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", "", "10", "", "", "",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", "blast", "", "", "",false,false); parameters.push_back(psearch);
  29                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  30                 CommandParameter prealign("realign", "Boolean", "", "T", "", "", "",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", "", "1000", "", "", "",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, numwanted, and realign.\n";
  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=1000.\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: 10) \n";
  80                 helpString += "The search parameter allows you to specify search method for finding the closest parent. Choices are blast, and kmer, default blast. \n";
  81                 helpString += "The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default true.  \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                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 116
 117                 else {
 118                         vector<string> myArray = setParameters();
 119
 120                         OptionParser parser(option);
 121                         map<string,string> parameters = parser.getParameters();
 122
 123                         ValidParameters validParameter("chimera.slayer");
 124                         map<string,string>::iterator it;
 125
 126                         //check to make sure all parameters are valid for command
 127                         for (it = parameters.begin(); it != parameters.end(); it++) {
 128                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 129                         }
 130
 131                         vector<string> tempOutNames;
 132                         outputTypes["chimera"] = tempOutNames;
 133                         outputTypes["accnos"] = tempOutNames;
 134                         outputTypes["fasta"] = tempOutNames;
 135
 136                         //if the user changes the input directory command factory will send this info to us in the output parameter
 137                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 138                         if (inputDir == "not found"){   inputDir = "";          }
 139
 140                         //check for required parameters
 141                         fastafile = validParameter.validFile(parameters, "fasta", false);
 142                         if (fastafile == "not found") {
 143                                 //if there is a current fasta file, use it
 144                                 string filename = m->getFastaFile();
 145                                 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 146                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 147                         }else {
 148                                 m->splitAtDash(fastafile, fastaFileNames);
 149
 150                                 //go through files and make sure they are good, if not, then disregard them
 151                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 152
 153                                         bool ignore = false;
 154                                         if (fastaFileNames[i] == "current") {
 155                                                 fastaFileNames[i] = m->getFastaFile();
 156                                                 if (fastaFileNames[i] != "") {  m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 157                                                 else {
 158                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 159                                                         //erase from file list
 160                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 161                                                         i--;
 162                                                 }
 163                                         }
 164
 165                                         if (!ignore) {
 166
 167                                                 if (inputDir != "") {
 168                                                         string path = m->hasPath(fastaFileNames[i]);
 169                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 170                                                         if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 171                                                 }
 172
 173                                                 int ableToOpen;
 174                                                 ifstream in;
 175
 176                                                 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 177
 178                                                 //if you can't open it, try default location
 179                                                 if (ableToOpen == 1) {
 180                                                         if (m->getDefaultPath() != "") { //default path is set
 181                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 182                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 183                                                                 ifstream in2;
 184                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 185                                                                 in2.close();
 186                                                                 fastaFileNames[i] = tryPath;
 187                                                         }
 188                                                 }
 189
 190                                                 if (ableToOpen == 1) {
 191                                                         if (m->getOutputDir() != "") { //default path is set
 192                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 193                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 194                                                                 ifstream in2;
 195                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 196                                                                 in2.close();
 197                                                                 fastaFileNames[i] = tryPath;
 198                                                         }
 199                                                 }
 200
 201                                                 in.close();
 202
 203                                                 if (ableToOpen == 1) {
 204                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 205                                                         //erase from file list
 206                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 207                                                         i--;
 208                                                 }
 209                                         }
 210                                 }
 211
 212                                 //make sure there is at least one valid file left
 213                                 if (fastaFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
 214                         }
 215
 216
 217                         //check for required parameters
 218                         bool hasName = true;
 219                         namefile = validParameter.validFile(parameters, "name", false);
 220                         if (namefile == "not found") { namefile = "";  hasName = false; }
 221                         else {
 222                                 m->splitAtDash(namefile, nameFileNames);
 223
 224                                 //go through files and make sure they are good, if not, then disregard them
 225                                 for (int i = 0; i < nameFileNames.size(); i++) {
 226
 227                                         bool ignore = false;
 228                                         if (nameFileNames[i] == "current") {
 229                                                 nameFileNames[i] = m->getNameFile();
 230                                                 if (nameFileNames[i] != "") {  m->mothurOut("Using " + nameFileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
 231                                                 else {
 232                                                         m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 233                                                         //erase from file list
 234                                                         nameFileNames.erase(nameFileNames.begin()+i);
 235                                                         i--;
 236                                                 }
 237                                         }
 238
 239                                         if (!ignore) {
 240
 241                                                 if (inputDir != "") {
 242                                                         string path = m->hasPath(nameFileNames[i]);
 243                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 244                                                         if (path == "") {       nameFileNames[i] = inputDir + nameFileNames[i];         }
 245                                                 }
 246
 247                                                 int ableToOpen;
 248                                                 ifstream in;
 249
 250                                                 ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror");
 251
 252                                                 //if you can't open it, try default location
 253                                                 if (ableToOpen == 1) {
 254                                                         if (m->getDefaultPath() != "") { //default path is set
 255                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]);
 256                                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 257                                                                 ifstream in2;
 258                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 259                                                                 in2.close();
 260                                                                 nameFileNames[i] = tryPath;
 261                                                         }
 262                                                 }
 263
 264                                                 if (ableToOpen == 1) {
 265                                                         if (m->getOutputDir() != "") { //default path is set
 266                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]);
 267                                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 268                                                                 ifstream in2;
 269                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 270                                                                 in2.close();
 271                                                                 nameFileNames[i] = tryPath;
 272                                                         }
 273                                                 }
 274
 275                                                 in.close();
 276
 277                                                 if (ableToOpen == 1) {
 278                                                         m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 279                                                         //erase from file list
 280                                                         nameFileNames.erase(nameFileNames.begin()+i);
 281                                                         i--;
 282                                                 }
 283                                         }
 284                                 }
 285
 286                                 //make sure there is at least one valid file left
 287                                 if (nameFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid name files."); m->mothurOutEndLine(); abort = true; }
 288                         }
 289
 290                         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; }
 291
 292                         //if the user changes the output directory command factory will send this info to us in the output parameter
 293                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 294
 295
 296                         string path;
 297                         it = parameters.find("reference");
 298                         //user has given a template file
 299                         if(it != parameters.end()){
 300                                 if (it->second == "self") { templatefile = "self"; }
 301                                 else {
 302                                         path = m->hasPath(it->second);
 303                                         //if the user has not given a path then, add inputdir. else leave path alone.
 304                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 305
 306                                         templatefile = validParameter.validFile(parameters, "reference", true);
 307                                         if (templatefile == "not open") { abort = true; }
 308                                         else if (templatefile == "not found") { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.slayer command, unless and namefile is given."); m->mothurOutEndLine(); abort = true;  }
 309                                 }
 310                         }else if (hasName) {  templatefile = "self"; }
 311                         else { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true;  }
 312
 313                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 314                         m->setProcessors(temp);
 315                         convert(temp, processors);
 316
 317                         temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
 318                         convert(temp, ksize);
 319
 320                         temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "50"; }
 321                         convert(temp, window);
 322
 323                         temp = validParameter.validFile(parameters, "match", false);                    if (temp == "not found") { temp = "5"; }
 324                         convert(temp, match);
 325
 326                         temp = validParameter.validFile(parameters, "mismatch", false);                 if (temp == "not found") { temp = "-4"; }
 327                         convert(temp, mismatch);
 328
 329                         temp = validParameter.validFile(parameters, "divergence", false);               if (temp == "not found") { temp = "1.007"; }
 330                         convert(temp, divR);
 331
 332                         temp = validParameter.validFile(parameters, "minsim", false);                   if (temp == "not found") { temp = "90"; }
 333                         convert(temp, minSimilarity);
 334
 335                         temp = validParameter.validFile(parameters, "mincov", false);                   if (temp == "not found") { temp = "70"; }
 336                         convert(temp, minCoverage);
 337
 338                         temp = validParameter.validFile(parameters, "minbs", false);                    if (temp == "not found") { temp = "90"; }
 339                         convert(temp, minBS);
 340
 341                         temp = validParameter.validFile(parameters, "minsnp", false);                   if (temp == "not found") { temp = "10"; }
 342                         convert(temp, minSNP);
 343
 344                         temp = validParameter.validFile(parameters, "parents", false);                  if (temp == "not found") { temp = "3"; }
 345                         convert(temp, parents);
 346
 347                         temp = validParameter.validFile(parameters, "realign", false);                  if (temp == "not found") { temp = "t"; }
 348                         realign = m->isTrue(temp);
 349
 350                         temp = validParameter.validFile(parameters, "trim", false);                             if (temp == "not found") { temp = "f"; }
 351                         trim = m->isTrue(temp);
 352
 353                         temp = validParameter.validFile(parameters, "split", false);                    if (temp == "not found") { temp = "f"; }
 354                         trimera = m->isTrue(temp);
 355
 356                         search = validParameter.validFile(parameters, "search", false);                 if (search == "not found") { search = "blast"; }
 357
 358                         temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
 359                         convert(temp, iters);
 360
 361                         temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "5"; }
 362                         convert(temp, increment);
 363
 364                         temp = validParameter.validFile(parameters, "numwanted", false);                if (temp == "not found") { temp = "15"; }
 365                         convert(temp, numwanted);
 366
 367                         if ((search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true;  }
 368                 }
 369         }
 370         catch(exception& e) {
 371                 m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
 372                 exit(1);
 373         }
 374 }
 375 //***************************************************************************************************************
 376
 377 int ChimeraSlayerCommand::execute(){
 378         try{
 379                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 380
 381                 for (int s = 0; s < fastaFileNames.size(); s++) {
 382
 383                         m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 384
 385                         int start = time(NULL);
 386
 387                         if (templatefile != "self") { //you want to run slayer with a refernce template
 388                                 chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
 389                         }else {
 390                                 if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
 391                                 string nameFile = "";
 392                                 if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
 393                                         nameFile = nameFileNames[s];
 394                                 }else {
 395                                         m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine();
 396
 397                                         //use unique.seqs to create new name and fastafile
 398                                         string inputString = "fasta=" + fastaFileNames[s];
 399                                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 400                                         m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
 401
 402                                         Command* uniqueCommand = new DeconvoluteCommand(inputString);
 403                                         uniqueCommand->execute();
 404
 405                                         map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 406
 407                                         delete uniqueCommand;
 408
 409                                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 410
 411                                         nameFile = filenames["name"][0];
 412                                         fastaFileNames[s] = filenames["fasta"][0];
 413                                 }
 414
 415                                 //sort fastafile by abundance, returns new sorted fastafile name
 416                                 m->mothurOut("Sorting fastafile according to abundance..."); cout.flush();
 417                                 map<string, int> priority = sortFastaFile(fastaFileNames[s], nameFile);
 418                                 m->mothurOut("Done."); m->mothurOutEndLine();
 419
 420                                 if (m->control_pressed) {  for (int j = 0; j < outputNames.size(); j++) {       remove(outputNames[j].c_str()); }  return 0;    }
 421
 422                                 chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
 423                         }
 424
 425                         if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it
 426                         string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimera";
 427                         string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "slayer.accnos";
 428                         string trimFastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "slayer.fasta";
 429
 430                         if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) {        remove(outputNames[j].c_str()); }  return 0;    }
 431
 432                         if (chimera->getUnaligned()) {
 433                                 m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine();
 434                                 delete chimera;
 435                                 return 0;
 436                         }
 437                         templateSeqsLength = chimera->getLength();
 438
 439                 #ifdef USE_MPI
 440                         int pid, numSeqsPerProcessor;
 441                                 int tag = 2001;
 442                                 vector<unsigned long int> MPIPos;
 443
 444                                 MPI_Status status;
 445                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 446                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 447
 448                                 MPI_File inMPI;
 449                                 MPI_File outMPI;
 450                                 MPI_File outMPIAccnos;
 451                                 MPI_File outMPIFasta;
 452
 453                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 454                                 int inMode=MPI_MODE_RDONLY;
 455
 456                                 char outFilename[1024];
 457                                 strcpy(outFilename, outputFileName.c_str());
 458
 459                                 char outAccnosFilename[1024];
 460                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 461
 462                                 char outFastaFilename[1024];
 463                                 strcpy(outFastaFilename, trimFastaFileName.c_str());
 464
 465                                 char inFileName[1024];
 466                                 strcpy(inFileName, fastaFileNames[s].c_str());
 467
 468                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 469                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 470                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 471                                 if (trim) { MPI_File_open(MPI_COMM_WORLD, outFastaFilename, outMode, MPI_INFO_NULL, &outMPIFasta); }
 472
 473                         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;  }
 474
 475                                 if (pid == 0) { //you are the root process
 476                                         m->mothurOutEndLine();
 477                                         m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
 478                                         m->mothurOutEndLine();
 479
 480                                         string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
 481
 482                                         //print header
 483                                         int length = outTemp.length();
 484                                         char* buf2 = new char[length];
 485                                         memcpy(buf2, outTemp.c_str(), length);
 486
 487                                         MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
 488                                         delete buf2;
 489
 490                                         MPIPos = m->setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs
 491
 492                                         if (templatefile != "self") { //if template=self we can only use 1 processor
 493                                                 //send file positions to all processes
 494                                                 for(int i = 1; i < processors; i++) {
 495                                                         MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 496                                                         MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 497                                                 }
 498                                         }
 499                                         //figure out how many sequences you have to align
 500                                         numSeqsPerProcessor = numSeqs / processors;
 501                                         int startIndex =  pid * numSeqsPerProcessor;
 502                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 503
 504                                         if (templatefile == "self") { //if template=self we can only use 1 processor
 505                                                 startIndex = 0;
 506                                                 numSeqsPerProcessor = numSeqs;
 507                                         }
 508
 509                                         //do your part
 510                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos);
 511
 512                                         int numNoParents = chimera->getNumNoParents();
 513                                         int temp;
 514                                         for(int i = 1; i < processors; i++) {
 515                                                 MPI_Recv(&temp, 1, MPI_INT, 1, tag, MPI_COMM_WORLD, &status);
 516                                                 numNoParents += temp;
 517                                         }
 518
 519
 520                                         if (numSeqs == numNoParents) {  m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
 521
 522                                         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;  }
 523
 524                                 }else{ //you are a child process
 525                                         if (templatefile != "self") { //if template=self we can only use 1 processor
 526                                                 MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 527                                                 MPIPos.resize(numSeqs+1);
 528                                                 MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 529
 530                                                 //figure out how many sequences you have to align
 531                                                 numSeqsPerProcessor = numSeqs / processors;
 532                                                 int startIndex =  pid * numSeqsPerProcessor;
 533                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 534
 535                                                 //do your part
 536                                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos);
 537
 538                                                 int numNoParents = chimera->getNumNoParents();
 539                                                 MPI_Send(&numNoParents, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 540
 541                                                 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;  }
 542
 543                                         }
 544                                 }
 545
 546                                 //close files
 547                                 MPI_File_close(&inMPI);
 548                                 MPI_File_close(&outMPI);
 549                                 MPI_File_close(&outMPIAccnos);
 550                                 if (trim) { MPI_File_close(&outMPIFasta); }
 551                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 552
 553                 #else
 554                         ofstream outHeader;
 555                         string tempHeader = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimeras.tempHeader";
 556                         m->openOutputFile(tempHeader, outHeader);
 557
 558                         chimera->printHeader(outHeader);
 559                         outHeader.close();
 560
 561                         vector<unsigned long int> positions = m->divideFile(fastaFileNames[s], processors);
 562
 563                         for (int i = 0; i < (positions.size()-1); i++) {
 564                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 565                         }
 566
 567                         //break up file
 568                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 569                                 if(processors == 1){
 570                                         numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
 571
 572                                         int numNoParents = chimera->getNumNoParents();
 573                                         if (numNoParents == numSeqs) { m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
 574
 575                                         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; }
 576
 577                                 }else{
 578                                         processIDS.resize(0);
 579
 580                                         numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
 581
 582                                         rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 583                                         rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
 584                                         if (trim) {  rename((trimFastaFileName + toString(processIDS[0]) + ".temp").c_str(), trimFastaFileName.c_str()); }
 585
 586                                         //append output files
 587                                         for(int i=1;i<processors;i++){
 588                                                 m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
 589                                                 remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
 590                                         }
 591
 592                                         //append output files
 593                                         for(int i=1;i<processors;i++){
 594                                                 m->appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
 595                                                 remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());
 596                                         }
 597
 598                                         if (trim) {
 599                                                 for(int i=1;i<processors;i++){
 600                                                         m->appendFiles((trimFastaFileName + toString(processIDS[i]) + ".temp"), trimFastaFileName);
 601                                                         remove((trimFastaFileName + toString(processIDS[i]) + ".temp").c_str());
 602                                                 }
 603                                         }
 604
 605                                         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; }
 606                                 }
 607
 608                         #else
 609                                 numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
 610
 611                                 int numNoParents = chimera->getNumNoParents();
 612                                 if (numNoParents == numSeqs) { m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
 613
 614
 615                                 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; }
 616
 617                         #endif
 618
 619                         m->appendFiles(outputFileName, tempHeader);
 620
 621                         remove(outputFileName.c_str());
 622                         rename(tempHeader.c_str(), outputFileName.c_str());
 623
 624                 #endif
 625                         delete chimera;
 626
 627
 628                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 629
 630                         outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
 631                         outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
 632                         if (trim) {  outputNames.push_back(trimFastaFileName); outputTypes["fasta"].push_back(trimFastaFileName); }
 633
 634                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 635                 }
 636
 637                 //set accnos file as new current accnosfile
 638                 string current = "";
 639                 itTypes = outputTypes.find("accnos");
 640                 if (itTypes != outputTypes.end()) {
 641                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 642                 }
 643
 644                 if (trim) {
 645                         itTypes = outputTypes.find("fasta");
 646                         if (itTypes != outputTypes.end()) {
 647                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 648                         }
 649                 }
 650
 651                 m->mothurOutEndLine();
 652                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 653                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 654                 m->mothurOutEndLine();
 655
 656                 return 0;
 657
 658         }
 659         catch(exception& e) {
 660                 m->errorOut(e, "ChimeraSlayerCommand", "execute");
 661                 exit(1);
 662         }
 663 }
 664 //**********************************************************************************************************************
 665
 666 int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string filename, string accnos, string fasta){
 667         try {
 668                 ofstream out;
 669                 m->openOutputFile(outputFName, out);
 670
 671                 ofstream out2;
 672                 m->openOutputFile(accnos, out2);
 673
 674                 ofstream out3;
 675                 if (trim) {  m->openOutputFile(fasta, out3); }
 676
 677                 ifstream inFASTA;
 678                 m->openInputFile(filename, inFASTA);
 679
 680                 inFASTA.seekg(filePos->start);
 681
 682                 bool done = false;
 683                 int count = 0;
 684
 685                 while (!done) {
 686
 687                         if (m->control_pressed) {       out.close(); out2.close(); if (trim) { out3.close(); } inFASTA.close(); return 1;       }
 688
 689                         Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
 690                         string candidateAligned = candidateSeq->getAligned();
 691
 692                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 693                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 694                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 695                                 }else{
 696                                         //find chimeras
 697                                         chimera->getChimeras(candidateSeq);
 698
 699                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 700
 701                                         //if you are not chimeric, then check each half
 702                                         data_results wholeResults = chimera->getResults();
 703
 704                                         //determine if we need to split
 705                                         bool isChimeric = false;
 706
 707                                         if (wholeResults.flag == "yes") {
 708                                                 string chimeraFlag = "no";
 709                                                 if(  (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
 710                                                    ||
 711                                                    (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
 712
 713
 714                                                 if (chimeraFlag == "yes") {
 715                                                         if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
 716                                                 }
 717                                         }
 718
 719                                         if ((!isChimeric) && trimera) {
 720
 721                                                 //split sequence in half by bases
 722                                                 string leftQuery, rightQuery;
 723                                                 Sequence tempSeq(candidateSeq->getName(), candidateAligned);
 724                                                 divideInHalf(tempSeq, leftQuery, rightQuery);
 725
 726                                                 //run chimeraSlayer on each piece
 727                                                 Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
 728                                                 Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
 729
 730                                                 //find chimeras
 731                                                 chimera->getChimeras(left);
 732                                                 data_results leftResults = chimera->getResults();
 733
 734                                                 chimera->getChimeras(right);
 735                                                 data_results rightResults = chimera->getResults();
 736
 737                                                 //if either piece is chimeric then report
 738                                                 Sequence trimmed = chimera->print(out, out2, leftResults, rightResults);
 739                                                 if (trim) { trimmed.printSequence(out3);  }
 740
 741                                                 delete left; delete right;
 742
 743                                         }else { //already chimeric
 744                                                 //print results
 745                                                 Sequence trimmed = chimera->print(out, out2);
 746                                                 if (trim) { trimmed.printSequence(out3);  }
 747                                         }
 748
 749
 750                                 }
 751                                 count++;
 752                         }
 753
 754                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 755                                 unsigned long int pos = inFASTA.tellg();
 756                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 757                         #else
 758                                 if (inFASTA.eof()) { break; }
 759                         #endif
 760
 761                         delete candidateSeq;
 762                         //report progress
 763                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 764                 }
 765                 //report progress
 766                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 767
 768                 out.close();
 769                 out2.close();
 770                 if (trim) { out3.close(); }
 771                 inFASTA.close();
 772
 773                 return count;
 774         }
 775         catch(exception& e) {
 776                 m->errorOut(e, "ChimeraSlayerCommand", "driver");
 777                 exit(1);
 778         }
 779 }
 780 //**********************************************************************************************************************
 781 #ifdef USE_MPI
 782 int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, MPI_File& outFastaMPI, vector<unsigned long int>& MPIPos){
 783         try {
 784                 MPI_Status status;
 785                 int pid;
 786                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 787
 788                 for(int i=0;i<num;i++){
 789
 790                         if (m->control_pressed) {       return 1;       }
 791
 792                         //read next sequence
 793                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 794
 795                         char* buf4 = new char[length];
 796                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 797
 798                         string tempBuf = buf4;
 799                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 800                         istringstream iss (tempBuf,istringstream::in);
 801
 802                         delete buf4;
 803
 804                         Sequence* candidateSeq = new Sequence(iss);  m->gobble(iss);
 805                         string candidateAligned = candidateSeq->getAligned();
 806
 807                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 808
 809                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 810                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 811                                 }else{
 812
 813                                         //find chimeras
 814                                         chimera->getChimeras(candidateSeq);
 815
 816                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 817
 818                                         //if you are not chimeric, then check each half
 819                                         data_results wholeResults = chimera->getResults();
 820
 821                                         //determine if we need to split
 822                                         bool isChimeric = false;
 823
 824                                         if (wholeResults.flag == "yes") {
 825                                                 string chimeraFlag = "no";
 826                                                 if(  (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
 827                                                    ||
 828                                                    (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
 829
 830
 831                                                 if (chimeraFlag == "yes") {
 832                                                         if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
 833                                                 }
 834                                         }
 835
 836                                         if ((!isChimeric) && trimera) {
 837                                                 //split sequence in half by bases
 838                                                 string leftQuery, rightQuery;
 839                                                 Sequence tempSeq(candidateSeq->getName(), candidateAligned);
 840                                                 divideInHalf(tempSeq, leftQuery, rightQuery);
 841
 842                                                 //run chimeraSlayer on each piece
 843                                                 Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
 844                                                 Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
 845
 846                                                 //find chimeras
 847                                                 chimera->getChimeras(left);
 848                                                 data_results leftResults = chimera->getResults();
 849
 850                                                 chimera->getChimeras(right);
 851                                                 data_results rightResults = chimera->getResults();
 852
 853                                                 //if either piece is chimeric then report
 854                                                 Sequence trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults);
 855                                                 if (trim) {
 856                                                         string outputString = ">" + trimmed.getName() + "\n" + trimmed.getAligned() + "\n";
 857
 858                                                         //write to accnos file
 859                                                         int length = outputString.length();
 860                                                         char* buf2 = new char[length];
 861                                                         memcpy(buf2, outputString.c_str(), length);
 862
 863                                                         MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
 864                                                         delete buf2;
 865                                                 }
 866
 867                                                 delete left; delete right;
 868
 869                                         }else {
 870                                                 //print results
 871                                                 Sequence trimmed = chimera->print(outMPI, outAccMPI);
 872
 873                                                 if (trim) {
 874                                                         string outputString = ">" + trimmed.getName() + "\n" + trimmed.getAligned() + "\n";
 875
 876                                                         //write to accnos file
 877                                                         int length = outputString.length();
 878                                                         char* buf2 = new char[length];
 879                                                         memcpy(buf2, outputString.c_str(), length);
 880
 881                                                         MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
 882                                                         delete buf2;
 883                                                 }
 884                                         }
 885
 886                                 }
 887                         }
 888                         delete candidateSeq;
 889
 890                         //report progress
 891                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 892                 }
 893                 //report progress
 894                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 895
 896
 897                 return 0;
 898         }
 899         catch(exception& e) {
 900                 m->errorOut(e, "ChimeraSlayerCommand", "driverMPI");
 901                 exit(1);
 902         }
 903 }
 904 #endif
 905
 906 /**************************************************************************************************/
 907
 908 int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos, string fasta) {
 909         try {
 910 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 911                 int process = 0;
 912                 int num = 0;
 913
 914                 //loop through and create all the processes you want
 915                 while (process != processors) {
 916                         int pid = fork();
 917
 918                         if (pid > 0) {
 919                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 920                                 process++;
 921                         }else if (pid == 0){
 922                                 num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp");
 923
 924                                 //pass numSeqs to parent
 925                                 ofstream out;
 926                                 string tempFile = outputFileName + toString(getpid()) + ".num.temp";
 927                                 m->openOutputFile(tempFile, out);
 928                                 out << num << '\t' << chimera->getNumNoParents() << endl;
 929                                 out.close();
 930                                 exit(0);
 931                         }else {
 932                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 933                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 934                                 exit(0);
 935                         }
 936                 }
 937
 938                 //force parent to wait until all the processes are done
 939                 for (int i=0;i<processors;i++) {
 940                         int temp = processIDS[i];
 941                         wait(&temp);
 942                 }
 943
 944                 int numNoParents = 0;
 945                 for (int i = 0; i < processIDS.size(); i++) {
 946                         ifstream in;
 947                         string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
 948                         m->openInputFile(tempFile, in);
 949                         if (!in.eof()) { int tempNum = 0; int tempNumParents = 0; in >> tempNum >> tempNumParents; num += tempNum; numNoParents += tempNumParents; }
 950                         in.close(); remove(tempFile.c_str());
 951                 }
 952
 953                 if (num == numNoParents) {  m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors."); m->mothurOutEndLine(); }
 954
 955                 return num;
 956 #endif
 957         }
 958         catch(exception& e) {
 959                 m->errorOut(e, "ChimeraSlayerCommand", "createProcesses");
 960                 exit(1);
 961         }
 962 }
 963
 964 /**************************************************************************************************/
 965
 966 int ChimeraSlayerCommand::divideInHalf(Sequence querySeq, string& leftQuery, string& rightQuery) {
 967         try {
 968
 969                 string queryUnAligned = querySeq.getUnaligned();
 970                 int numBases = int(queryUnAligned.length() * 0.5);
 971
 972                 string queryAligned = querySeq.getAligned();
 973                 leftQuery = querySeq.getAligned();
 974                 rightQuery = querySeq.getAligned();
 975
 976                 int baseCount = 0;
 977                 int leftSpot = 0;
 978                 for (int i = 0; i < queryAligned.length(); i++) {
 979                         //if you are a base
 980                         if (isalpha(queryAligned[i])) {
 981                                 baseCount++;
 982                         }
 983
 984                         //if you have half
 985                         if (baseCount >= numBases) {  leftSpot = i; break; } //first half
 986                 }
 987
 988                 //blank out right side
 989                 for (int i = leftSpot; i < leftQuery.length(); i++) { leftQuery[i] = '.'; }
 990
 991                 //blank out left side
 992                 for (int i = 0; i < leftSpot; i++) { rightQuery[i] = '.'; }
 993
 994                 return 0;
 995
 996         }
 997         catch(exception& e) {
 998                 m->errorOut(e, "ChimeraSlayerCommand", "divideInHalf");
 999                 exit(1);
1000         }
1001 }
1002 /**************************************************************************************************/
1003 map<string, int> ChimeraSlayerCommand::sortFastaFile(string fastaFile, string nameFile) {
1004         try {
1005                 map<string, int> nameAbund;
1006
1007                 //read through fastafile and store info
1008                 map<string, string> seqs;
1009                 ifstream in;
1010                 m->openInputFile(fastaFile, in);
1011
1012                 while (!in.eof()) {
1013
1014                         if (m->control_pressed) { in.close(); return nameAbund; }
1015
1016                         Sequence seq(in); m->gobble(in);
1017                         seqs[seq.getName()] = seq.getAligned();
1018                 }
1019
1020                 in.close();
1021
1022                 //read namefile
1023                 vector<seqPriorityNode> nameMapCount;
1024                 int error = m->readNames(nameFile, nameMapCount, seqs);
1025
1026                 if (m->control_pressed) { return nameAbund; }
1027
1028                 if (error == 1) { m->control_pressed = true; return nameAbund; }
1029                 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; }
1030
1031                 sort(nameMapCount.begin(), nameMapCount.end(), compareSeqPriorityNodes);
1032
1033                 string newFasta = fastaFile + ".temp";
1034                 ofstream out;
1035                 m->openOutputFile(newFasta, out);
1036
1037                 //print new file in order of
1038                 for (int i = 0; i < nameMapCount.size(); i++) {
1039                         out << ">" << nameMapCount[i].name << endl << nameMapCount[i].seq << endl;
1040                         nameAbund[nameMapCount[i].name] = nameMapCount[i].numIdentical;
1041                 }
1042                 out.close();
1043
1044                 rename(newFasta.c_str(), fastaFile.c_str());
1045
1046                 return nameAbund;
1047
1048         }
1049         catch(exception& e) {
1050                 m->errorOut(e, "ChimeraSlayerCommand", "sortFastaFile");
1051                 exit(1);
1052         }
1053 }
1054
1055 /**************************************************************************************************/
1056