removelineagecommand.cpp

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