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 #include "referencedb.h"
  14
  15 //**********************************************************************************************************************
  16 vector<string> ChimeraSlayerCommand::setParameters(){
  17         try {
  18                 CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
  19                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  20                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  21                 CommandParameter pwindow("window", "Number", "", "50", "", "", "",false,false); parameters.push_back(pwindow);
  22                 CommandParameter pksize("ksize", "Number", "", "7", "", "", "",false,false); parameters.push_back(pksize);
  23                 CommandParameter pmatch("match", "Number", "", "5.0", "", "", "",false,false); parameters.push_back(pmatch);
  24                 CommandParameter pmismatch("mismatch", "Number", "", "-4.0", "", "", "",false,false); parameters.push_back(pmismatch);
  25                 CommandParameter pminsim("minsim", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminsim);
  26                 CommandParameter pmincov("mincov", "Number", "", "70", "", "", "",false,false); parameters.push_back(pmincov);
  27                 CommandParameter pminsnp("minsnp", "Number", "", "10", "", "", "",false,false); parameters.push_back(pminsnp);
  28                 CommandParameter pminbs("minbs", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminbs);
  29                 CommandParameter psearch("search", "Multiple", "kmer-blast", "blast", "", "", "",false,false); parameters.push_back(psearch);
  30                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  31                 CommandParameter prealign("realign", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(prealign);
  32                 CommandParameter ptrim("trim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptrim);
  33                 CommandParameter psplit("split", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psplit);
  34                 CommandParameter pnumwanted("numwanted", "Number", "", "15", "", "", "",false,false); parameters.push_back(pnumwanted);
  35                 CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
  36                 CommandParameter pdivergence("divergence", "Number", "", "1.007", "", "", "",false,false); parameters.push_back(pdivergence);
  37                 CommandParameter pparents("parents", "Number", "", "3", "", "", "",false,false); parameters.push_back(pparents);
  38                 CommandParameter pincrement("increment", "Number", "", "5", "", "", "",false,false); parameters.push_back(pincrement);
  39                 CommandParameter pblastlocation("blastlocation", "String", "", "", "", "", "",false,false); parameters.push_back(pblastlocation);
  40                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  41                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  42                 CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
  43
  44                 vector<string> myArray;
  45                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  46                 return myArray;
  47         }
  48         catch(exception& e) {
  49                 m->errorOut(e, "ChimeraSlayerCommand", "setParameters");
  50                 exit(1);
  51         }
  52 }
  53 //**********************************************************************************************************************
  54 string ChimeraSlayerCommand::getHelpString(){
  55         try {
  56                 string helpString = "";
  57                 helpString += "The chimera.slayer command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
  58                 helpString += "This command was modeled after the chimeraSlayer written by the Broad Institute.\n";
  59                 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, blastlocation and realign.\n";
  60                 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";
  61                 helpString += "The name parameter allows you to provide a name file, if you are using reference=self. \n";
  62                 helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n";
  63                 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";
  64                 helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
  65 #ifdef USE_MPI
  66                 helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
  67 #endif
  68                 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";
  69                 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";
  70                 helpString += "The window parameter allows you to specify the window size for searching for chimeras, default=50. \n";
  71                 helpString += "The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n";
  72                 helpString += "The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n";
  73                 helpString += "The ksize parameter allows you to input kmersize, default is 7, used if search is kmer. \n";
  74                 helpString += "The match parameter allows you to reward matched bases in blast search, default is 5. \n";
  75                 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";
  76                 helpString += "The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n";
  77                 helpString += "The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n";
  78                 helpString += "The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=1000.\n";
  79                 helpString += "The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n";
  80                 helpString += "The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n";
  81                 helpString += "The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n";
  82                 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";
  83                 helpString += "The search parameter allows you to specify search method for finding the closest parent. Choices are blast, and kmer, default blast. \n";
  84                 helpString += "The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default true.  \n";
  85                 helpString += "The blastlocation parameter allows you to specify the location of your blast executable. By default mothur will look in ./blast/bin relative to mothur's executable.  \n";
  86                 helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
  87                 helpString += "The chimera.slayer command should be in the following format: \n";
  88                 helpString += "chimera.slayer(fasta=yourFastaFile, reference=yourTemplate, search=yourSearch) \n";
  89                 helpString += "Example: chimera.slayer(fasta=AD.align, reference=core_set_aligned.imputed.fasta, search=kmer) \n";
  90                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
  91                 return helpString;
  92         }
  93         catch(exception& e) {
  94                 m->errorOut(e, "ChimeraSlayerCommand", "getHelpString");
  95                 exit(1);
  96         }
  97 }
  98 //**********************************************************************************************************************
  99 ChimeraSlayerCommand::ChimeraSlayerCommand(){
 100         try {
 101                 abort = true; calledHelp = true;
 102                 setParameters();
 103                 vector<string> tempOutNames;
 104                 outputTypes["chimera"] = tempOutNames;
 105                 outputTypes["accnos"] = tempOutNames;
 106                 outputTypes["fasta"] = tempOutNames;
 107         }
 108         catch(exception& e) {
 109                 m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
 110                 exit(1);
 111         }
 112 }
 113 //***************************************************************************************************************
 114 ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
 115         try {
 116                 abort = false; calledHelp = false;
 117                 ReferenceDB* rdb = ReferenceDB::getInstance();
 118
 119                 //allow user to run help
 120                 if(option == "help") { help(); abort = true; calledHelp = true; }
 121                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 122
 123                 else {
 124                         vector<string> myArray = setParameters();
 125
 126                         OptionParser parser(option);
 127                         map<string,string> parameters = parser.getParameters();
 128
 129                         ValidParameters validParameter("chimera.slayer");
 130                         map<string,string>::iterator it;
 131
 132                         //check to make sure all parameters are valid for command
 133                         for (it = parameters.begin(); it != parameters.end(); it++) {
 134                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 135                         }
 136
 137                         vector<string> tempOutNames;
 138                         outputTypes["chimera"] = tempOutNames;
 139                         outputTypes["accnos"] = tempOutNames;
 140                         outputTypes["fasta"] = tempOutNames;
 141
 142                         //if the user changes the input directory command factory will send this info to us in the output parameter
 143                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 144                         if (inputDir == "not found"){   inputDir = "";          }
 145
 146                         //check for required parameters
 147                         fastafile = validParameter.validFile(parameters, "fasta", false);
 148                         if (fastafile == "not found") {
 149                                 //if there is a current fasta file, use it
 150                                 string filename = m->getFastaFile();
 151                                 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 152                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 153                         }else {
 154                                 m->splitAtDash(fastafile, fastaFileNames);
 155
 156                                 //go through files and make sure they are good, if not, then disregard them
 157                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 158
 159                                         bool ignore = false;
 160                                         if (fastaFileNames[i] == "current") {
 161                                                 fastaFileNames[i] = m->getFastaFile();
 162                                                 if (fastaFileNames[i] != "") {  m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 163                                                 else {
 164                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 165                                                         //erase from file list
 166                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 167                                                         i--;
 168                                                 }
 169                                         }
 170
 171                                         if (!ignore) {
 172
 173                                                 if (inputDir != "") {
 174                                                         string path = m->hasPath(fastaFileNames[i]);
 175                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 176                                                         if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 177                                                 }
 178
 179                                                 int ableToOpen;
 180                                                 ifstream in;
 181
 182                                                 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 183
 184                                                 //if you can't open it, try default location
 185                                                 if (ableToOpen == 1) {
 186                                                         if (m->getDefaultPath() != "") { //default path is set
 187                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 188                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 189                                                                 ifstream in2;
 190                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 191                                                                 in2.close();
 192                                                                 fastaFileNames[i] = tryPath;
 193                                                         }
 194                                                 }
 195
 196                                                 if (ableToOpen == 1) {
 197                                                         if (m->getOutputDir() != "") { //default path is set
 198                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 199                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 200                                                                 ifstream in2;
 201                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 202                                                                 in2.close();
 203                                                                 fastaFileNames[i] = tryPath;
 204                                                         }
 205                                                 }
 206
 207                                                 in.close();
 208
 209                                                 if (ableToOpen == 1) {
 210                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 211                                                         //erase from file list
 212                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 213                                                         i--;
 214                                                 }else {
 215                                                         m->setFastaFile(fastaFileNames[i]);
 216                                                 }
 217                                         }
 218                                 }
 219
 220                                 //make sure there is at least one valid file left
 221                                 if (fastaFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
 222                         }
 223
 224
 225                         //check for required parameters
 226                         bool hasName = true;
 227                         namefile = validParameter.validFile(parameters, "name", false);
 228                         if (namefile == "not found") { namefile = "";  hasName = false; }
 229                         else {
 230                                 m->splitAtDash(namefile, nameFileNames);
 231
 232                                 //go through files and make sure they are good, if not, then disregard them
 233                                 for (int i = 0; i < nameFileNames.size(); i++) {
 234
 235                                         bool ignore = false;
 236                                         if (nameFileNames[i] == "current") {
 237                                                 nameFileNames[i] = m->getNameFile();
 238                                                 if (nameFileNames[i] != "") {  m->mothurOut("Using " + nameFileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
 239                                                 else {
 240                                                         m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 241                                                         //erase from file list
 242                                                         nameFileNames.erase(nameFileNames.begin()+i);
 243                                                         i--;
 244                                                 }
 245                                         }
 246
 247                                         if (!ignore) {
 248
 249                                                 if (inputDir != "") {
 250                                                         string path = m->hasPath(nameFileNames[i]);
 251                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 252                                                         if (path == "") {       nameFileNames[i] = inputDir + nameFileNames[i];         }
 253                                                 }
 254
 255                                                 int ableToOpen;
 256                                                 ifstream in;
 257
 258                                                 ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror");
 259
 260                                                 //if you can't open it, try default location
 261                                                 if (ableToOpen == 1) {
 262                                                         if (m->getDefaultPath() != "") { //default path is set
 263                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]);
 264                                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 265                                                                 ifstream in2;
 266                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 267                                                                 in2.close();
 268                                                                 nameFileNames[i] = tryPath;
 269                                                         }
 270                                                 }
 271
 272                                                 if (ableToOpen == 1) {
 273                                                         if (m->getOutputDir() != "") { //default path is set
 274                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]);
 275                                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 276                                                                 ifstream in2;
 277                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 278                                                                 in2.close();
 279                                                                 nameFileNames[i] = tryPath;
 280                                                         }
 281                                                 }
 282
 283                                                 in.close();
 284
 285                                                 if (ableToOpen == 1) {
 286                                                         m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 287                                                         //erase from file list
 288                                                         nameFileNames.erase(nameFileNames.begin()+i);
 289                                                         i--;
 290                                                 }else {
 291                                                         m->setNameFile(nameFileNames[i]);
 292                                                 }
 293                                         }
 294                                 }
 295
 296                                 //make sure there is at least one valid file left
 297                                 if (nameFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid name files."); m->mothurOutEndLine(); abort = true; }
 298                         }
 299
 300                         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; }
 301
 302                         //if the user changes the output directory command factory will send this info to us in the output parameter
 303                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 304
 305                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 306                         m->setProcessors(temp);
 307                         convert(temp, processors);
 308
 309                         temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
 310                         save = m->isTrue(temp);
 311                         rdb->save = save;
 312                         if (save) { //clear out old references
 313                                 rdb->clearMemory();
 314                         }
 315
 316                         string path;
 317                         it = parameters.find("reference");
 318                         //user has given a template file
 319                         if(it != parameters.end()){
 320                                 if (it->second == "self") {
 321                                         templatefile = "self";
 322                                         if (save) {
 323                                                 m->mothurOut("[WARNING]: You can't save reference=self, ignoring save.");
 324                                                 m->mothurOutEndLine();
 325                                                 save = false;
 326                                         }
 327                                 }
 328                                 else {
 329                                         path = m->hasPath(it->second);
 330                                         //if the user has not given a path then, add inputdir. else leave path alone.
 331                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 332
 333                                         templatefile = validParameter.validFile(parameters, "reference", true);
 334                                         if (templatefile == "not open") { abort = true; }
 335                                         else if (templatefile == "not found") { //check for saved reference sequences
 336                                                 if (rdb->referenceSeqs.size() != 0) {
 337                                                         templatefile = "saved";
 338                                                 }else {
 339                                                         m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required.");
 340                                                         m->mothurOutEndLine();
 341                                                         abort = true;
 342                                                 }
 343                                         }else { if (save) {     rdb->setSavedReference(templatefile);   }       }
 344                                 }
 345                         }else if (hasName) {  templatefile = "self";
 346                                 if (save) {
 347                                         m->mothurOut("[WARNING]: You can't save reference=self, ignoring save.");
 348                                         m->mothurOutEndLine();
 349                                         save = false;
 350                                 }
 351                         }
 352                         else {
 353                                 if (rdb->referenceSeqs.size() != 0) {
 354                                         templatefile = "saved";
 355                                 }else {
 356                                         m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required.");
 357                                         m->mothurOutEndLine();
 358                                         templatefile = ""; abort = true;
 359                                 }
 360                         }
 361
 362
 363
 364                         temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
 365                         convert(temp, ksize);
 366
 367                         temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "50"; }
 368                         convert(temp, window);
 369
 370                         temp = validParameter.validFile(parameters, "match", false);                    if (temp == "not found") { temp = "5"; }
 371                         convert(temp, match);
 372
 373                         temp = validParameter.validFile(parameters, "mismatch", false);                 if (temp == "not found") { temp = "-4"; }
 374                         convert(temp, mismatch);
 375
 376                         temp = validParameter.validFile(parameters, "divergence", false);               if (temp == "not found") { temp = "1.007"; }
 377                         convert(temp, divR);
 378
 379                         temp = validParameter.validFile(parameters, "minsim", false);                   if (temp == "not found") { temp = "90"; }
 380                         convert(temp, minSimilarity);
 381
 382                         temp = validParameter.validFile(parameters, "mincov", false);                   if (temp == "not found") { temp = "70"; }
 383                         convert(temp, minCoverage);
 384
 385                         temp = validParameter.validFile(parameters, "minbs", false);                    if (temp == "not found") { temp = "90"; }
 386                         convert(temp, minBS);
 387
 388                         temp = validParameter.validFile(parameters, "minsnp", false);                   if (temp == "not found") { temp = "10"; }
 389                         convert(temp, minSNP);
 390
 391                         temp = validParameter.validFile(parameters, "parents", false);                  if (temp == "not found") { temp = "3"; }
 392                         convert(temp, parents);
 393
 394                         temp = validParameter.validFile(parameters, "realign", false);                  if (temp == "not found") { temp = "t"; }
 395                         realign = m->isTrue(temp);
 396
 397                         temp = validParameter.validFile(parameters, "trim", false);                             if (temp == "not found") { temp = "f"; }
 398                         trim = m->isTrue(temp);
 399
 400                         temp = validParameter.validFile(parameters, "split", false);                    if (temp == "not found") { temp = "f"; }
 401                         trimera = m->isTrue(temp);
 402
 403                         search = validParameter.validFile(parameters, "search", false);                 if (search == "not found") { search = "blast"; }
 404
 405                         temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
 406                         convert(temp, iters);
 407
 408                         temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "5"; }
 409                         convert(temp, increment);
 410
 411                         temp = validParameter.validFile(parameters, "numwanted", false);                if (temp == "not found") { temp = "15"; }
 412                         convert(temp, numwanted);
 413
 414                         blastlocation = validParameter.validFile(parameters, "blastlocation", false);
 415                         if (blastlocation == "not found") { blastlocation = ""; }
 416                         else {
 417                                 //add / to name if needed
 418                                 string lastChar = blastlocation.substr(blastlocation.length()-1);
 419 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 420                                 if (lastChar != "/") { blastlocation += "/"; }
 421 #else
 422                                 if (lastChar != "\\") { blastlocation += "\\"; }
 423 #endif
 424                                 blastlocation = m->getFullPathName(blastlocation);
 425                                 string formatdbCommand = "";
 426 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 427                                 formatdbCommand = blastlocation + "formatdb";
 428 #else
 429                                 formatdbCommand = blastlocation + "formatdb.exe";
 430 #endif
 431
 432                                 //test to make sure formatdb exists
 433                                 ifstream in;
 434                                 formatdbCommand = m->getFullPathName(formatdbCommand);
 435                                 int ableToOpen = m->openInputFile(formatdbCommand, in, "no error"); in.close();
 436                                 if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe to run chimera.slayer."); m->mothurOutEndLine(); abort = true; }
 437
 438                                 string blastCommand = "";
 439 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 440                                 blastCommand = blastlocation + "megablast";
 441 #else
 442                                 blastCommand = blastlocation + "megablast.exe";
 443 #endif
 444                                 //test to make sure formatdb exists
 445                                 ifstream in2;
 446                                 blastCommand = m->getFullPathName(blastCommand);
 447                                 ableToOpen = m->openInputFile(blastCommand, in2, "no error"); in2.close();
 448                                 if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " + blastCommand + " file does not exist. mothur requires blastall.exe to run chimera.slayer."); m->mothurOutEndLine(); abort = true; }
 449                         }
 450
 451                         if ((search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true;  }
 452
 453                         if (hasName && (templatefile != "self")) { m->mothurOut("You have provided a namefile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
 454                 }
 455         }
 456         catch(exception& e) {
 457                 m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
 458                 exit(1);
 459         }
 460 }
 461 //***************************************************************************************************************
 462
 463 int ChimeraSlayerCommand::execute(){
 464         try{
 465                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 466
 467                 for (int s = 0; s < fastaFileNames.size(); s++) {
 468
 469                         m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 470
 471                         int start = time(NULL);
 472
 473                         if (templatefile != "self") { //you want to run slayer with a refernce template
 474                                 chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation);
 475                         }else {
 476                                 if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
 477                                 string nameFile = "";
 478                                 if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
 479                                         nameFile = nameFileNames[s];
 480                                 }else {
 481                                         m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine();
 482
 483                                         //use unique.seqs to create new name and fastafile
 484                                         string inputString = "fasta=" + fastaFileNames[s];
 485                                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 486                                         m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
 487
 488                                         Command* uniqueCommand = new DeconvoluteCommand(inputString);
 489                                         uniqueCommand->execute();
 490
 491                                         map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 492
 493                                         delete uniqueCommand;
 494
 495                                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 496
 497                                         nameFile = filenames["name"][0];
 498                                         fastaFileNames[s] = filenames["fasta"][0];
 499                                 }
 500
 501                                 //sort fastafile by abundance, returns new sorted fastafile name
 502                                 m->mothurOut("Sorting fastafile according to abundance..."); cout.flush();
 503                                 map<string, int> priority = sortFastaFile(fastaFileNames[s], nameFile);
 504                                 m->mothurOut("Done."); m->mothurOutEndLine();
 505
 506                                 if (m->control_pressed) {  for (int j = 0; j < outputNames.size(); j++) {       m->mothurRemove(outputNames[j]);        }  return 0;    }
 507
 508                                 chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation);
 509                         }
 510
 511                         if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it
 512                         string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimera";
 513                         string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "slayer.accnos";
 514                         string trimFastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "slayer.fasta";
 515
 516                         if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) {        m->mothurRemove(outputNames[j]);        }  return 0;    }
 517
 518                         if (chimera->getUnaligned()) {
 519                                 m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine();
 520                                 delete chimera;
 521                                 return 0;
 522                         }
 523                         templateSeqsLength = chimera->getLength();
 524
 525                 #ifdef USE_MPI
 526                         int pid, numSeqsPerProcessor;
 527                                 int tag = 2001;
 528                                 vector<unsigned long int> MPIPos;
 529
 530                                 MPI_Status status;
 531                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 532                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 533
 534                                 MPI_File inMPI;
 535                                 MPI_File outMPI;
 536                                 MPI_File outMPIAccnos;
 537                                 MPI_File outMPIFasta;
 538
 539                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 540                                 int inMode=MPI_MODE_RDONLY;
 541
 542                                 char outFilename[1024];
 543                                 strcpy(outFilename, outputFileName.c_str());
 544
 545                                 char outAccnosFilename[1024];
 546                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 547
 548                                 char outFastaFilename[1024];
 549                                 strcpy(outFastaFilename, trimFastaFileName.c_str());
 550
 551                                 char inFileName[1024];
 552                                 strcpy(inFileName, fastaFileNames[s].c_str());
 553
 554                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 555                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 556                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 557                                 if (trim) { MPI_File_open(MPI_COMM_WORLD, outFastaFilename, outMode, MPI_INFO_NULL, &outMPIFasta); }
 558
 559                         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++) {   m->mothurRemove(outputNames[j]);        }   delete chimera; return 0;  }
 560
 561                                 if (pid == 0) { //you are the root process
 562                                         m->mothurOutEndLine();
 563                                         m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
 564                                         m->mothurOutEndLine();
 565
 566                                         string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
 567
 568                                         //print header
 569                                         int length = outTemp.length();
 570                                         char* buf2 = new char[length];
 571                                         memcpy(buf2, outTemp.c_str(), length);
 572
 573                                         MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
 574                                         delete buf2;
 575
 576                                         MPIPos = m->setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs
 577
 578                                         if (templatefile != "self") { //if template=self we can only use 1 processor
 579                                                 //send file positions to all processes
 580                                                 for(int i = 1; i < processors; i++) {
 581                                                         MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 582                                                         MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 583                                                 }
 584                                         }
 585                                         //figure out how many sequences you have to align
 586                                         numSeqsPerProcessor = numSeqs / processors;
 587                                         int startIndex =  pid * numSeqsPerProcessor;
 588                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 589
 590                                         if (templatefile == "self") { //if template=self we can only use 1 processor
 591                                                 startIndex = 0;
 592                                                 numSeqsPerProcessor = numSeqs;
 593                                         }
 594
 595                                         //do your part
 596                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos);
 597
 598                                         int numNoParents = chimera->getNumNoParents();
 599                                         int temp;
 600                                         for(int i = 1; i < processors; i++) {
 601                                                 MPI_Recv(&temp, 1, MPI_INT, 1, tag, MPI_COMM_WORLD, &status);
 602                                                 numNoParents += temp;
 603                                         }
 604
 605
 606                                         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(); }
 607
 608                                         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++) {   m->mothurRemove(outputNames[j]);        }  m->mothurRemove(outputFileName);  m->mothurRemove(accnosFileName);  delete chimera; return 0;  }
 609
 610                                 }else{ //you are a child process
 611                                         if (templatefile != "self") { //if template=self we can only use 1 processor
 612                                                 MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 613                                                 MPIPos.resize(numSeqs+1);
 614                                                 MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 615
 616                                                 //figure out how many sequences you have to align
 617                                                 numSeqsPerProcessor = numSeqs / processors;
 618                                                 int startIndex =  pid * numSeqsPerProcessor;
 619                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 620
 621                                                 //do your part
 622                                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos);
 623
 624                                                 int numNoParents = chimera->getNumNoParents();
 625                                                 MPI_Send(&numNoParents, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 626
 627                                                 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++) {   m->mothurRemove(outputNames[j]);        }  delete chimera; return 0;  }
 628
 629                                         }
 630                                 }
 631
 632                                 //close files
 633                                 MPI_File_close(&inMPI);
 634                                 MPI_File_close(&outMPI);
 635                                 MPI_File_close(&outMPIAccnos);
 636                                 if (trim) { MPI_File_close(&outMPIFasta); }
 637                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 638
 639                 #else
 640                         ofstream outHeader;
 641                         string tempHeader = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimeras.tempHeader";
 642                         m->openOutputFile(tempHeader, outHeader);
 643
 644                         chimera->printHeader(outHeader);
 645                         outHeader.close();
 646
 647                         vector<unsigned long int> positions = m->divideFile(fastaFileNames[s], processors);
 648
 649                         for (int i = 0; i < (positions.size()-1); i++) {
 650                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 651                         }
 652
 653                         //break up file
 654                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 655                                 if(processors == 1){
 656                                         numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
 657
 658                                         int numNoParents = chimera->getNumNoParents();
 659                                         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(); }
 660
 661                                         if (m->control_pressed) { outputTypes.clear(); if (trim) { m->mothurRemove(trimFastaFileName); } m->mothurRemove(outputFileName); m->mothurRemove(tempHeader); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) {  m->mothurRemove(outputNames[j]);        } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear(); delete chimera; return 0; }
 662
 663                                 }else{
 664                                         processIDS.resize(0);
 665
 666                                         numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
 667
 668                                         rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 669                                         rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
 670                                         if (trim) {  rename((trimFastaFileName + toString(processIDS[0]) + ".temp").c_str(), trimFastaFileName.c_str()); }
 671
 672                                         //append output files
 673                                         for(int i=1;i<processors;i++){
 674                                                 m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
 675                                                 m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp"));
 676                                         }
 677
 678                                         //append output files
 679                                         for(int i=1;i<processors;i++){
 680                                                 m->appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
 681                                                 m->mothurRemove((accnosFileName + toString(processIDS[i]) + ".temp"));
 682                                         }
 683
 684                                         if (trim) {
 685                                                 for(int i=1;i<processors;i++){
 686                                                         m->appendFiles((trimFastaFileName + toString(processIDS[i]) + ".temp"), trimFastaFileName);
 687                                                         m->mothurRemove((trimFastaFileName + toString(processIDS[i]) + ".temp"));
 688                                                 }
 689                                         }
 690
 691                                         if (m->control_pressed) { outputTypes.clear(); if (trim) { m->mothurRemove(trimFastaFileName); } m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) {       m->mothurRemove(outputNames[j]);        } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear(); delete chimera; return 0; }
 692                                 }
 693
 694                         #else
 695                                 numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
 696
 697                                 int numNoParents = chimera->getNumNoParents();
 698                                 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(); }
 699
 700
 701                                 if (m->control_pressed) { outputTypes.clear(); if (trim) { m->mothurRemove(trimFastaFileName); } m->mothurRemove(outputFileName); m->mothurRemove(tempHeader); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) {  m->mothurRemove(outputNames[j]);        } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear(); delete chimera; return 0; }
 702
 703                         #endif
 704
 705                         m->appendFiles(outputFileName, tempHeader);
 706
 707                         m->mothurRemove(outputFileName);
 708                         rename(tempHeader.c_str(), outputFileName.c_str());
 709
 710                 #endif
 711                         delete chimera;
 712
 713
 714                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 715
 716                         outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
 717                         outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
 718                         if (trim) {  outputNames.push_back(trimFastaFileName); outputTypes["fasta"].push_back(trimFastaFileName); }
 719
 720                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 721                 }
 722
 723                 //set accnos file as new current accnosfile
 724                 string current = "";
 725                 itTypes = outputTypes.find("accnos");
 726                 if (itTypes != outputTypes.end()) {
 727                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 728                 }
 729
 730                 if (trim) {
 731                         itTypes = outputTypes.find("fasta");
 732                         if (itTypes != outputTypes.end()) {
 733                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 734                         }
 735                 }
 736
 737                 m->mothurOutEndLine();
 738                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 739                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 740                 m->mothurOutEndLine();
 741
 742                 return 0;
 743
 744         }
 745         catch(exception& e) {
 746                 m->errorOut(e, "ChimeraSlayerCommand", "execute");
 747                 exit(1);
 748         }
 749 }
 750 //**********************************************************************************************************************
 751
 752 int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string filename, string accnos, string fasta){
 753         try {
 754                 ofstream out;
 755                 m->openOutputFile(outputFName, out);
 756
 757                 ofstream out2;
 758                 m->openOutputFile(accnos, out2);
 759
 760                 ofstream out3;
 761                 if (trim) {  m->openOutputFile(fasta, out3); }
 762
 763                 ifstream inFASTA;
 764                 m->openInputFile(filename, inFASTA);
 765
 766                 inFASTA.seekg(filePos->start);
 767
 768                 bool done = false;
 769                 int count = 0;
 770
 771                 while (!done) {
 772
 773                         if (m->control_pressed) {       out.close(); out2.close(); if (trim) { out3.close(); } inFASTA.close(); return 1;       }
 774
 775                         Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
 776                         string candidateAligned = candidateSeq->getAligned();
 777
 778                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 779                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 780                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 781                                 }else{
 782                                         //find chimeras
 783                                         chimera->getChimeras(candidateSeq);
 784
 785                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 786
 787                                         //if you are not chimeric, then check each half
 788                                         data_results wholeResults = chimera->getResults();
 789
 790                                         //determine if we need to split
 791                                         bool isChimeric = false;
 792
 793                                         if (wholeResults.flag == "yes") {
 794                                                 string chimeraFlag = "no";
 795                                                 if(  (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
 796                                                    ||
 797                                                    (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
 798
 799
 800                                                 if (chimeraFlag == "yes") {
 801                                                         if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
 802                                                 }
 803                                         }
 804
 805                                         if ((!isChimeric) && trimera) {
 806
 807                                                 //split sequence in half by bases
 808                                                 string leftQuery, rightQuery;
 809                                                 Sequence tempSeq(candidateSeq->getName(), candidateAligned);
 810                                                 divideInHalf(tempSeq, leftQuery, rightQuery);
 811
 812                                                 //run chimeraSlayer on each piece
 813                                                 Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
 814                                                 Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
 815
 816                                                 //find chimeras
 817                                                 chimera->getChimeras(left);
 818                                                 data_results leftResults = chimera->getResults();
 819
 820                                                 chimera->getChimeras(right);
 821                                                 data_results rightResults = chimera->getResults();
 822
 823                                                 //if either piece is chimeric then report
 824                                                 Sequence trimmed = chimera->print(out, out2, leftResults, rightResults);
 825                                                 if (trim) { trimmed.printSequence(out3);  }
 826
 827                                                 delete left; delete right;
 828
 829                                         }else { //already chimeric
 830                                                 //print results
 831                                                 Sequence trimmed = chimera->print(out, out2);
 832                                                 if (trim) { trimmed.printSequence(out3);  }
 833                                         }
 834
 835
 836                                 }
 837                                 count++;
 838                         }
 839
 840                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 841                                 unsigned long int pos = inFASTA.tellg();
 842                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 843                         #else
 844                                 if (inFASTA.eof()) { break; }
 845                         #endif
 846
 847                         delete candidateSeq;
 848                         //report progress
 849                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 850                 }
 851                 //report progress
 852                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 853
 854                 out.close();
 855                 out2.close();
 856                 if (trim) { out3.close(); }
 857                 inFASTA.close();
 858
 859                 return count;
 860         }
 861         catch(exception& e) {
 862                 m->errorOut(e, "ChimeraSlayerCommand", "driver");
 863                 exit(1);
 864         }
 865 }
 866 //**********************************************************************************************************************
 867 #ifdef USE_MPI
 868 int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, MPI_File& outFastaMPI, vector<unsigned long int>& MPIPos){
 869         try {
 870                 MPI_Status status;
 871                 int pid;
 872                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 873
 874                 for(int i=0;i<num;i++){
 875
 876                         if (m->control_pressed) {       return 1;       }
 877
 878                         //read next sequence
 879                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 880
 881                         char* buf4 = new char[length];
 882                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 883
 884                         string tempBuf = buf4;
 885                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 886                         istringstream iss (tempBuf,istringstream::in);
 887
 888                         delete buf4;
 889
 890                         Sequence* candidateSeq = new Sequence(iss);  m->gobble(iss);
 891                         string candidateAligned = candidateSeq->getAligned();
 892
 893                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 894
 895                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 896                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 897                                 }else{
 898
 899                                         //find chimeras
 900                                         chimera->getChimeras(candidateSeq);
 901
 902                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 903
 904                                         //if you are not chimeric, then check each half
 905                                         data_results wholeResults = chimera->getResults();
 906
 907                                         //determine if we need to split
 908                                         bool isChimeric = false;
 909
 910                                         if (wholeResults.flag == "yes") {
 911                                                 string chimeraFlag = "no";
 912                                                 if(  (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
 913                                                    ||
 914                                                    (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
 915
 916
 917                                                 if (chimeraFlag == "yes") {
 918                                                         if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
 919                                                 }
 920                                         }
 921
 922                                         if ((!isChimeric) && trimera) {
 923                                                 //split sequence in half by bases
 924                                                 string leftQuery, rightQuery;
 925                                                 Sequence tempSeq(candidateSeq->getName(), candidateAligned);
 926                                                 divideInHalf(tempSeq, leftQuery, rightQuery);
 927
 928                                                 //run chimeraSlayer on each piece
 929                                                 Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
 930                                                 Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
 931
 932                                                 //find chimeras
 933                                                 chimera->getChimeras(left);
 934                                                 data_results leftResults = chimera->getResults();
 935
 936                                                 chimera->getChimeras(right);
 937                                                 data_results rightResults = chimera->getResults();
 938
 939                                                 //if either piece is chimeric then report
 940                                                 Sequence trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults);
 941                                                 if (trim) {
 942                                                         string outputString = ">" + trimmed.getName() + "\n" + trimmed.getAligned() + "\n";
 943
 944                                                         //write to accnos file
 945                                                         int length = outputString.length();
 946                                                         char* buf2 = new char[length];
 947                                                         memcpy(buf2, outputString.c_str(), length);
 948
 949                                                         MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
 950                                                         delete buf2;
 951                                                 }
 952
 953                                                 delete left; delete right;
 954
 955                                         }else {
 956                                                 //print results
 957                                                 Sequence trimmed = chimera->print(outMPI, outAccMPI);
 958
 959                                                 if (trim) {
 960                                                         string outputString = ">" + trimmed.getName() + "\n" + trimmed.getAligned() + "\n";
 961
 962                                                         //write to accnos file
 963                                                         int length = outputString.length();
 964                                                         char* buf2 = new char[length];
 965                                                         memcpy(buf2, outputString.c_str(), length);
 966
 967                                                         MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
 968                                                         delete buf2;
 969                                                 }
 970                                         }
 971
 972                                 }
 973                         }
 974                         delete candidateSeq;
 975
 976                         //report progress
 977                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 978                 }
 979                 //report progress
 980                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 981
 982
 983                 return 0;
 984         }
 985         catch(exception& e) {
 986                 m->errorOut(e, "ChimeraSlayerCommand", "driverMPI");
 987                 exit(1);
 988         }
 989 }
 990 #endif
 991
 992 /**************************************************************************************************/
 993
 994 int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos, string fasta) {
 995         try {
 996 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 997                 int process = 0;
 998                 int num = 0;
 999
1000                 //loop through and create all the processes you want
1001                 while (process != processors) {
1002                         int pid = fork();
1003
1004                         if (pid > 0) {
1005                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1006                                 process++;
1007                         }else if (pid == 0){
1008                                 num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp");
1009
1010                                 //pass numSeqs to parent
1011                                 ofstream out;
1012                                 string tempFile = outputFileName + toString(getpid()) + ".num.temp";
1013                                 m->openOutputFile(tempFile, out);
1014                                 out << num << '\t' << chimera->getNumNoParents() << endl;
1015                                 out.close();
1016                                 exit(0);
1017                         }else {
1018                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1019                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1020                                 exit(0);
1021                         }
1022                 }
1023
1024                 //force parent to wait until all the processes are done
1025                 for (int i=0;i<processors;i++) {
1026                         int temp = processIDS[i];
1027                         wait(&temp);
1028                 }
1029
1030                 int numNoParents = 0;
1031                 for (int i = 0; i < processIDS.size(); i++) {
1032                         ifstream in;
1033                         string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
1034                         m->openInputFile(tempFile, in);
1035                         if (!in.eof()) { int tempNum = 0; int tempNumParents = 0; in >> tempNum >> tempNumParents; num += tempNum; numNoParents += tempNumParents; }
1036                         in.close(); m->mothurRemove(tempFile);
1037                 }
1038
1039                 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(); }
1040
1041                 return num;
1042 #endif
1043         }
1044         catch(exception& e) {
1045                 m->errorOut(e, "ChimeraSlayerCommand", "createProcesses");
1046                 exit(1);
1047         }
1048 }
1049
1050 /**************************************************************************************************/
1051
1052 int ChimeraSlayerCommand::divideInHalf(Sequence querySeq, string& leftQuery, string& rightQuery) {
1053         try {
1054
1055                 string queryUnAligned = querySeq.getUnaligned();
1056                 int numBases = int(queryUnAligned.length() * 0.5);
1057
1058                 string queryAligned = querySeq.getAligned();
1059                 leftQuery = querySeq.getAligned();
1060                 rightQuery = querySeq.getAligned();
1061
1062                 int baseCount = 0;
1063                 int leftSpot = 0;
1064                 for (int i = 0; i < queryAligned.length(); i++) {
1065                         //if you are a base
1066                         if (isalpha(queryAligned[i])) {
1067                                 baseCount++;
1068                         }
1069
1070                         //if you have half
1071                         if (baseCount >= numBases) {  leftSpot = i; break; } //first half
1072                 }
1073
1074                 //blank out right side
1075                 for (int i = leftSpot; i < leftQuery.length(); i++) { leftQuery[i] = '.'; }
1076
1077                 //blank out left side
1078                 for (int i = 0; i < leftSpot; i++) { rightQuery[i] = '.'; }
1079
1080                 return 0;
1081
1082         }
1083         catch(exception& e) {
1084                 m->errorOut(e, "ChimeraSlayerCommand", "divideInHalf");
1085                 exit(1);
1086         }
1087 }
1088 /**************************************************************************************************/
1089 map<string, int> ChimeraSlayerCommand::sortFastaFile(string fastaFile, string nameFile) {
1090         try {
1091                 map<string, int> nameAbund;
1092
1093                 //read through fastafile and store info
1094                 map<string, string> seqs;
1095                 ifstream in;
1096                 m->openInputFile(fastaFile, in);
1097
1098                 while (!in.eof()) {
1099
1100                         if (m->control_pressed) { in.close(); return nameAbund; }
1101
1102                         Sequence seq(in); m->gobble(in);
1103                         seqs[seq.getName()] = seq.getAligned();
1104                 }
1105
1106                 in.close();
1107
1108                 //read namefile
1109                 vector<seqPriorityNode> nameMapCount;
1110                 int error = m->readNames(nameFile, nameMapCount, seqs);
1111
1112                 if (m->control_pressed) { return nameAbund; }
1113
1114                 if (error == 1) { m->control_pressed = true; return nameAbund; }
1115                 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; }
1116
1117                 sort(nameMapCount.begin(), nameMapCount.end(), compareSeqPriorityNodes);
1118
1119                 string newFasta = fastaFile + ".temp";
1120                 ofstream out;
1121                 m->openOutputFile(newFasta, out);
1122
1123                 //print new file in order of
1124                 for (int i = 0; i < nameMapCount.size(); i++) {
1125                         out << ">" << nameMapCount[i].name << endl << nameMapCount[i].seq << endl;
1126                         nameAbund[nameMapCount[i].name] = nameMapCount[i].numIdentical;
1127                 }
1128                 out.close();
1129
1130                 rename(newFasta.c_str(), fastaFile.c_str());
1131
1132                 return nameAbund;
1133
1134         }
1135         catch(exception& e) {
1136                 m->errorOut(e, "ChimeraSlayerCommand", "sortFastaFile");
1137                 exit(1);
1138         }
1139 }
1140
1141 /**************************************************************************************************/
1142