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