673 }
 674 //**********************************************************************************************************************
 675
 676
 677
 678