chimeraslayercommand.cpp

   1 /*
   2  *  chimeraslayercommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 3/31/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "chimeraslayercommand.h"
  11 #include "chimeraslayer.h"
  12 #include "deconvolutecommand.h"
  13
  14 //**********************************************************************************************************************
  15 vector<string> ChimeraSlayerCommand::setParameters(){
  16         try {
  17                 CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
  18                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  19                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  20                 CommandParameter pwindow("window", "Number", "", "50", "", "", "",false,false); parameters.push_back(pwindow);
  21                 CommandParameter pksize("ksize", "Number", "", "7", "", "", "",false,false); parameters.push_back(pksize);
  22                 CommandParameter pmatch("match", "Number", "", "5.0", "", "", "",false,false); parameters.push_back(pmatch);
  23                 CommandParameter pmismatch("mismatch", "Number", "", "-4.0", "", "", "",false,false); parameters.push_back(pmismatch);
  24                 CommandParameter pminsim("minsim", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminsim);
  25                 CommandParameter pmincov("mincov", "Number", "", "70", "", "", "",false,false); parameters.push_back(pmincov);
  26                 CommandParameter pminsnp("minsnp", "Number", "", "100", "", "", "",false,false); parameters.push_back(pminsnp);
  27                 CommandParameter pminbs("minbs", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminbs);
  28                 CommandParameter psearch("search", "Multiple", "kmer-blast-distance", "distance", "", "", "",false,false); parameters.push_back(psearch);
  29                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  30                 CommandParameter prealign("realign", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(prealign);
  31                 CommandParameter ptrim("trim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptrim);
  32                 CommandParameter psplit("split", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psplit);
  33                 CommandParameter pnumwanted("numwanted", "Number", "", "15", "", "", "",false,false); parameters.push_back(pnumwanted);
  34                 CommandParameter piters("iters", "Number", "", "100", "", "", "",false,false); parameters.push_back(piters);
  35                 CommandParameter pdivergence("divergence", "Number", "", "1.007", "", "", "",false,false); parameters.push_back(pdivergence);
  36                 CommandParameter pparents("parents", "Number", "", "3", "", "", "",false,false); parameters.push_back(pparents);
  37                 CommandParameter pincrement("increment", "Number", "", "5", "", "", "",false,false); parameters.push_back(pincrement);
  38                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  39                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  40
  41                 vector<string> myArray;
  42                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  43                 return myArray;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "ChimeraSlayerCommand", "setParameters");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 string ChimeraSlayerCommand::getHelpString(){
  52         try {
  53                 string helpString = "";
  54                 helpString += "The chimera.slayer command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
  55                 helpString += "This command was modeled after the chimeraSlayer written by the Broad Institute.\n";
  56                 helpString += "The chimera.slayer command parameters are fasta, name, template, processors, trim, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment and numwanted.\n"; //realign,
  57                 helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required, unless you have a valid current fasta file. \n";
  58                 helpString += "The name parameter allows you to provide a name file, if you are using template=self. \n";
  59                 helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n";
  60                 helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. You may also set template=self, in this case the abundant sequences will be used as potential parents. \n";
  61                 helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
  62 #ifdef USE_MPI
  63                 helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
  64 #endif
  65                 helpString += "The trim parameter allows you to output a new fasta file containing your sequences with the chimeric ones trimmed to include only their longest piece, default=F. \n";
  66                 helpString += "The split parameter allows you to check both pieces of non-chimeric sequence for chimeras, thus looking for trimeras and quadmeras. default=F. \n";
  67                 helpString += "The window parameter allows you to specify the window size for searching for chimeras, default=50. \n";
  68                 helpString += "The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n";
  69                 helpString += "The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n";
  70                 helpString += "The ksize parameter allows you to input kmersize, default is 7, used if search is kmer. \n";
  71                 helpString += "The match parameter allows you to reward matched bases in blast search, default is 5. \n";
  72                 helpString += "The parents parameter allows you to select the number of potential parents to investigate from the numwanted best matches after rating them, default is 3. \n";
  73                 helpString += "The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n";
  74                 helpString += "The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n";
  75                 helpString += "The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=100.\n";
  76                 helpString += "The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n";
  77                 helpString += "The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n";
  78                 helpString += "The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n";
  79                 helpString += "The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 100) \n";
  80                 helpString += "The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. \n";
  81                 helpString += "The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default false.  \n";
  82                 helpString += "The chimera.slayer command should be in the following format: \n";
  83                 helpString += "chimera.slayer(fasta=yourFastaFile, reference=yourTemplate, search=yourSearch) \n";
  84                 helpString += "Example: chimera.slayer(fasta=AD.align, reference=core_set_aligned.imputed.fasta, search=kmer) \n";
  85                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
  86                 return helpString;
  87         }
  88         catch(exception& e) {
  89                 m->errorOut(e, "ChimeraSlayerCommand", "getHelpString");
  90                 exit(1);
  91         }
  92 }
  93 //**********************************************************************************************************************
  94 ChimeraSlayerCommand::ChimeraSlayerCommand(){
  95         try {
  96                 abort = true; calledHelp = true;
  97                 setParameters();
  98                 vector<string> tempOutNames;
  99                 outputTypes["chimera"] = tempOutNames;
 100                 outputTypes["accnos"] = tempOutNames;
 101                 outputTypes["fasta"] = tempOutNames;
 102         }
 103         catch(exception& e) {
 104                 m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
 105                 exit(1);
 106         }
 107 }
 108 //***************************************************************************************************************
 109 ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
 110         try {
 111                 abort = false; calledHelp = false;
 112
 113                 //allow user to run help
 114                 if(option == "help") { help(); abort = true; calledHelp = true; }
 115
 116                 else {
 117                         vector<string> myArray = setParameters();
 118
 119                         OptionParser parser(option);
 120                         map<string,string> parameters = parser.getParameters();
 121
 122                         ValidParameters validParameter("chimera.slayer");
 123                         map<string,string>::iterator it;
 124
 125                         //check to make sure all parameters are valid for command
 126                         for (it = parameters.begin(); it != parameters.end(); it++) {
 127                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 128                         }
 129
 130                         vector<string> tempOutNames;
 131                         outputTypes["chimera"] = tempOutNames;
 132                         outputTypes["accnos"] = tempOutNames;
 133                         outputTypes["fasta"] = tempOutNames;
 134
 135                         //if the user changes the input directory command factory will send this info to us in the output parameter
 136                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 137                         if (inputDir == "not found"){   inputDir = "";          }
 138
 139                         //check for required parameters
 140                         fastafile = validParameter.validFile(parameters, "fasta", false);
 141                         if (fastafile == "not found") {
 142                                 //if there is a current fasta file, use it
 143                                 string filename = m->getFastaFile();
 144                                 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 145                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 146                         }else {
 147                                 m->splitAtDash(fastafile, fastaFileNames);
 148
 149                                 //go through files and make sure they are good, if not, then disregard them
 150                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 151                                         if (inputDir != "") {
 152                                                 string path = m->hasPath(fastaFileNames[i]);
 153                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 154                                                 if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 155                                         }
 156
 157                                         int ableToOpen;
 158                                         ifstream in;
 159
 160                                         ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 161
 162                                         //if you can't open it, try default location
 163                                         if (ableToOpen == 1) {
 164                                                 if (m->getDefaultPath() != "") { //default path is set
 165                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 166                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 167                                                         ifstream in2;
 168                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 169                                                         in2.close();
 170                                                         fastaFileNames[i] = tryPath;
 171                                                 }
 172                                         }
 173
 174                                         if (ableToOpen == 1) {
 175                                                 if (m->getOutputDir() != "") { //default path is set
 176                                                         string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 177                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 178                                                         ifstream in2;
 179                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 180                                                         in2.close();
 181                                                         fastaFileNames[i] = tryPath;
 182                                                 }
 183                                         }
 184
 185                                         in.close();
 186
 187                                         if (ableToOpen == 1) {
 188                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 189                                                 //erase from file list
 190                                                 fastaFileNames.erase(fastaFileNames.begin()+i);
 191                                                 i--;
 192                                         }
 193                                 }
 194
 195                                 //make sure there is at least one valid file left
 196                                 if (fastaFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
 197                         }
 198
 199
 200                         //check for required parameters
 201                         bool hasName = true;
 202                         namefile = validParameter.validFile(parameters, "name", false);
 203                         if (namefile == "not found") { namefile = "";  hasName = false; }
 204                         else {
 205                                 m->splitAtDash(namefile, nameFileNames);
 206
 207                                 //go through files and make sure they are good, if not, then disregard them
 208                                 for (int i = 0; i < nameFileNames.size(); i++) {
 209                                         if (inputDir != "") {
 210                                                 string path = m->hasPath(nameFileNames[i]);
 211                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 212                                                 if (path == "") {       nameFileNames[i] = inputDir + nameFileNames[i];         }
 213                                         }
 214
 215                                         int ableToOpen;
 216                                         ifstream in;
 217
 218                                         ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror");
 219
 220                                         //if you can't open it, try default location
 221                                         if (ableToOpen == 1) {
 222                                                 if (m->getDefaultPath() != "") { //default path is set
 223                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]);
 224                                                         m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 225                                                         ifstream in2;
 226                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 227                                                         in2.close();
 228                                                         nameFileNames[i] = tryPath;
 229                                                 }
 230                                         }
 231
 232                                         if (ableToOpen == 1) {
 233                                                 if (m->getOutputDir() != "") { //default path is set
 234                                                         string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]);
 235                                                         m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 236                                                         ifstream in2;
 237                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 238                                                         in2.close();
 239                                                         nameFileNames[i] = tryPath;
 240                                                 }
 241                                         }
 242
 243                                         in.close();
 244
 245                                         if (ableToOpen == 1) {
 246                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 247                                                 //erase from file list
 248                                                 nameFileNames.erase(nameFileNames.begin()+i);
 249                                                 i--;
 250                                         }
 251                                 }
 252
 253                                 //make sure there is at least one valid file left
 254                                 if (nameFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid name files."); m->mothurOutEndLine(); abort = true; }
 255                         }
 256
 257                         if (hasName && (nameFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of namefiles does not match the number of fastafiles, please correct."); m->mothurOutEndLine(); abort=true; }
 258
 259                         //if the user changes the output directory command factory will send this info to us in the output parameter
 260                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 261
 262
 263                         string path;
 264                         it = parameters.find("reference");
 265                         //user has given a template file
 266                         if(it != parameters.end()){
 267                                 if (it->second == "self") { templatefile = "self"; }
 268                                 else {
 269                                         path = m->hasPath(it->second);
 270                                         //if the user has not given a path then, add inputdir. else leave path alone.
 271                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 272
 273                                         templatefile = validParameter.validFile(parameters, "reference", true);
 274                                         if (templatefile == "not open") { abort = true; }
 275                                         else if (templatefile == "not found") { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true;  }
 276                                 }
 277                         }
 278
 279                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 280                         m->setProcessors(temp);
 281                         convert(temp, processors);
 282
 283                         temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
 284                         convert(temp, ksize);
 285
 286                         temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "50"; }
 287                         convert(temp, window);
 288
 289                         temp = validParameter.validFile(parameters, "match", false);                    if (temp == "not found") { temp = "5"; }
 290                         convert(temp, match);
 291
 292                         temp = validParameter.validFile(parameters, "mismatch", false);                 if (temp == "not found") { temp = "-4"; }
 293                         convert(temp, mismatch);
 294
 295                         temp = validParameter.validFile(parameters, "divergence", false);               if (temp == "not found") { temp = "1.007"; }
 296                         convert(temp, divR);
 297
 298                         temp = validParameter.validFile(parameters, "minsim", false);                   if (temp == "not found") { temp = "90"; }
 299                         convert(temp, minSimilarity);
 300
 301                         temp = validParameter.validFile(parameters, "mincov", false);                   if (temp == "not found") { temp = "70"; }
 302                         convert(temp, minCoverage);
 303
 304                         temp = validParameter.validFile(parameters, "minbs", false);                    if (temp == "not found") { temp = "90"; }
 305                         convert(temp, minBS);
 306
 307                         temp = validParameter.validFile(parameters, "minsnp", false);                   if (temp == "not found") { temp = "100"; }
 308                         convert(temp, minSNP);
 309
 310                         temp = validParameter.validFile(parameters, "parents", false);                  if (temp == "not found") { temp = "3"; }
 311                         convert(temp, parents);
 312
 313                         temp = validParameter.validFile(parameters, "realign", false);                  if (temp == "not found") { temp = "f"; }
 314                         realign = m->isTrue(temp);
 315
 316                         temp = validParameter.validFile(parameters, "trim", false);                             if (temp == "not found") { temp = "f"; }
 317                         trim = m->isTrue(temp);
 318
 319                         temp = validParameter.validFile(parameters, "split", false);                    if (temp == "not found") { temp = "f"; }
 320                         trimera = m->isTrue(temp);
 321
 322                         search = validParameter.validFile(parameters, "search", false);                 if (search == "not found") { search = "distance"; }
 323
 324                         temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "100"; }
 325                         convert(temp, iters);
 326
 327                         temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "5"; }
 328                         convert(temp, increment);
 329
 330                         temp = validParameter.validFile(parameters, "numwanted", false);                if (temp == "not found") { temp = "15"; }
 331                         convert(temp, numwanted);
 332
 333                         if ((search != "distance") && (search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true;  }
 334                 }
 335         }
 336         catch(exception& e) {
 337                 m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
 338                 exit(1);
 339         }
 340 }
 341 //***************************************************************************************************************
 342
 343 int ChimeraSlayerCommand::execute(){
 344         try{
 345
 346                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 347
 348                 for (int s = 0; s < fastaFileNames.size(); s++) {
 349
 350                         m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 351
 352                         int start = time(NULL);
 353
 354                         if (templatefile != "self") { //you want to run slayer with a refernce template
 355                                 chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
 356                         }else {
 357                                 if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
 358                                 string nameFile = "";
 359                                 if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
 360                                         nameFile = nameFileNames[s];
 361                                 }else {
 362                                         m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine();
 363
 364                                         //use unique.seqs to create new name and fastafile
 365                                         string inputString = "fasta=" + fastaFileNames[s];
 366                                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 367                                         m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
 368
 369                                         Command* uniqueCommand = new DeconvoluteCommand(inputString);
 370                                         uniqueCommand->execute();
 371
 372                                         map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 373
 374                                         delete uniqueCommand;
 375
 376                                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 377
 378                                         nameFile = filenames["name"][0];
 379                                         fastaFileNames[s] = filenames["fasta"][0];
 380                                 }
 381
 382                                 //sort fastafile by abundance, returns new sorted fastafile name
 383                                 m->mothurOut("Sorting fastafile according to abundance..."); cout.flush();
 384                                 map<string, int> priority = sortFastaFile(fastaFileNames[s], nameFile);
 385                                 m->mothurOut("Done."); m->mothurOutEndLine();
 386
 387                                 if (m->control_pressed) {  for (int j = 0; j < outputNames.size(); j++) {       remove(outputNames[j].c_str()); }  return 0;    }
 388
 389                                 chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
 390                         }
 391
 392                         if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it
 393                         string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimera";
 394                         string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "slayer.accnos";
 395                         string trimFastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "slayer.fasta";
 396
 397                         if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) {        remove(outputNames[j].c_str()); }  return 0;    }
 398
 399                         if (chimera->getUnaligned()) {
 400                                 m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine();
 401                                 delete chimera;
 402                                 return 0;
 403                         }
 404                         templateSeqsLength = chimera->getLength();
 405
 406                 #ifdef USE_MPI
 407                         int pid, numSeqsPerProcessor;
 408                                 int tag = 2001;
 409                                 vector<unsigned long int> MPIPos;
 410
 411                                 MPI_Status status;
 412                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 413                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 414
 415                                 MPI_File inMPI;
 416                                 MPI_File outMPI;
 417                                 MPI_File outMPIAccnos;
 418                                 MPI_File outMPIFasta;
 419
 420                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 421                                 int inMode=MPI_MODE_RDONLY;
 422
 423                                 char outFilename[1024];
 424                                 strcpy(outFilename, outputFileName.c_str());
 425
 426                                 char outAccnosFilename[1024];
 427                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 428
 429                                 char outFastaFilename[1024];
 430                                 strcpy(outFastaFilename, trimFastaFileName.c_str());
 431
 432                                 char inFileName[1024];
 433                                 strcpy(inFileName, fastaFileNames[s].c_str());
 434
 435                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 436                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 437                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 438                                 if (trim) { MPI_File_open(MPI_COMM_WORLD, outFastaFilename, outMode, MPI_INFO_NULL, &outMPIFasta); }
 439
 440                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) {  MPI_File_close(&outMPIFasta);  } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }   delete chimera; return 0;  }
 441
 442                                 if (pid == 0) { //you are the root process
 443                                         m->mothurOutEndLine();
 444                                         m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
 445                                         m->mothurOutEndLine();
 446
 447                                         string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
 448
 449                                         //print header
 450                                         int length = outTemp.length();
 451                                         char* buf2 = new char[length];
 452                                         memcpy(buf2, outTemp.c_str(), length);
 453
 454                                         MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
 455                                         delete buf2;
 456
 457                                         MPIPos = m->setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs
 458
 459                                         if (templatefile != "self") { //if template=self we can only use 1 processor
 460                                                 //send file positions to all processes
 461                                                 for(int i = 1; i < processors; i++) {
 462                                                         MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 463                                                         MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 464                                                 }
 465                                         }
 466                                         //figure out how many sequences you have to align
 467                                         numSeqsPerProcessor = numSeqs / processors;
 468                                         int startIndex =  pid * numSeqsPerProcessor;
 469                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 470
 471                                         if (templatefile == "self") { //if template=self we can only use 1 processor
 472                                                 startIndex = 0;
 473                                                 numSeqsPerProcessor = numSeqs;
 474                                         }
 475
 476                                         //do your part
 477                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos);
 478
 479                                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); }  MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  remove(outputFileName.c_str());  remove(accnosFileName.c_str());  delete chimera; return 0;  }
 480
 481                                 }else{ //you are a child process
 482                                         if (templatefile != "self") { //if template=self we can only use 1 processor
 483                                                 MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 484                                                 MPIPos.resize(numSeqs+1);
 485                                                 MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 486
 487                                                 //figure out how many sequences you have to align
 488                                                 numSeqsPerProcessor = numSeqs / processors;
 489                                                 int startIndex =  pid * numSeqsPerProcessor;
 490                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 491
 492                                                 //do your part
 493                                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos);
 494
 495                                                 if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); }  MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  delete chimera; return 0;  }
 496
 497                                         }
 498                                 }
 499
 500                                 //close files
 501                                 MPI_File_close(&inMPI);
 502                                 MPI_File_close(&outMPI);
 503                                 MPI_File_close(&outMPIAccnos);
 504                                 if (trim) { MPI_File_close(&outMPIFasta); }
 505                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 506
 507                 #else
 508                         ofstream outHeader;
 509                         string tempHeader = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimeras.tempHeader";
 510                         m->openOutputFile(tempHeader, outHeader);
 511
 512                         chimera->printHeader(outHeader);
 513                         outHeader.close();
 514
 515                         vector<unsigned long int> positions = m->divideFile(fastaFileNames[s], processors);
 516
 517                         for (int i = 0; i < (positions.size()-1); i++) {
 518                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 519                         }
 520
 521                         //break up file
 522                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 523                                 if(processors == 1){
 524                                         numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
 525
 526                                         if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) {      remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear(); delete chimera; return 0; }
 527
 528                                 }else{
 529                                         processIDS.resize(0);
 530
 531                                         numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
 532
 533                                         rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 534                                         rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
 535                                         if (trim) {  rename((trimFastaFileName + toString(processIDS[0]) + ".temp").c_str(), trimFastaFileName.c_str()); }
 536
 537                                         //append output files
 538                                         for(int i=1;i<processors;i++){
 539                                                 m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
 540                                                 remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
 541                                         }
 542
 543                                         //append output files
 544                                         for(int i=1;i<processors;i++){
 545                                                 m->appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
 546                                                 remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());
 547                                         }
 548
 549                                         if (trim) {
 550                                                 for(int i=1;i<processors;i++){
 551                                                         m->appendFiles((trimFastaFileName + toString(processIDS[i]) + ".temp"), trimFastaFileName);
 552                                                         remove((trimFastaFileName + toString(processIDS[i]) + ".temp").c_str());
 553                                                 }
 554                                         }
 555
 556                                         if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear(); delete chimera; return 0; }
 557                                 }
 558
 559                         #else
 560                                 numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
 561
 562                                 if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) {      remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear(); delete chimera; return 0; }
 563
 564                         #endif
 565
 566                         m->appendFiles(outputFileName, tempHeader);
 567
 568                         remove(outputFileName.c_str());
 569                         rename(tempHeader.c_str(), outputFileName.c_str());
 570
 571                 #endif
 572                         delete chimera;
 573
 574
 575                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 576
 577                         outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
 578                         outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
 579                         if (trim) {  outputNames.push_back(trimFastaFileName); outputTypes["fasta"].push_back(trimFastaFileName); }
 580
 581                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 582                 }
 583
 584                 //set accnos file as new current accnosfile
 585                 string current = "";
 586                 itTypes = outputTypes.find("accnos");
 587                 if (itTypes != outputTypes.end()) {
 588                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 589                 }
 590
 591                 if (trim) {
 592                         itTypes = outputTypes.find("fasta");
 593                         if (itTypes != outputTypes.end()) {
 594                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 595                         }
 596                 }
 597
 598                 m->mothurOutEndLine();
 599                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 600                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 601                 m->mothurOutEndLine();
 602
 603                 return 0;
 604
 605         }
 606         catch(exception& e) {
 607                 m->errorOut(e, "ChimeraSlayerCommand", "execute");
 608                 exit(1);
 609         }
 610 }
 611 //**********************************************************************************************************************
 612
 613 int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string filename, string accnos, string fasta){
 614         try {
 615                 ofstream out;
 616                 m->openOutputFile(outputFName, out);
 617
 618                 ofstream out2;
 619                 m->openOutputFile(accnos, out2);
 620
 621                 ofstream out3;
 622                 if (trim) {  m->openOutputFile(fasta, out3); }
 623
 624                 ifstream inFASTA;
 625                 m->openInputFile(filename, inFASTA);
 626
 627                 inFASTA.seekg(filePos->start);
 628
 629                 bool done = false;
 630                 int count = 0;
 631
 632                 while (!done) {
 633
 634                         if (m->control_pressed) {       out.close(); out2.close(); if (trim) { out3.close(); } inFASTA.close(); return 1;       }
 635
 636                         Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
 637                         string candidateAligned = candidateSeq->getAligned();
 638
 639                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 640
 641                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 642                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 643                                 }else{
 644                                         //find chimeras
 645                                         chimera->getChimeras(candidateSeq);
 646
 647                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 648
 649                                         //if you are not chimeric, then check each half
 650                                         data_results wholeResults = chimera->getResults();
 651
 652                                         //determine if we need to split
 653                                         bool isChimeric = false;
 654
 655                                         if (wholeResults.flag == "yes") {
 656                                                 string chimeraFlag = "no";
 657                                                 if(  (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
 658                                                    ||
 659                                                    (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
 660
 661
 662                                                 if (chimeraFlag == "yes") {
 663                                                         if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
 664                                                 }
 665                                         }
 666
 667                                         if ((!isChimeric) && trimera) {
 668
 669                                                 //split sequence in half by bases
 670                                                 string leftQuery, rightQuery;
 671                                                 Sequence tempSeq(candidateSeq->getName(), candidateAligned);
 672                                                 divideInHalf(tempSeq, leftQuery, rightQuery);
 673
 674                                                 //run chimeraSlayer on each piece
 675                                                 Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
 676                                                 Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
 677
 678                                                 //find chimeras
 679                                                 chimera->getChimeras(left);
 680                                                 data_results leftResults = chimera->getResults();
 681
 682                                                 chimera->getChimeras(right);
 683                                                 data_results rightResults = chimera->getResults();
 684
 685                                                 //if either piece is chimeric then report
 686                                                 Sequence* trimmed = chimera->print(out, out2, leftResults, rightResults);
 687                                                 if (trim) { trimmed->printSequence(out3); delete trimmed; }
 688
 689                                                 delete left; delete right;
 690
 691                                         }else { //already chimeric
 692                                                 //print results
 693                                                 Sequence* trimmed = chimera->print(out, out2);
 694                                                 if (trim) { trimmed->printSequence(out3); delete trimmed; }
 695                                         }
 696
 697
 698                                 }
 699                                 count++;
 700                         }
 701                         delete candidateSeq;
 702
 703                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 704                                 unsigned long int pos = inFASTA.tellg();
 705                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 706                         #else
 707                                 if (inFASTA.eof()) { break; }
 708                         #endif
 709
 710                         //report progress
 711                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 712                 }
 713                 //report progress
 714                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 715
 716                 out.close();
 717                 out2.close();
 718                 if (trim) { out3.close(); }
 719                 inFASTA.close();
 720
 721                 return count;
 722         }
 723         catch(exception& e) {
 724                 m->errorOut(e, "ChimeraSlayerCommand", "driver");
 725                 exit(1);
 726         }
 727 }
 728 //**********************************************************************************************************************
 729 #ifdef USE_MPI
 730 int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, MPI_File& outFastaMPI, vector<unsigned long int>& MPIPos){
 731         try {
 732                 MPI_Status status;
 733                 int pid;
 734                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 735
 736                 for(int i=0;i<num;i++){
 737
 738                         if (m->control_pressed) {       return 1;       }
 739
 740                         //read next sequence
 741                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 742
 743                         char* buf4 = new char[length];
 744                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 745
 746                         string tempBuf = buf4;
 747                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 748                         istringstream iss (tempBuf,istringstream::in);
 749
 750                         delete buf4;
 751
 752                         Sequence* candidateSeq = new Sequence(iss);  m->gobble(iss);
 753                         string candidateAligned = candidateSeq->getAligned();
 754
 755                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 756
 757                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 758                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 759                                 }else{
 760
 761                                         //find chimeras
 762                                         chimera->getChimeras(candidateSeq);
 763
 764                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 765
 766                                         //if you are not chimeric, then check each half
 767                                         data_results wholeResults = chimera->getResults();
 768
 769                                         //determine if we need to split
 770                                         bool isChimeric = false;
 771
 772                                         if (wholeResults.flag == "yes") {
 773                                                 string chimeraFlag = "no";
 774                                                 if(  (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
 775                                                    ||
 776                                                    (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
 777
 778
 779                                                 if (chimeraFlag == "yes") {
 780                                                         if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
 781                                                 }
 782                                         }
 783
 784                                         if ((!isChimeric) && trimera) {
 785                                                 //split sequence in half by bases
 786                                                 string leftQuery, rightQuery;
 787                                                 Sequence tempSeq(candidateSeq->getName(), candidateAligned);
 788                                                 divideInHalf(tempSeq, leftQuery, rightQuery);
 789
 790                                                 //run chimeraSlayer on each piece
 791                                                 Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
 792                                                 Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
 793
 794                                                 //find chimeras
 795                                                 chimera->getChimeras(left);
 796                                                 data_results leftResults = chimera->getResults();
 797
 798                                                 chimera->getChimeras(right);
 799                                                 data_results rightResults = chimera->getResults();
 800
 801                                                 //if either piece is chimeric then report
 802                                                 Sequence* trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults);
 803                                                 if (trim) {
 804                                                         string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n";
 805                                                         delete trimmed;
 806
 807                                                         //write to accnos file
 808                                                         int length = outputString.length();
 809                                                         char* buf2 = new char[length];
 810                                                         memcpy(buf2, outputString.c_str(), length);
 811
 812                                                         MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
 813                                                         delete buf2;
 814                                                 }
 815
 816                                                 delete left; delete right;
 817
 818                                         }else {
 819                                                 //print results
 820                                                 Sequence* trimmed = chimera->print(outMPI, outAccMPI);
 821
 822                                                 if (trim) {
 823                                                         string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n";
 824                                                         delete trimmed;
 825
 826                                                         //write to accnos file
 827                                                         int length = outputString.length();
 828                                                         char* buf2 = new char[length];
 829                                                         memcpy(buf2, outputString.c_str(), length);
 830
 831                                                         MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
 832                                                         delete buf2;
 833                                                 }
 834                                         }
 835
 836                                 }
 837                         }
 838                         delete candidateSeq;
 839
 840                         //report progress
 841                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 842                 }
 843                 //report progress
 844                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 845
 846
 847                 return 0;
 848         }
 849         catch(exception& e) {
 850                 m->errorOut(e, "ChimeraSlayerCommand", "driverMPI");
 851                 exit(1);
 852         }
 853 }
 854 #endif
 855
 856 /**************************************************************************************************/
 857
 858 int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos, string fasta) {
 859         try {
 860 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 861                 int process = 0;
 862                 int num = 0;
 863
 864                 //loop through and create all the processes you want
 865                 while (process != processors) {
 866                         int pid = fork();
 867
 868                         if (pid > 0) {
 869                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 870                                 process++;
 871                         }else if (pid == 0){
 872                                 num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp");
 873
 874                                 //pass numSeqs to parent
 875                                 ofstream out;
 876                                 string tempFile = outputFileName + toString(getpid()) + ".num.temp";
 877                                 m->openOutputFile(tempFile, out);
 878                                 out << num << endl;
 879                                 out.close();
 880
 881                                 exit(0);
 882                         }else {
 883                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 884                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 885                                 exit(0);
 886                         }
 887                 }
 888
 889                 //force parent to wait until all the processes are done
 890                 for (int i=0;i<processors;i++) {
 891                         int temp = processIDS[i];
 892                         wait(&temp);
 893                 }
 894
 895                 for (int i = 0; i < processIDS.size(); i++) {
 896                         ifstream in;
 897                         string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
 898                         m->openInputFile(tempFile, in);
 899                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 900                         in.close(); remove(tempFile.c_str());
 901                 }
 902
 903                 return num;
 904 #endif
 905         }
 906         catch(exception& e) {
 907                 m->errorOut(e, "ChimeraSlayerCommand", "createProcesses");
 908                 exit(1);
 909         }
 910 }
 911
 912 /**************************************************************************************************/
 913
 914 int ChimeraSlayerCommand::divideInHalf(Sequence querySeq, string& leftQuery, string& rightQuery) {
 915         try {
 916
 917                 string queryUnAligned = querySeq.getUnaligned();
 918                 int numBases = int(queryUnAligned.length() * 0.5);
 919
 920                 string queryAligned = querySeq.getAligned();
 921                 leftQuery = querySeq.getAligned();
 922                 rightQuery = querySeq.getAligned();
 923
 924                 int baseCount = 0;
 925                 int leftSpot = 0;
 926                 for (int i = 0; i < queryAligned.length(); i++) {
 927                         //if you are a base
 928                         if (isalpha(queryAligned[i])) {
 929                                 baseCount++;
 930                         }
 931
 932                         //if you have half
 933                         if (baseCount >= numBases) {  leftSpot = i; break; } //first half
 934                 }
 935
 936                 //blank out right side
 937                 for (int i = leftSpot; i < leftQuery.length(); i++) { leftQuery[i] = '.'; }
 938
 939                 //blank out left side
 940                 for (int i = 0; i < leftSpot; i++) { rightQuery[i] = '.'; }
 941
 942                 return 0;
 943
 944         }
 945         catch(exception& e) {
 946                 m->errorOut(e, "ChimeraSlayerCommand", "divideInHalf");
 947                 exit(1);
 948         }
 949 }
 950 /**************************************************************************************************/
 951 map<string, int> ChimeraSlayerCommand::sortFastaFile(string fastaFile, string nameFile) {
 952         try {
 953                 map<string, int> nameAbund;
 954
 955                 //read through fastafile and store info
 956                 map<string, string> seqs;
 957                 ifstream in;
 958                 m->openInputFile(fastaFile, in);
 959
 960                 while (!in.eof()) {
 961
 962                         if (m->control_pressed) { in.close(); return nameAbund; }
 963
 964                         Sequence seq(in); m->gobble(in);
 965                         seqs[seq.getName()] = seq.getAligned();
 966                 }
 967
 968                 in.close();
 969
 970                 //read namefile
 971                 vector<seqPriorityNode> nameMapCount;
 972                 int error = m->readNames(nameFile, nameMapCount, seqs);
 973
 974                 if (m->control_pressed) { return nameAbund; }
 975
 976                 if (error == 1) { m->control_pressed = true; return nameAbund; }
 977                 if (seqs.size() != nameMapCount.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your namefile, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return nameAbund; }
 978
 979                 sort(nameMapCount.begin(), nameMapCount.end(), compareSeqPriorityNodes);
 980
 981                 string newFasta = fastaFile + ".temp";
 982                 ofstream out;
 983                 m->openOutputFile(newFasta, out);
 984
 985                 //print new file in order of
 986                 for (int i = 0; i < nameMapCount.size(); i++) {
 987                         out << ">" << nameMapCount[i].name << endl << nameMapCount[i].seq << endl;
 988                         nameAbund[nameMapCount[i].name] = nameMapCount[i].numIdentical;
 989                 }
 990                 out.close();
 991
 992                 rename(newFasta.c_str(), fastaFile.c_str());
 993
 994                 return nameAbund;
 995
 996         }
 997         catch(exception& e) {
 998                 m->errorOut(e, "ChimeraSlayerCommand", "sortFastaFile");
 999                 exit(1);
1000         }
1001 }
1002
1003 /**************************************************************************************************/
1004