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);      if (temp == "not found") { temp = "false"; usedDups = ""; }
 186                         dups = m->isTrue(temp);
 187
 188                         taxons = validParameter.validFile(parameters, "taxon", false);
 189                         if (taxons == "not found") { taxons = "";  m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine();  abort = true;  }
 190                         else {
 191                                 //rip off quotes
 192                                 if (taxons[0] == '\'') {  taxons = taxons.substr(1); }
 193                                 if (taxons[(taxons.length()-1)] == '\'') {  taxons = taxons.substr(0, (taxons.length()-1)); }
 194                         }
 195
 196
 197                         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; }
 198
 199                         if ((usedDups != "") && (namefile == "")) {  m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine();  abort = true; }
 200
 201                 }
 202
 203         }
 204         catch(exception& e) {
 205                 m->errorOut(e, "GetLineageCommand", "GetLineageCommand");
 206                 exit(1);
 207         }
 208 }
 209 //**********************************************************************************************************************
 210
 211 void GetLineageCommand::help(){
 212         try {
 213                 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");
 214                 m->mothurOut("It outputs a file containing only the sequences from the taxonomy file that are from the taxon requested.\n");
 215                 m->mothurOut("The get.lineage command parameters are taxon, fasta, name, group, list, taxonomy, alignreport and dups.  You must provide taxonomy and taxon.\n");
 216                 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");
 217                 m->mothurOut("The taxon parameter allows you to select the taxons you would like to get.\n");
 218                 m->mothurOut("The get.lineage command should be in the following format: get.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n");
 219                 m->mothurOut("Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n");
 220                 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");
 221                 m->mothurOut("Example get.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n");
 222                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 223         }
 224         catch(exception& e) {
 225                 m->errorOut(e, "GetLineageCommand", "help");
 226                 exit(1);
 227         }
 228 }
 229
 230 //**********************************************************************************************************************
 231
 232 int GetLineageCommand::execute(){
 233         try {
 234
 235                 if (abort == true) { return 0; }
 236
 237                 if (m->control_pressed) { return 0; }
 238
 239                 //read through the correct file and output lines you want to keep
 240                 if (taxfile != "")                      {               readTax();              }  //fills the set of names to get
 241                 if (namefile != "")                     {               readName();             }
 242                 if (fastafile != "")            {               readFasta();    }
 243                 if (groupfile != "")            {               readGroup();    }
 244                 if (alignfile != "")            {               readAlign();    }
 245                 if (listfile != "")                     {               readList();             }
 246
 247
 248                 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str());  } return 0; }
 249
 250                 if (outputNames.size() != 0) {
 251                         m->mothurOutEndLine();
 252                         m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 253                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 254                         m->mothurOutEndLine();
 255                 }
 256
 257                 return 0;
 258         }
 259
 260         catch(exception& e) {
 261                 m->errorOut(e, "GetLineageCommand", "execute");
 262                 exit(1);
 263         }
 264 }
 265
 266 //**********************************************************************************************************************
 267 int GetLineageCommand::readFasta(){
 268         try {
 269                 string thisOutputDir = outputDir;
 270                 if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
 271                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" +  m->getExtension(fastafile);
 272                 ofstream out;
 273                 m->openOutputFile(outputFileName, out);
 274
 275
 276                 ifstream in;
 277                 m->openInputFile(fastafile, in);
 278                 string name;
 279
 280                 bool wroteSomething = false;
 281
 282                 while(!in.eof()){
 283
 284                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 285
 286                         Sequence currSeq(in);
 287                         name = currSeq.getName();
 288
 289                         if (name != "") {
 290                                 //if this name is in the accnos file
 291                                 if (names.count(name) != 0) {
 292                                         wroteSomething = true;
 293
 294                                         currSeq.printSequence(out);
 295                                 }
 296                         }
 297                         m->gobble(in);
 298                 }
 299                 in.close();
 300                 out.close();
 301
 302                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 303                 outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName);
 304
 305                 return 0;
 306
 307         }
 308         catch(exception& e) {
 309                 m->errorOut(e, "GetLineageCommand", "readFasta");
 310                 exit(1);
 311         }
 312 }
 313 //**********************************************************************************************************************
 314 int GetLineageCommand::readList(){
 315         try {
 316                 string thisOutputDir = outputDir;
 317                 if (outputDir == "") {  thisOutputDir += m->hasPath(listfile);  }
 318                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" +  m->getExtension(listfile);
 319                 ofstream out;
 320                 m->openOutputFile(outputFileName, out);
 321
 322                 ifstream in;
 323                 m->openInputFile(listfile, in);
 324
 325                 bool wroteSomething = false;
 326
 327                 while(!in.eof()){
 328
 329                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 330
 331                         //read in list vector
 332                         ListVector list(in);
 333
 334                         //make a new list vector
 335                         ListVector newList;
 336                         newList.setLabel(list.getLabel());
 337
 338                         //for each bin
 339                         for (int i = 0; i < list.getNumBins(); i++) {
 340
 341                                 //parse out names that are in accnos file
 342                                 string binnames = list.get(i);
 343
 344                                 string newNames = "";
 345                                 while (binnames.find_first_of(',') != -1) {
 346                                         string name = binnames.substr(0,binnames.find_first_of(','));
 347                                         binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
 348
 349                                         //if that name is in the .accnos file, add it
 350                                         if (names.count(name) != 0) {  newNames += name + ",";  }
 351                                 }
 352
 353                                 //get last name
 354                                 if (names.count(binnames) != 0) {  newNames += binnames + ",";  }
 355
 356                                 //if there are names in this bin add to new list
 357                                 if (newNames != "") {
 358                                         newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
 359                                         newList.push_back(newNames);
 360                                 }
 361                         }
 362
 363                         //print new listvector
 364                         if (newList.getNumBins() != 0) {
 365                                 wroteSomething = true;
 366                                 newList.print(out);
 367                         }
 368
 369                         m->gobble(in);
 370                 }
 371                 in.close();
 372                 out.close();
 373
 374                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 375                 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
 376
 377                 return 0;
 378
 379         }
 380         catch(exception& e) {
 381                 m->errorOut(e, "GetLineageCommand", "readList");
 382                 exit(1);
 383         }
 384 }
 385 //**********************************************************************************************************************
 386 int GetLineageCommand::readName(){
 387         try {
 388                 string thisOutputDir = outputDir;
 389                 if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
 390                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" +  m->getExtension(namefile);
 391                 ofstream out;
 392                 m->openOutputFile(outputFileName, out);
 393
 394
 395                 ifstream in;
 396                 m->openInputFile(namefile, in);
 397                 string name, firstCol, secondCol;
 398
 399                 bool wroteSomething = false;
 400
 401
 402                 while(!in.eof()){
 403
 404                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 405
 406                         in >> firstCol;
 407                         in >> secondCol;
 408
 409                         string hold = "";
 410                         if (dups) { hold = secondCol; }
 411
 412                         vector<string> parsedNames;
 413                         //parse second column saving each name
 414                         while (secondCol.find_first_of(',') != -1) {
 415                                 name = secondCol.substr(0,secondCol.find_first_of(','));
 416                                 secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
 417                                 parsedNames.push_back(name);
 418                         }
 419
 420                         //get name after last ,
 421                         parsedNames.push_back(secondCol);
 422
 423                         vector<string> validSecond;
 424                         for (int i = 0; i < parsedNames.size(); i++) {
 425                                 if (names.count(parsedNames[i]) != 0) {
 426                                         validSecond.push_back(parsedNames[i]);
 427                                 }
 428                         }
 429
 430                         if ((dups) && (validSecond.size() != 0)) { //dups = true and we want to add someone, then add everyone
 431                                 for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
 432                                 out << firstCol << '\t' << hold << endl;
 433                                 wroteSomething = true;
 434                         }else {
 435                                 //if the name in the first column is in the set then print it and any other names in second column also in set
 436                                 if (names.count(firstCol) != 0) {
 437
 438                                         wroteSomething = true;
 439
 440                                         out << firstCol << '\t';
 441
 442                                         //you know you have at least one valid second since first column is valid
 443                                         for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 444                                         out << validSecond[validSecond.size()-1] << endl;
 445
 446
 447                                 //make first name in set you come to first column and then add the remaining names to second column
 448                                 }else {
 449                                         //you want part of this row
 450                                         if (validSecond.size() != 0) {
 451
 452                                                 wroteSomething = true;
 453
 454                                                 out << validSecond[0] << '\t';
 455
 456                                                 //you know you have at least one valid second since first column is valid
 457                                                 for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
 458                                                 out << validSecond[validSecond.size()-1] << endl;
 459                                         }
 460                                 }
 461                         }
 462                         m->gobble(in);
 463                 }
 464                 in.close();
 465                 out.close();
 466
 467                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 468                 outputNames.push_back(outputFileName);  outputTypes["name"].push_back(outputFileName);
 469
 470                 return 0;
 471
 472         }
 473         catch(exception& e) {
 474                 m->errorOut(e, "GetLineageCommand", "readName");
 475                 exit(1);
 476         }
 477 }
 478
 479 //**********************************************************************************************************************
 480 int GetLineageCommand::readGroup(){
 481         try {
 482                 string thisOutputDir = outputDir;
 483                 if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
 484                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
 485                 ofstream out;
 486                 m->openOutputFile(outputFileName, out);
 487
 488
 489                 ifstream in;
 490                 m->openInputFile(groupfile, in);
 491                 string name, group;
 492
 493                 bool wroteSomething = false;
 494
 495                 while(!in.eof()){
 496
 497                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 498
 499
 500                         in >> name;                             //read from first column
 501                         in >> group;                    //read from second column
 502
 503                         //if this name is in the accnos file
 504                         if (names.count(name) != 0) {
 505                                 wroteSomething = true;
 506
 507                                 out << name << '\t' << group << endl;
 508                         }
 509
 510                         m->gobble(in);
 511                 }
 512                 in.close();
 513                 out.close();
 514
 515                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 516                 outputNames.push_back(outputFileName);  outputTypes["group"].push_back(outputFileName);
 517
 518                 return 0;
 519
 520         }
 521         catch(exception& e) {
 522                 m->errorOut(e, "GetLineageCommand", "readGroup");
 523                 exit(1);
 524         }
 525 }
 526 //**********************************************************************************************************************
 527 int GetLineageCommand::readTax(){
 528         try {
 529                 string thisOutputDir = outputDir;
 530                 if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
 531                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
 532                 ofstream out;
 533                 m->openOutputFile(outputFileName, out);
 534
 535                 ifstream in;
 536                 m->openInputFile(taxfile, in);
 537                 string name, tax;
 538
 539                 bool wroteSomething = false;
 540
 541                 while(!in.eof()){
 542
 543                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 544
 545                         in >> name;                             //read from first column
 546                         in >> tax;                      //read from second column
 547
 548                         string newtax = tax;
 549
 550                         //if the users file contains confidence scores we want to ignore them when searching for the taxons
 551                         int hasConfidences = tax.find_first_of('(');
 552                         if (hasConfidences != string::npos) {
 553                                 newtax = removeConfidences(tax);
 554                         }
 555
 556                         int pos = newtax.find(taxons);
 557
 558                         if (pos != string::npos) { //this sequence contains the taxon the user wants
 559                                 names.insert(name);
 560                                 out << name << '\t' << tax << endl;
 561                         }
 562
 563                         m->gobble(in);
 564                 }
 565                 in.close();
 566                 out.close();
 567
 568                 if (names.size() == 0) { m->mothurOut("Your taxonomy file does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
 569                 outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
 570
 571                 return 0;
 572
 573         }
 574         catch(exception& e) {
 575                 m->errorOut(e, "GetLineageCommand", "readTax");
 576                 exit(1);
 577         }
 578 }
 579 /**************************************************************************************************/
 580 string GetLineageCommand::removeConfidences(string tax) {
 581         try {
 582
 583                 string taxon = "";
 584                 int taxLength = tax.length();
 585                 for(int i=0;i<taxLength;i++){
 586                         if(tax[i] == ';'){
 587                                 taxon = taxon.substr(0, taxon.find_first_of('(')); //rip off confidence
 588                                 taxon += ";";
 589                         }
 590                         else{
 591                                 taxon += tax[i];
 592                         }
 593                 }
 594
 595                 return taxon;
 596         }
 597         catch(exception& e) {
 598                 m->errorOut(e, "GetLineageCommand", "removeConfidences");
 599                 exit(1);
 600         }
 601 }
 602 //**********************************************************************************************************************
 603 //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
 604 int GetLineageCommand::readAlign(){
 605         try {
 606                 string thisOutputDir = outputDir;
 607                 if (outputDir == "") {  thisOutputDir += m->hasPath(alignfile);  }
 608                 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
 609                 ofstream out;
 610                 m->openOutputFile(outputFileName, out);
 611
 612
 613                 ifstream in;
 614                 m->openInputFile(alignfile, in);
 615                 string name, junk;
 616
 617                 bool wroteSomething = false;
 618
 619                 //read column headers
 620                 for (int i = 0; i < 16; i++) {
 621                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 622                         else                    {       break;                  }
 623                 }
 624                 out << endl;
 625
 626                 while(!in.eof()){
 627
 628                         if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
 629
 630
 631                         in >> name;                             //read from first column
 632
 633                         //if this name is in the accnos file
 634                         if (names.count(name) != 0) {
 635                                 wroteSomething = true;
 636
 637                                 out << name << '\t';
 638
 639                                 //read rest
 640                                 for (int i = 0; i < 15; i++) {
 641                                         if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
 642                                         else                    {       break;                  }
 643                                 }
 644                                 out << endl;
 645
 646                         }else {//still read just don't do anything with it
 647                                 //read rest
 648                                 for (int i = 0; i < 15; i++) {
 649                                         if (!in.eof())  {       in >> junk;             }
 650                                         else                    {       break;                  }
 651                                 }
 652                         }
 653
 654                         m->gobble(in);
 655                 }
 656                 in.close();
 657                 out.close();
 658
 659                 if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
 660                 outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
 661
 662                 return 0;
 663
 664         }
 665         catch(exception& e) {
 666                 m->errorOut(e, "GetLineageCommand", "readAlign");
 667                 exit(1);
 668         }
 669 }
 670 //**********************************************************************************************************************
 671
 672
 673
 674