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 "deconvolutecommand.h"
  12 #include "referencedb.h"
  13 #include "sequenceparser.h"
  14 #include "counttable.h"
  15
  16 //**********************************************************************************************************************
  17 vector<string> ChimeraSlayerCommand::setParameters(){
  18         try {
  19                 CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
  20                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera-accnos",false,true,true); parameters.push_back(pfasta);
  21                 CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
  22          CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
  23                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
  24                 CommandParameter pwindow("window", "Number", "", "50", "", "", "","",false,false); parameters.push_back(pwindow);
  25                 CommandParameter pksize("ksize", "Number", "", "7", "", "", "","",false,false); parameters.push_back(pksize);
  26                 CommandParameter pmatch("match", "Number", "", "5.0", "", "", "","",false,false); parameters.push_back(pmatch);
  27                 CommandParameter pmismatch("mismatch", "Number", "", "-4.0", "", "", "","",false,false); parameters.push_back(pmismatch);
  28                 CommandParameter pminsim("minsim", "Number", "", "90", "", "", "","",false,false); parameters.push_back(pminsim);
  29                 CommandParameter pmincov("mincov", "Number", "", "70", "", "", "","",false,false); parameters.push_back(pmincov);
  30                 CommandParameter pminsnp("minsnp", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pminsnp);
  31                 CommandParameter pminbs("minbs", "Number", "", "90", "", "", "","",false,false); parameters.push_back(pminbs);
  32                 CommandParameter psearch("search", "Multiple", "kmer-blast", "blast", "", "", "","",false,false); parameters.push_back(psearch);
  33                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
  34
  35                 CommandParameter prealign("realign", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(prealign);
  36                 CommandParameter ptrim("trim", "Boolean", "", "F", "", "", "","fasta",false,false); parameters.push_back(ptrim);
  37                 CommandParameter psplit("split", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psplit);
  38                 CommandParameter pnumwanted("numwanted", "Number", "", "15", "", "", "","",false,false); parameters.push_back(pnumwanted);
  39                 CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
  40                 CommandParameter pdivergence("divergence", "Number", "", "1.007", "", "", "","",false,false); parameters.push_back(pdivergence);
  41         CommandParameter pdups("dereplicate", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pdups);
  42                 CommandParameter pparents("parents", "Number", "", "3", "", "", "","",false,false); parameters.push_back(pparents);
  43                 CommandParameter pincrement("increment", "Number", "", "5", "", "", "","",false,false); parameters.push_back(pincrement);
  44                 CommandParameter pblastlocation("blastlocation", "String", "", "", "", "", "","",false,false); parameters.push_back(pblastlocation);
  45                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  46                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  47                 CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
  48
  49                 vector<string> myArray;
  50                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  51                 return myArray;
  52         }
  53         catch(exception& e) {
  54                 m->errorOut(e, "ChimeraSlayerCommand", "setParameters");
  55                 exit(1);
  56         }
  57 }
  58 //**********************************************************************************************************************
  59 string ChimeraSlayerCommand::getHelpString(){
  60         try {
  61                 string helpString = "";
  62                 helpString += "The chimera.slayer command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
  63                 helpString += "This command was modeled after the chimeraSlayer written by the Broad Institute.\n";
  64                 helpString += "The chimera.slayer command parameters are fasta, name, group, template, processors, dereplicate, trim, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment, numwanted, blastlocation and realign.\n";
  65                 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";
  66                 helpString += "The name parameter allows you to provide a name file, if you are using reference=self. \n";
  67                 helpString += "The group parameter allows you to provide a group file. The group file can be used with a namesfile and reference=self. When checking sequences, only sequences from the same group as the query sequence will be used as the reference. \n";
  68         helpString += "The count parameter allows you to provide a count file. The count file reference=self. If your count file contains group information, when checking sequences, only sequences from the same group as the query sequence will be used as the reference. When you use a count file with group info and dereplicate=T, mothur will create a *.pick.count_table file containing seqeunces after chimeras are removed. \n";
  69                 helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n";
  70                 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";
  71                 helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
  72 #ifdef USE_MPI
  73                 helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
  74 #endif
  75         helpString += "If the dereplicate parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric, default=f.\n";
  76                 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";
  77                 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";
  78                 helpString += "The window parameter allows you to specify the window size for searching for chimeras, default=50. \n";
  79                 helpString += "The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n";
  80                 helpString += "The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n";
  81                 helpString += "The ksize parameter allows you to input kmersize, default is 7, used if search is kmer. \n";
  82                 helpString += "The match parameter allows you to reward matched bases in blast search, default is 5. \n";
  83                 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";
  84                 helpString += "The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n";
  85                 helpString += "The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n";
  86                 helpString += "The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=1000.\n";
  87                 helpString += "The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n";
  88                 helpString += "The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n";
  89                 helpString += "The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n";
  90                 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";
  91                 helpString += "The search parameter allows you to specify search method for finding the closest parent. Choices are blast, and kmer, default blast. \n";
  92                 helpString += "The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default true.  \n";
  93                 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";
  94                 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.";
  95                 helpString += "The chimera.slayer command should be in the following format: \n";
  96                 helpString += "chimera.slayer(fasta=yourFastaFile, reference=yourTemplate, search=yourSearch) \n";
  97                 helpString += "Example: chimera.slayer(fasta=AD.align, reference=core_set_aligned.imputed.fasta, search=kmer) \n";
  98                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
  99                 return helpString;
 100         }
 101         catch(exception& e) {
 102                 m->errorOut(e, "ChimeraSlayerCommand", "getHelpString");
 103                 exit(1);
 104         }
 105 }
 106 //**********************************************************************************************************************
 107 string ChimeraSlayerCommand::getOutputPattern(string type) {
 108     try {
 109         string pattern = "";
 110
 111         if (type == "chimera") {  pattern = "[filename],slayer.chimeras"; }
 112         else if (type == "accnos") {  pattern = "[filename],slayer.accnos"; }
 113         else if (type == "fasta") {  pattern = "[filename],slayer.fasta"; }
 114         else if (type == "count") {  pattern = "[filename],slayer.pick.count_table"; }
 115         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
 116
 117         return pattern;
 118     }
 119     catch(exception& e) {
 120         m->errorOut(e, "ChimeraSlayerCommand", "getOutputPattern");
 121         exit(1);
 122     }
 123 }
 124 //**********************************************************************************************************************
 125 ChimeraSlayerCommand::ChimeraSlayerCommand(){
 126         try {
 127                 abort = true; calledHelp = true;
 128                 setParameters();
 129                 vector<string> tempOutNames;
 130                 outputTypes["chimera"] = tempOutNames;
 131                 outputTypes["accnos"] = tempOutNames;
 132                 outputTypes["fasta"] = tempOutNames;
 133         outputTypes["count"] = tempOutNames;
 134         }
 135         catch(exception& e) {
 136                 m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
 137                 exit(1);
 138         }
 139 }
 140 //***************************************************************************************************************
 141 ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
 142         try {
 143                 abort = false; calledHelp = false;
 144                 ReferenceDB* rdb = ReferenceDB::getInstance();
 145         hasCount = false;
 146         hasName = false;
 147
 148                 //allow user to run help
 149                 if(option == "help") { help(); abort = true; calledHelp = true; }
 150                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 151
 152                 else {
 153                         vector<string> myArray = setParameters();
 154
 155                         OptionParser parser(option);
 156                         map<string,string> parameters = parser.getParameters();
 157
 158                         ValidParameters validParameter("chimera.slayer");
 159                         map<string,string>::iterator it;
 160
 161                         //check to make sure all parameters are valid for command
 162                         for (it = parameters.begin(); it != parameters.end(); it++) {
 163                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 164                         }
 165
 166                         vector<string> tempOutNames;
 167                         outputTypes["chimera"] = tempOutNames;
 168                         outputTypes["accnos"] = tempOutNames;
 169                         outputTypes["fasta"] = tempOutNames;
 170             outputTypes["count"] = tempOutNames;
 171
 172                         //if the user changes the input directory command factory will send this info to us in the output parameter
 173                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 174                         if (inputDir == "not found"){   inputDir = "";          }
 175
 176                         //check for required parameters
 177                         fastafile = validParameter.validFile(parameters, "fasta", false);
 178                         if (fastafile == "not found") {
 179                                 //if there is a current fasta file, use it
 180                                 string filename = m->getFastaFile();
 181                                 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 182                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 183                         }else {
 184                                 m->splitAtDash(fastafile, fastaFileNames);
 185
 186                                 //go through files and make sure they are good, if not, then disregard them
 187                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 188
 189                                         bool ignore = false;
 190                                         if (fastaFileNames[i] == "current") {
 191                                                 fastaFileNames[i] = m->getFastaFile();
 192                                                 if (fastaFileNames[i] != "") {  m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 193                                                 else {
 194                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 195                                                         //erase from file list
 196                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 197                                                         i--;
 198                                                 }
 199                                         }
 200
 201                                         if (!ignore) {
 202
 203                                                 if (inputDir != "") {
 204                                                         string path = m->hasPath(fastaFileNames[i]);
 205                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 206                                                         if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 207                                                 }
 208
 209                                                 int ableToOpen;
 210                                                 ifstream in;
 211
 212                                                 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 213
 214                                                 //if you can't open it, try default location
 215                                                 if (ableToOpen == 1) {
 216                                                         if (m->getDefaultPath() != "") { //default path is set
 217                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 218                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 219                                                                 ifstream in2;
 220                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 221                                                                 in2.close();
 222                                                                 fastaFileNames[i] = tryPath;
 223                                                         }
 224                                                 }
 225
 226                                                 if (ableToOpen == 1) {
 227                                                         if (m->getOutputDir() != "") { //default path is set
 228                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 229                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 230                                                                 ifstream in2;
 231                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 232                                                                 in2.close();
 233                                                                 fastaFileNames[i] = tryPath;
 234                                                         }
 235                                                 }
 236
 237                                                 in.close();
 238
 239                                                 if (ableToOpen == 1) {
 240                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 241                                                         //erase from file list
 242                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 243                                                         i--;
 244                                                 }else {
 245                                                         m->setFastaFile(fastaFileNames[i]);
 246                                                 }
 247                                         }
 248                                 }
 249
 250                                 //make sure there is at least one valid file left
 251                                 if (fastaFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
 252                         }
 253
 254
 255                         //check for required parameters
 256                         namefile = validParameter.validFile(parameters, "name", false);
 257                         if (namefile == "not found") { namefile = "";   }
 258                         else {
 259                                 m->splitAtDash(namefile, nameFileNames);
 260
 261                                 //go through files and make sure they are good, if not, then disregard them
 262                                 for (int i = 0; i < nameFileNames.size(); i++) {
 263
 264                                         bool ignore = false;
 265                                         if (nameFileNames[i] == "current") {
 266                                                 nameFileNames[i] = m->getNameFile();
 267                                                 if (nameFileNames[i] != "") {  m->mothurOut("Using " + nameFileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
 268                                                 else {
 269                                                         m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 270                                                         //erase from file list
 271                                                         nameFileNames.erase(nameFileNames.begin()+i);
 272                                                         i--;
 273                                                 }
 274                                         }
 275
 276                                         if (!ignore) {
 277
 278                                                 if (inputDir != "") {
 279                                                         string path = m->hasPath(nameFileNames[i]);
 280                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 281                                                         if (path == "") {       nameFileNames[i] = inputDir + nameFileNames[i];         }
 282                                                 }
 283
 284                                                 int ableToOpen;
 285                                                 ifstream in;
 286
 287                                                 ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror");
 288
 289                                                 //if you can't open it, try default location
 290                                                 if (ableToOpen == 1) {
 291                                                         if (m->getDefaultPath() != "") { //default path is set
 292                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]);
 293                                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 294                                                                 ifstream in2;
 295                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 296                                                                 in2.close();
 297                                                                 nameFileNames[i] = tryPath;
 298                                                         }
 299                                                 }
 300
 301                                                 if (ableToOpen == 1) {
 302                                                         if (m->getOutputDir() != "") { //default path is set
 303                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]);
 304                                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 305                                                                 ifstream in2;
 306                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 307                                                                 in2.close();
 308                                                                 nameFileNames[i] = tryPath;
 309                                                         }
 310                                                 }
 311
 312                                                 in.close();
 313
 314                                                 if (ableToOpen == 1) {
 315                                                         m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 316                                                         //erase from file list
 317                                                         nameFileNames.erase(nameFileNames.begin()+i);
 318                                                         i--;
 319                                                 }else {
 320                                                         m->setNameFile(nameFileNames[i]);
 321                                                 }
 322                                         }
 323                                 }
 324                         }
 325
 326             if (nameFileNames.size() != 0) { hasName = true; }
 327
 328             //check for required parameters
 329             vector<string> countfileNames;
 330                         countfile = validParameter.validFile(parameters, "count", false);
 331                         if (countfile == "not found") {
 332                 countfile = "";
 333                         }else {
 334                                 m->splitAtDash(countfile, countfileNames);
 335
 336                                 //go through files and make sure they are good, if not, then disregard them
 337                                 for (int i = 0; i < countfileNames.size(); i++) {
 338
 339                                         bool ignore = false;
 340                                         if (countfileNames[i] == "current") {
 341                                                 countfileNames[i] = m->getCountTableFile();
 342                                                 if (nameFileNames[i] != "") {  m->mothurOut("Using " + countfileNames[i] + " as input file for the count parameter where you had given current."); m->mothurOutEndLine(); }
 343                                                 else {
 344                                                         m->mothurOut("You have no current count file, ignoring current."); m->mothurOutEndLine(); ignore=true;
 345                                                         //erase from file list
 346                                                         countfileNames.erase(countfileNames.begin()+i);
 347                                                         i--;
 348                                                 }
 349                                         }
 350
 351                                         if (!ignore) {
 352
 353                                                 if (inputDir != "") {
 354                                                         string path = m->hasPath(countfileNames[i]);
 355                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 356                                                         if (path == "") {       countfileNames[i] = inputDir + countfileNames[i];               }
 357                                                 }
 358
 359                                                 int ableToOpen;
 360                                                 ifstream in;
 361
 362                                                 ableToOpen = m->openInputFile(countfileNames[i], in, "noerror");
 363
 364                                                 //if you can't open it, try default location
 365                                                 if (ableToOpen == 1) {
 366                                                         if (m->getDefaultPath() != "") { //default path is set
 367                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(countfileNames[i]);
 368                                                                 m->mothurOut("Unable to open " + countfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 369                                                                 ifstream in2;
 370                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 371                                                                 in2.close();
 372                                                                 countfileNames[i] = tryPath;
 373                                                         }
 374                                                 }
 375
 376                                                 if (ableToOpen == 1) {
 377                                                         if (m->getOutputDir() != "") { //default path is set
 378                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(countfileNames[i]);
 379                                                                 m->mothurOut("Unable to open " + countfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 380                                                                 ifstream in2;
 381                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 382                                                                 in2.close();
 383                                                                 countfileNames[i] = tryPath;
 384                                                         }
 385                                                 }
 386
 387                                                 in.close();
 388
 389                                                 if (ableToOpen == 1) {
 390                                                         m->mothurOut("Unable to open " + countfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 391                                                         //erase from file list
 392                                                         countfileNames.erase(countfileNames.begin()+i);
 393                                                         i--;
 394                                                 }else {
 395                                                         m->setCountTableFile(countfileNames[i]);
 396                                                 }
 397                                         }
 398                                 }
 399                         }
 400
 401             if (countfileNames.size() != 0) { hasCount = true; }
 402
 403                         //make sure there is at least one valid file left
 404             if (hasName && hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
 405
 406             if (!hasName && hasCount) { nameFileNames = countfileNames; }
 407
 408                         if ((hasCount || hasName) && (nameFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of name or count files does not match the number of fastafiles, please correct."); m->mothurOutEndLine(); abort=true; }
 409
 410                         bool hasGroup = true;
 411                         groupfile = validParameter.validFile(parameters, "group", false);
 412                         if (groupfile == "not found") { groupfile = "";  hasGroup = false; }
 413                         else {
 414                                 m->splitAtDash(groupfile, groupFileNames);
 415
 416                                 //go through files and make sure they are good, if not, then disregard them
 417                                 for (int i = 0; i < groupFileNames.size(); i++) {
 418
 419                                         bool ignore = false;
 420                                         if (groupFileNames[i] == "current") {
 421                                                 groupFileNames[i] = m->getGroupFile();
 422                                                 if (groupFileNames[i] != "") {  m->mothurOut("Using " + groupFileNames[i] + " as input file for the group parameter where you had given current."); m->mothurOutEndLine(); }
 423                                                 else {
 424                                                         m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 425                                                         //erase from file list
 426                                                         groupFileNames.erase(groupFileNames.begin()+i);
 427                                                         i--;
 428                                                 }
 429                                         }
 430
 431                                         if (!ignore) {
 432
 433                                                 if (inputDir != "") {
 434                                                         string path = m->hasPath(groupFileNames[i]);
 435                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 436                                                         if (path == "") {       groupFileNames[i] = inputDir + groupFileNames[i];               }
 437                                                 }
 438
 439                                                 int ableToOpen;
 440                                                 ifstream in;
 441
 442                                                 ableToOpen = m->openInputFile(groupFileNames[i], in, "noerror");
 443
 444                                                 //if you can't open it, try default location
 445                                                 if (ableToOpen == 1) {
 446                                                         if (m->getDefaultPath() != "") { //default path is set
 447                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(groupFileNames[i]);
 448                                                                 m->mothurOut("Unable to open " + groupFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 449                                                                 ifstream in2;
 450                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 451                                                                 in2.close();
 452                                                                 groupFileNames[i] = tryPath;
 453                                                         }
 454                                                 }
 455
 456                                                 if (ableToOpen == 1) {
 457                                                         if (m->getOutputDir() != "") { //default path is set
 458                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(groupFileNames[i]);
 459                                                                 m->mothurOut("Unable to open " + groupFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 460                                                                 ifstream in2;
 461                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 462                                                                 in2.close();
 463                                                                 groupFileNames[i] = tryPath;
 464                                                         }
 465                                                 }
 466
 467                                                 in.close();
 468
 469                                                 if (ableToOpen == 1) {
 470                                                         m->mothurOut("Unable to open " + groupFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 471                                                         //erase from file list
 472                                                         groupFileNames.erase(groupFileNames.begin()+i);
 473                                                         i--;
 474                                                 }else {
 475                                                         m->setGroupFile(groupFileNames[i]);
 476                                                 }
 477                                         }
 478                                 }
 479
 480                                 //make sure there is at least one valid file left
 481                                 if (groupFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid group files."); m->mothurOutEndLine(); abort = true; }
 482                         }
 483
 484                         if (hasGroup && (groupFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of groupfiles does not match the number of fastafiles, please correct."); m->mothurOutEndLine(); abort=true; }
 485
 486             if (hasGroup && hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or group."); m->mothurOutEndLine(); abort = true; }
 487                         //if the user changes the output directory command factory will send this info to us in the output parameter
 488                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 489
 490                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 491                         m->setProcessors(temp);
 492                         m->mothurConvert(temp, processors);
 493
 494                         temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
 495                         save = m->isTrue(temp);
 496                         rdb->save = save;
 497                         if (save) { //clear out old references
 498                                 rdb->clearMemory();
 499                         }
 500
 501                         string path;
 502                         it = parameters.find("reference");
 503                         //user has given a template file
 504                         if(it != parameters.end()){
 505                                 if (it->second == "self") {
 506                                         templatefile = "self";
 507                                         if (save) {
 508                                                 m->mothurOut("[WARNING]: You can't save reference=self, ignoring save.");
 509                                                 m->mothurOutEndLine();
 510                                                 save = false;
 511                                         }
 512                                 }
 513                                 else {
 514                                         path = m->hasPath(it->second);
 515                                         //if the user has not given a path then, add inputdir. else leave path alone.
 516                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 517
 518                                         templatefile = validParameter.validFile(parameters, "reference", true);
 519                                         if (templatefile == "not open") { abort = true; }
 520                                         else if (templatefile == "not found") { //check for saved reference sequences
 521                                                 if (rdb->referenceSeqs.size() != 0) {
 522                                                         templatefile = "saved";
 523                                                 }else {
 524                                                         m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required.");
 525                                                         m->mothurOutEndLine();
 526                                                         abort = true;
 527                                                 }
 528                                         }else { if (save) {     rdb->setSavedReference(templatefile);   }       }
 529                                 }
 530                         }else if (hasName) {  templatefile = "self";
 531                                 if (save) {
 532                                         m->mothurOut("[WARNING]: You can't save reference=self, ignoring save.");
 533                                         m->mothurOutEndLine();
 534                                         save = false;
 535                                 }
 536                         }else if (hasCount) {  templatefile = "self";
 537                                 if (save) {
 538                                         m->mothurOut("[WARNING]: You can't save reference=self, ignoring save.");
 539                                         m->mothurOutEndLine();
 540                                         save = false;
 541                                 }
 542                         }
 543                         else {
 544                                 if (rdb->referenceSeqs.size() != 0) {
 545                                         templatefile = "saved";
 546                                 }else {
 547                                         m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required.");
 548                                         m->mothurOutEndLine();
 549                                         templatefile = ""; abort = true;
 550                                 }
 551                         }
 552
 553
 554
 555                         temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
 556                         m->mothurConvert(temp, ksize);
 557
 558                         temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "50"; }
 559                         m->mothurConvert(temp, window);
 560
 561                         temp = validParameter.validFile(parameters, "match", false);                    if (temp == "not found") { temp = "5"; }
 562                         m->mothurConvert(temp, match);
 563
 564                         temp = validParameter.validFile(parameters, "mismatch", false);                 if (temp == "not found") { temp = "-4"; }
 565                         m->mothurConvert(temp, mismatch);
 566
 567                         temp = validParameter.validFile(parameters, "divergence", false);               if (temp == "not found") { temp = "1.007"; }
 568                         m->mothurConvert(temp, divR);
 569
 570                         temp = validParameter.validFile(parameters, "minsim", false);                   if (temp == "not found") { temp = "90"; }
 571                         m->mothurConvert(temp, minSimilarity);
 572
 573                         temp = validParameter.validFile(parameters, "mincov", false);                   if (temp == "not found") { temp = "70"; }
 574                         m->mothurConvert(temp, minCoverage);
 575
 576                         temp = validParameter.validFile(parameters, "minbs", false);                    if (temp == "not found") { temp = "90"; }
 577                         m->mothurConvert(temp, minBS);
 578
 579                         temp = validParameter.validFile(parameters, "minsnp", false);                   if (temp == "not found") { temp = "10"; }
 580                         m->mothurConvert(temp, minSNP);
 581
 582                         temp = validParameter.validFile(parameters, "parents", false);                  if (temp == "not found") { temp = "3"; }
 583                         m->mothurConvert(temp, parents);
 584
 585                         temp = validParameter.validFile(parameters, "realign", false);                  if (temp == "not found") { temp = "t"; }
 586                         realign = m->isTrue(temp);
 587
 588                         temp = validParameter.validFile(parameters, "trim", false);                             if (temp == "not found") { temp = "f"; }
 589                         trim = m->isTrue(temp);
 590
 591                         temp = validParameter.validFile(parameters, "split", false);                    if (temp == "not found") { temp = "f"; }
 592                         trimera = m->isTrue(temp);
 593
 594                         search = validParameter.validFile(parameters, "search", false);                 if (search == "not found") { search = "blast"; }
 595
 596                         temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
 597                         m->mothurConvert(temp, iters);
 598
 599                         temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "5"; }
 600                         m->mothurConvert(temp, increment);
 601
 602                         temp = validParameter.validFile(parameters, "numwanted", false);                if (temp == "not found") { temp = "15"; }
 603                         m->mothurConvert(temp, numwanted);
 604
 605                         temp = validParameter.validFile(parameters, "dereplicate", false);
 606                         if (temp == "not found") {
 607                                 if (groupfile != "")    {  temp = "false";                                      }
 608                                 else                    {  temp = "true";       }
 609                         }
 610                         dups = m->isTrue(temp);
 611
 612                         blastlocation = validParameter.validFile(parameters, "blastlocation", false);
 613                         if (blastlocation == "not found") { blastlocation = ""; }
 614                         else {
 615                                 //add / to name if needed
 616                                 string lastChar = blastlocation.substr(blastlocation.length()-1);
 617 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 618                                 if (lastChar != "/") { blastlocation += "/"; }
 619 #else
 620                                 if (lastChar != "\\") { blastlocation += "\\"; }
 621 #endif
 622                                 blastlocation = m->getFullPathName(blastlocation);
 623                                 string formatdbCommand = "";
 624 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 625                                 formatdbCommand = blastlocation + "formatdb";
 626 #else
 627                                 formatdbCommand = blastlocation + "formatdb.exe";
 628 #endif
 629
 630                                 //test to make sure formatdb exists
 631                                 ifstream in;
 632                                 formatdbCommand = m->getFullPathName(formatdbCommand);
 633                                 int ableToOpen = m->openInputFile(formatdbCommand, in, "no error"); in.close();
 634                                 if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe to run chimera.slayer."); m->mothurOutEndLine(); abort = true; }
 635
 636                                 string blastCommand = "";
 637 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 638                                 blastCommand = blastlocation + "megablast";
 639 #else
 640                                 blastCommand = blastlocation + "megablast.exe";
 641 #endif
 642                                 //test to make sure formatdb exists
 643                                 ifstream in2;
 644                                 blastCommand = m->getFullPathName(blastCommand);
 645                                 ableToOpen = m->openInputFile(blastCommand, in2, "no error"); in2.close();
 646                                 if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " + blastCommand + " file does not exist. mothur requires blastall.exe to run chimera.slayer."); m->mothurOutEndLine(); abort = true; }
 647                         }
 648
 649                         if ((search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true;  }
 650
 651                         if ((hasName || hasCount) && (templatefile != "self")) { m->mothurOut("You have provided a namefile or countfile 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; }
 652                         if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file 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; }
 653
 654                         //until we resolve the issue 10-18-11
 655 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 656 #else
 657                         //processors=1;
 658 #endif
 659                 }
 660         }
 661         catch(exception& e) {
 662                 m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
 663                 exit(1);
 664         }
 665 }
 666 //***************************************************************************************************************
 667
 668 int ChimeraSlayerCommand::execute(){
 669         try{
 670                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 671
 672                 for (int s = 0; s < fastaFileNames.size(); s++) {
 673
 674                         m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 675
 676                         int start = time(NULL);
 677                         if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it
 678                         map<string, string> variables;
 679             variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
 680                         string outputFileName = getOutputFileName("chimera", variables);
 681                         string accnosFileName = getOutputFileName("accnos", variables);
 682                         string trimFastaFileName = getOutputFileName("fasta", variables);
 683             string newCountFile = "";
 684
 685                         //clears files
 686                         ofstream out, out1, out2;
 687                         m->openOutputFile(outputFileName, out); out.close();
 688                         m->openOutputFile(accnosFileName, out1); out1.close();
 689                         if (trim) { m->openOutputFile(trimFastaFileName, out2); out2.close(); }
 690                         outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
 691                         outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
 692                         if (trim) {  outputNames.push_back(trimFastaFileName); outputTypes["fasta"].push_back(trimFastaFileName); }
 693
 694                         //maps a filename to priority map.
 695                         //if no groupfile this is fastafileNames[s] -> prioirity
 696                         //if groupfile then this is each groups seqs -> priority
 697                         map<string, map<string, int> > fileToPriority;
 698                         map<string, map<string, int> >::iterator itFile;
 699                         map<string, string> fileGroup;
 700                         fileToPriority[fastaFileNames[s]] = priority; //default
 701                         fileGroup[fastaFileNames[s]] = "noGroup";
 702             map<string, string> uniqueNames;
 703                         int totalChimeras = 0;
 704                         lines.clear();
 705
 706                         if (templatefile == "self") {
 707                 if (hasCount) {
 708                     SequenceCountParser* parser = NULL;
 709                     setUpForSelfReference(parser, fileGroup, fileToPriority, s);
 710                     if (parser != NULL) { uniqueNames = parser->getAllSeqsMap(); delete parser; }
 711                 }else {
 712                     SequenceParser* parser = NULL;
 713                     setUpForSelfReference(parser, fileGroup, fileToPriority, s);
 714                     if (parser != NULL) { uniqueNames = parser->getAllSeqsMap(); delete parser; }
 715                 }
 716             }
 717
 718                         if (m->control_pressed) {   for (int j = 0; j < outputNames.size(); j++) {      m->mothurRemove(outputNames[j]);        }  return 0;    }
 719
 720                         if (fileToPriority.size() == 1) { //you running without a groupfile
 721                                 itFile = fileToPriority.begin();
 722                                 string thisFastaName = itFile->first;
 723                                 map<string, int> thisPriority = itFile->second;
 724 #ifdef USE_MPI
 725                                 MPIExecute(thisFastaName, outputFileName, accnosFileName, trimFastaFileName, thisPriority);
 726 #else
 727                                 //break up file
 728                                 vector<unsigned long long> positions;
 729 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 730                                 positions = m->divideFile(thisFastaName, processors);
 731                                 for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(linePair(positions[i], positions[(i+1)]));      }
 732 #else
 733                                 if (processors == 1) {  lines.push_back(linePair(0, 1000)); }
 734                                 else {
 735                                         positions = m->setFilePosFasta(thisFastaName, numSeqs);
 736                     if (positions.size() < processors) { processors = positions.size(); }
 737
 738                                         //figure out how many sequences you have to process
 739                                         int numSeqsPerProcessor = numSeqs / processors;
 740                                         for (int i = 0; i < processors; i++) {
 741                                                 int startIndex =  i * numSeqsPerProcessor;
 742                                                 if(i == (processors - 1)){      numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;        }
 743                                                 lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
 744                                         }
 745                                 }
 746 #endif
 747                                 if(processors == 1){ numSeqs = driver(lines[0], outputFileName, thisFastaName, accnosFileName, trimFastaFileName, thisPriority);  }
 748                                 else{ numSeqs = createProcesses(outputFileName, thisFastaName, accnosFileName, trimFastaFileName, thisPriority); }
 749
 750                                 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]);        }  return 0; }
 751 #endif
 752                         }else { //you have provided a groupfile
 753                 string countFile = "";
 754                 if (hasCount) {
 755                     countFile = nameFileNames[s];
 756                     variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(nameFileNames[s]));
 757                     newCountFile = getOutputFileName("count", variables);
 758                 }
 759 #ifdef USE_MPI
 760                                 MPIExecuteGroups(outputFileName, accnosFileName, trimFastaFileName, fileToPriority, fileGroup, newCountFile, countFile);
 761 #else
 762                                 if (processors == 1) {
 763                     numSeqs = driverGroups(outputFileName, accnosFileName, trimFastaFileName, fileToPriority, fileGroup, newCountFile);
 764                     if (hasCount && dups) {
 765                         CountTable c; c.readTable(nameFileNames[s]);
 766                         if (!m->isBlank(newCountFile)) {
 767                             ifstream in2;
 768                             m->openInputFile(newCountFile, in2);
 769
 770                             string name, group;
 771                             while (!in2.eof()) {
 772                                 in2 >> name >> group; m->gobble(in2);
 773                                 c.setAbund(name, group, 0);
 774                             }
 775                             in2.close();
 776                         }
 777                         m->mothurRemove(newCountFile);
 778                         c.printTable(newCountFile);
 779                     }
 780
 781                 }
 782                                 else {  numSeqs = createProcessesGroups(outputFileName, accnosFileName, trimFastaFileName, fileToPriority, fileGroup, newCountFile, countFile);                 } //destroys fileToPriority
 783 #endif
 784
 785 #ifdef USE_MPI
 786                                 int pid;
 787                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 788
 789                                 if (pid == 0) {
 790 #endif
 791                     if (!dups) {
 792                         totalChimeras = deconvoluteResults(uniqueNames, outputFileName, accnosFileName, trimFastaFileName);
 793                         m->mothurOutEndLine(); m->mothurOut(toString(totalChimeras) + " chimera found."); m->mothurOutEndLine();
 794                     }else {
 795                         if (hasCount) {
 796                             set<string> doNotRemove;
 797                             CountTable c; c.readTable(newCountFile);
 798                             vector<string> namesInTable = c.getNamesOfSeqs();
 799                             for (int i = 0; i < namesInTable.size(); i++) {
 800                                 int temp = c.getNumSeqs(namesInTable[i]);
 801                                 if (temp == 0) {  c.remove(namesInTable[i]);  }
 802                                 else { doNotRemove.insert((namesInTable[i])); }
 803                             }
 804                             //remove names we want to keep from accnos file.
 805                             set<string> accnosNames = m->readAccnos(accnosFileName);
 806                             ofstream out2;
 807                             m->openOutputFile(accnosFileName, out2);
 808                             for (set<string>::iterator it = accnosNames.begin(); it != accnosNames.end(); it++) {
 809                                 if (doNotRemove.count(*it) == 0) {  out2 << (*it) << endl; }
 810                             }
 811                             out2.close();
 812                             c.printTable(newCountFile);
 813                             outputNames.push_back(newCountFile); outputTypes["count"].push_back(newCountFile);
 814                         }
 815                     }
 816
 817 #ifdef USE_MPI
 818                                 }
 819                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait
 820 #endif
 821                         }
 822
 823             m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences.");    m->mothurOutEndLine();
 824                 }
 825
 826                 //set accnos file as new current accnosfile
 827                 string current = "";
 828                 itTypes = outputTypes.find("accnos");
 829                 if (itTypes != outputTypes.end()) {
 830                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 831                 }
 832
 833                 if (trim) {
 834                         itTypes = outputTypes.find("fasta");
 835                         if (itTypes != outputTypes.end()) {
 836                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 837                         }
 838                 }
 839
 840         itTypes = outputTypes.find("count");
 841                 if (itTypes != outputTypes.end()) {
 842                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 843                 }
 844
 845                 m->mothurOutEndLine();
 846                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 847                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 848                 m->mothurOutEndLine();
 849
 850                 return 0;
 851
 852         }
 853         catch(exception& e) {
 854                 m->errorOut(e, "ChimeraSlayerCommand", "execute");
 855                 exit(1);
 856         }
 857 }
 858 //**********************************************************************************************************************
 859 int ChimeraSlayerCommand::MPIExecuteGroups(string outputFileName, string accnosFileName, string trimFastaFileName, map<string, map<string, int> >& fileToPriority, map<string, string>& fileGroup, string countlist, string countfile){
 860         try {
 861 #ifdef USE_MPI
 862                 int pid;
 863                 int tag = 2001;
 864
 865                 MPI_Status status;
 866                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 867                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 868
 869                 //put filenames in a vector, then pass each process a starting and ending point in the vector
 870                 //all processes already have the fileToPriority and fileGroup, they just need to know which files to process
 871                 map<string, map<string, int> >::iterator itFile;
 872                 vector<string> filenames;
 873                 for(itFile = fileToPriority.begin(); itFile != fileToPriority.end(); itFile++) { filenames.push_back(itFile->first); }
 874
 875                 int numGroupsPerProcessor = filenames.size() / processors;
 876                 int startIndex =  pid * numGroupsPerProcessor;
 877                 int endIndex = (pid+1) * numGroupsPerProcessor;
 878                 if(pid == (processors - 1)){    endIndex = filenames.size();    }
 879
 880                 vector<unsigned long long> MPIPos;
 881
 882                 MPI_File outMPI;
 883                 MPI_File outMPIAccnos;
 884                 MPI_File outMPIFasta;
 885         MPI_File outMPICount;
 886
 887                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 888                 int inMode=MPI_MODE_RDONLY;
 889
 890                 char outFilename[1024];
 891                 strcpy(outFilename, outputFileName.c_str());
 892
 893                 char outAccnosFilename[1024];
 894                 strcpy(outAccnosFilename, accnosFileName.c_str());
 895
 896                 char outFastaFilename[1024];
 897                 strcpy(outFastaFilename, trimFastaFileName.c_str());
 898
 899         char outCountFilename[1024];
 900                 strcpy(outCountFilename, countlist.c_str());
 901
 902                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 903                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 904                 if (trim) { MPI_File_open(MPI_COMM_WORLD, outFastaFilename, outMode, MPI_INFO_NULL, &outMPIFasta); }
 905         if (hasCount && dups) {  MPI_File_open(MPI_COMM_WORLD, outCountFilename, outMode, MPI_INFO_NULL, &outMPICount); }
 906
 907                 if (m->control_pressed) {   MPI_File_close(&outMPI); if (trim) {  MPI_File_close(&outMPIFasta);  } MPI_File_close(&outMPIAccnos); if (hasCount && dups) { MPI_File_close(&outMPICount); } return 0;  }
 908
 909                 //print headers
 910                 if (pid == 0) { //you are the root process
 911                         m->mothurOutEndLine();
 912                         m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
 913                         m->mothurOutEndLine();
 914
 915                         string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
 916
 917                         //print header
 918                         int length = outTemp.length();
 919                         char* buf2 = new char[length];
 920                         memcpy(buf2, outTemp.c_str(), length);
 921
 922                         MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
 923                         delete buf2;
 924                 }
 925                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait
 926
 927                 for (int i = startIndex; i < endIndex; i++) {
 928
 929                         int start = time(NULL);
 930                         int num = 0;
 931                         string thisFastaName = filenames[i];
 932                         map<string, int> thisPriority = fileToPriority[thisFastaName];
 933
 934                         char inFileName[1024];
 935                         strcpy(inFileName, thisFastaName.c_str());
 936                         MPI_File inMPI;
 937                         MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 938
 939                         MPIPos = m->setFilePosFasta(thisFastaName, num); //fills MPIPos, returns numSeqs
 940
 941                         cout << endl << "Checking sequences from group: " << fileGroup[thisFastaName] << "." << endl;
 942
 943             set<string> cnames;
 944                         driverMPI(0, num, inMPI, outMPI, outMPIAccnos, outMPIFasta, cnames, MPIPos, thisFastaName, thisPriority, true);
 945                         numSeqs += num;
 946
 947                         MPI_File_close(&inMPI);
 948                         m->mothurRemove(thisFastaName);
 949
 950             if (dups) {
 951                 if (cnames.size() != 0) {
 952                     if (hasCount) {
 953                         for (set<string>::iterator it = cnames.begin(); it != cnames.end(); it++) {
 954                             string outputString = (*it) + "\t" + fileGroup[thisFastaName] + "\n";
 955                             int length = outputString.length();
 956                             char* buf2 = new char[length];
 957                             memcpy(buf2, outputString.c_str(), length);
 958                             MPI_File_write_shared(outMPICount, buf2, length, MPI_CHAR, &status);
 959                             delete buf2;
 960                         }
 961                     }else {
 962                         map<string, map<string, string> >::iterator itGroupNameMap = group2NameMap.find(fileGroup[thisFastaName]);
 963                         if (itGroupNameMap != group2NameMap.end()) {
 964                             map<string, string> thisnamemap = itGroupNameMap->second;
 965                             map<string, string>::iterator itN;
 966                             for (set<string>::iterator it = cnames.begin(); it != cnames.end(); it++) {
 967                                 itN = thisnamemap.find(*it);
 968                                 if (itN != thisnamemap.end()) {
 969                                     vector<string> tempNames; m->splitAtComma(itN->second, tempNames);
 970                                     for (int j = 0; j < tempNames.size(); j++) { //write to accnos file
 971                                         string outputString = tempNames[j] + "\n";
 972                                         int length = outputString.length();
 973                                         char* buf2 = new char[length];
 974                                         memcpy(buf2, outputString.c_str(), length);
 975
 976                                         MPI_File_write_shared(outMPIAccnos, buf2, length, MPI_CHAR, &status);
 977                                         delete buf2;
 978                                     }
 979
 980                                 }else { m->mothurOut("[ERROR]: parsing cannot find " + *it + ".\n"); m->control_pressed = true; }
 981                             }
 982                         }else { m->mothurOut("[ERROR]: parsing cannot find " + fileGroup[thisFastaName] + ".\n"); m->control_pressed = true; }
 983                     }
 984
 985                 }
 986             }
 987
 988                         cout << endl << "It took " << toString(time(NULL) - start) << " secs to check " + toString(num) + " sequences from group " << fileGroup[thisFastaName] << "." << endl;
 989                 }
 990
 991                 if (pid == 0) {
 992                         for(int i = 1; i < processors; i++) {
 993                                 int temp = 0;
 994                                 MPI_Recv(&temp, 1, MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 995                                 numSeqs += temp;
 996                         }
 997                 }else{ MPI_Send(&numSeqs, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD); }
 998
 999                 MPI_File_close(&outMPI);
1000                 MPI_File_close(&outMPIAccnos);
1001                 if (trim) { MPI_File_close(&outMPIFasta); }
1002         if (hasCount && dups) { MPI_File_close(&outMPICount); }
1003
1004                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait
1005 #endif
1006                 return 0;
1007
1008         }catch(exception& e) {
1009                 m->errorOut(e, "ChimeraSlayerCommand", "MPIExecuteGroups");
1010                 exit(1);
1011         }
1012 }
1013 //**********************************************************************************************************************
1014 int ChimeraSlayerCommand::MPIExecute(string inputFile, string outputFileName, string accnosFileName, string trimFastaFileName, map<string, int>& priority){
1015         try {
1016
1017 #ifdef USE_MPI
1018                 int pid, numSeqsPerProcessor;
1019                 int tag = 2001;
1020                 vector<unsigned long long> MPIPos;
1021
1022                 MPI_Status status;
1023                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
1024                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
1025
1026                 MPI_File inMPI;
1027                 MPI_File outMPI;
1028                 MPI_File outMPIAccnos;
1029                 MPI_File outMPIFasta;
1030
1031                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
1032                 int inMode=MPI_MODE_RDONLY;
1033
1034                 char outFilename[1024];
1035                 strcpy(outFilename, outputFileName.c_str());
1036
1037                 char outAccnosFilename[1024];
1038                 strcpy(outAccnosFilename, accnosFileName.c_str());
1039
1040                 char outFastaFilename[1024];
1041                 strcpy(outFastaFilename, trimFastaFileName.c_str());
1042
1043                 char inFileName[1024];
1044                 strcpy(inFileName, inputFile.c_str());
1045
1046                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
1047                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
1048                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
1049                 if (trim) { MPI_File_open(MPI_COMM_WORLD, outFastaFilename, outMode, MPI_INFO_NULL, &outMPIFasta); }
1050
1051                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) {  MPI_File_close(&outMPIFasta);  } MPI_File_close(&outMPIAccnos);  return 0;  }
1052
1053                 if (pid == 0) { //you are the root process
1054                         m->mothurOutEndLine();
1055                         m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
1056                         m->mothurOutEndLine();
1057
1058                         string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
1059
1060                         //print header
1061                         int length = outTemp.length();
1062                         char* buf2 = new char[length];
1063                         memcpy(buf2, outTemp.c_str(), length);
1064
1065                         MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
1066                         delete buf2;
1067
1068                         MPIPos = m->setFilePosFasta(inputFile, numSeqs); //fills MPIPos, returns numSeqs
1069
1070                         if (templatefile != "self") { //if template=self we can only use 1 processor
1071                                 //send file positions to all processes
1072                                 for(int i = 1; i < processors; i++) {
1073                                         MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
1074                                         MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
1075                                 }
1076                         }
1077                         //figure out how many sequences you have to align
1078                         numSeqsPerProcessor = numSeqs / processors;
1079                         int startIndex =  pid * numSeqsPerProcessor;
1080                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
1081
1082                         if (templatefile == "self") { //if template=self we can only use 1 processor
1083                                 startIndex = 0;
1084                                 numSeqsPerProcessor = numSeqs;
1085                         }
1086
1087                         //do your part
1088             set<string> cnames;
1089                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, cnames, MPIPos, inputFile, priority, false);
1090
1091                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); }  MPI_File_close(&outMPIAccnos);   return 0;  }
1092
1093                 }else{ //you are a child process
1094                         if (templatefile != "self") { //if template=self we can only use 1 processor
1095                                 MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
1096                                 MPIPos.resize(numSeqs+1);
1097                                 MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
1098
1099                                 //figure out how many sequences you have to align
1100                                 numSeqsPerProcessor = numSeqs / processors;
1101                                 int startIndex =  pid * numSeqsPerProcessor;
1102                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
1103
1104                                 //do your part
1105                 set<string> cnames;
1106                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, cnames, MPIPos, inputFile, priority, false);
1107
1108                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); }  MPI_File_close(&outMPIAccnos);  return 0;  }
1109
1110                         }
1111                 }
1112
1113                 //close files
1114                 MPI_File_close(&inMPI);
1115                 MPI_File_close(&outMPI);
1116                 MPI_File_close(&outMPIAccnos);
1117                 if (trim) { MPI_File_close(&outMPIFasta); }
1118                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
1119
1120
1121 #endif
1122                 return numSeqs;
1123         }
1124         catch(exception& e) {
1125                 m->errorOut(e, "ChimeraSlayerCommand", "MPIExecute");
1126                 exit(1);
1127         }
1128 }
1129 //**********************************************************************************************************************
1130 int ChimeraSlayerCommand::deconvoluteResults(map<string, string>& uniqueNames, string outputFileName, string accnosFileName, string trimFileName){
1131         try {
1132                 map<string, string>::iterator itUnique;
1133                 int total = 0;
1134
1135         if (trimera) { //add in more potential uniqueNames
1136             map<string, string> newUniqueNames = uniqueNames;
1137             for (map<string, string>::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) {
1138                 newUniqueNames[(it->first)+"_LEFT"] = (it->first)+"_LEFT";
1139                 newUniqueNames[(it->first)+"_RIGHT"] = (it->first)+"_RIGHT";
1140             }
1141             uniqueNames = newUniqueNames;
1142             newUniqueNames.clear();
1143         }
1144
1145                 //edit accnos file
1146                 ifstream in2;
1147                 m->openInputFile(accnosFileName, in2, "no error");
1148
1149                 ofstream out2;
1150                 m->openOutputFile(accnosFileName+".temp", out2);
1151
1152                 string name; name = "";
1153                 set<string> chimerasInFile;
1154                 set<string>::iterator itChimeras;
1155
1156                 while (!in2.eof()) {
1157                         if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; }
1158
1159                         in2 >> name; m->gobble(in2);
1160
1161                         //find unique name
1162                         itUnique = uniqueNames.find(name);
1163
1164                         if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
1165                         else {
1166                                 itChimeras = chimerasInFile.find((itUnique->second));
1167
1168                                 if (itChimeras == chimerasInFile.end()) {
1169                                         out2 << itUnique->second << endl;
1170                                         chimerasInFile.insert((itUnique->second));
1171                                         total++;
1172                                 }
1173                         }
1174                 }
1175                 in2.close();
1176                 out2.close();
1177
1178                 m->mothurRemove(accnosFileName);
1179                 rename((accnosFileName+".temp").c_str(), accnosFileName.c_str());
1180
1181
1182                 //edit chimera file
1183                 ifstream in;
1184                 m->openInputFile(outputFileName, in);
1185
1186                 ofstream out;
1187                 m->openOutputFile(outputFileName+".temp", out); out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
1188
1189                 string rest, parent1, parent2, line;
1190                 set<string> namesInFile; //this is so if a sequence is found to be chimera in several samples we dont write it to the results file more than once
1191                 set<string>::iterator itNames;
1192
1193                 //assumptions - in file each read will always look like...
1194                 /*
1195                  F11Fcsw_92754  no
1196                  F11Fcsw_63104  F11Fcsw_33372   F11Fcsw_37007   0.89441 80.4469 0.2     1.03727 93.2961 52.2    no      0-241   243-369
1197                  */
1198
1199                 //get header line
1200                 if (!in.eof()) {
1201                         line = m->getline(in); m->gobble(in);
1202                         out << line << endl;
1203                 }
1204
1205                 //for the chimera file, we want to make sure if any group finds a sequence to be chimeric then all groups do,
1206                 //so if this is a report that did not find it to be chimeric, but it appears in the accnos file,
1207                 //then ignore this report and continue until we find the report that found it to be chimeric
1208
1209                 while (!in.eof()) {
1210
1211                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove((outputFileName+".temp")); return 0; }
1212
1213                         in >> name;             m->gobble(in);
1214                         in >> parent1;  m->gobble(in);
1215
1216                         if (name == "Name") { //name = "Name" because we append the header line each time we add results from the groups
1217                                 line = m->getline(in); m->gobble(in);
1218                         }else {
1219                                 if (parent1 == "no") {
1220                                         //find unique name
1221                                         itUnique = uniqueNames.find(name);
1222
1223                                         if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
1224                                         else {
1225                                                 //is this sequence really not chimeric??
1226                                                 itChimeras = chimerasInFile.find(itUnique->second);
1227
1228                                                 if (itChimeras == chimerasInFile.end()) {
1229                                                         //is this sequence not already in the file
1230                                                         itNames = namesInFile.find((itUnique->second));
1231
1232                                                         if (itNames == namesInFile.end()) { out << itUnique->second << '\t' << "no" << endl; namesInFile.insert(itUnique->second); }
1233                                                 }
1234                                         }
1235                                 }else { //read the rest of the line
1236                                         double DivQLAQRB,PerIDQLAQRB,BootStrapA,DivQLBQRA,PerIDQLBQRA,BootStrapB;
1237                                         string flag, range1, range2;
1238                                         bool print = false;
1239                                         in >> parent2 >> DivQLAQRB >> PerIDQLAQRB >> BootStrapA >> DivQLBQRA >> PerIDQLBQRA >> BootStrapB >> flag >> range1 >> range2;  m->gobble(in);
1240
1241                                         //find unique name
1242                                         itUnique = uniqueNames.find(name);
1243
1244                                         if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
1245                                         else {
1246                                                 name = itUnique->second;
1247                                                 //is this name already in the file
1248                                                 itNames = namesInFile.find((name));
1249
1250                                                 if (itNames == namesInFile.end()) { //no not in file
1251                                                         if (flag == "no") { //are you really a no??
1252                                                                 //is this sequence really not chimeric??
1253                                                                 itChimeras = chimerasInFile.find(name);
1254
1255                                                                 //then you really are a no so print, otherwise skip
1256                                                                 if (itChimeras == chimerasInFile.end()) { print = true; }
1257
1258                                                         }else{ print = true; }
1259                                                 }
1260                                         }
1261
1262                                         if (print) {
1263                                                 out << name << '\t';
1264
1265                                                 namesInFile.insert(name);
1266
1267                                                 //output parent1's name
1268                                                 itUnique = uniqueNames.find(parent1);
1269                                                 if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parentA "+ parent1 + "."); m->mothurOutEndLine(); m->control_pressed = true; }
1270                                                 else { out << itUnique->second << '\t'; }
1271
1272                                                 //output parent2's name
1273                                                 itUnique = uniqueNames.find(parent2);
1274                                                 if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parentA "+ parent2 + "."); m->mothurOutEndLine(); m->control_pressed = true; }
1275                                                 else { out << itUnique->second << '\t'; }
1276
1277                                                 out << DivQLAQRB << '\t' << PerIDQLAQRB << '\t' << BootStrapA << '\t' << DivQLBQRA << '\t' << PerIDQLBQRA << '\t' << BootStrapB << '\t' << flag << '\t' << range1 << '\t' << range2 << endl;
1278                                         }
1279                                 }
1280                         }
1281                 }
1282                 in.close();
1283                 out.close();
1284
1285                 m->mothurRemove(outputFileName);
1286                 rename((outputFileName+".temp").c_str(), outputFileName.c_str());
1287
1288                 //edit fasta file
1289                 if (trim) {
1290                         ifstream in3;
1291                         m->openInputFile(trimFileName, in3);
1292
1293                         ofstream out3;
1294                         m->openOutputFile(trimFileName+".temp", out3);
1295
1296                         namesInFile.clear();
1297
1298                         while (!in3.eof()) {
1299                                 if (m->control_pressed) { in3.close(); out3.close(); m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); m->mothurRemove((trimFileName+".temp")); return 0; }
1300
1301                                 Sequence seq(in3); m->gobble(in3);
1302
1303                                 if (seq.getName() != "") {
1304                                         //find unique name
1305                                         itUnique = uniqueNames.find(seq.getName());
1306
1307                                         if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find "+ seq.getName() + "."); m->mothurOutEndLine(); m->control_pressed = true; }
1308                                         else {
1309                                                 itNames = namesInFile.find((itUnique->second));
1310
1311                                                 if (itNames == namesInFile.end()) {
1312                                                         seq.printSequence(out3);
1313                                                 }
1314                                         }
1315                                 }
1316                         }
1317                         in3.close();
1318                         out3.close();
1319
1320                         m->mothurRemove(trimFileName);
1321                         rename((trimFileName+".temp").c_str(), trimFileName.c_str());
1322                 }
1323
1324                 return total;
1325         }
1326         catch(exception& e) {
1327                 m->errorOut(e, "ChimeraSlayerCommand", "deconvoluteResults");
1328                 exit(1);
1329         }
1330 }
1331 //**********************************************************************************************************************
1332 int ChimeraSlayerCommand::setUpForSelfReference(SequenceParser*& parser, map<string, string>& fileGroup, map<string, map<string, int> >& fileToPriority, int s){
1333         try {
1334                 fileGroup.clear();
1335                 fileToPriority.clear();
1336
1337                 string nameFile = "";
1338                 if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
1339                         nameFile = nameFileNames[s];
1340                 }else {  nameFile = getNamesFile(fastaFileNames[s]); }
1341
1342                 //you provided a groupfile
1343                 string groupFile = "";
1344                 if (groupFileNames.size() != 0) { groupFile = groupFileNames[s]; }
1345
1346                 if (groupFile == "") {
1347                         if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
1348
1349                         //sort fastafile by abundance, returns new sorted fastafile name
1350                         m->mothurOut("Sorting fastafile according to abundance..."); cout.flush();
1351                         priority = sortFastaFile(fastaFileNames[s], nameFile);
1352                         m->mothurOut("Done."); m->mothurOutEndLine();
1353
1354                         fileToPriority[fastaFileNames[s]] = priority;
1355                         fileGroup[fastaFileNames[s]] = "noGroup";
1356                 }else {
1357                         //Parse sequences by group
1358                         parser = new SequenceParser(groupFile, fastaFileNames[s], nameFile);
1359                         vector<string> groups = parser->getNamesOfGroups();
1360
1361                         for (int i = 0; i < groups.size(); i++) {
1362                                 vector<Sequence> thisGroupsSeqs = parser->getSeqs(groups[i]);
1363                                 map<string, string> thisGroupsMap = parser->getNameMap(groups[i]);
1364                 group2NameMap[groups[i]] = thisGroupsMap;
1365                                 string newFastaFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + groups[i] + "-sortedTemp.fasta";
1366                                 priority = sortFastaFile(thisGroupsSeqs, thisGroupsMap, newFastaFile);
1367                                 fileToPriority[newFastaFile] = priority;
1368                                 fileGroup[newFastaFile] = groups[i];
1369                         }
1370                 }
1371
1372
1373                 return 0;
1374         }
1375         catch(exception& e) {
1376                 m->errorOut(e, "ChimeraSlayerCommand", "setUpForSelfReference");
1377                 exit(1);
1378         }
1379 }
1380 //**********************************************************************************************************************
1381 int ChimeraSlayerCommand::setUpForSelfReference(SequenceCountParser*& parser, map<string, string>& fileGroup, map<string, map<string, int> >& fileToPriority, int s){
1382         try {
1383                 fileGroup.clear();
1384                 fileToPriority.clear();
1385
1386                 string nameFile = "";
1387                 if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
1388                         nameFile = nameFileNames[s];
1389                 }else {  m->control_pressed = true; return 0; }
1390
1391                 CountTable ct;
1392                 if (!ct.testGroups(nameFile)) {
1393                         if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
1394
1395                         //sort fastafile by abundance, returns new sorted fastafile name
1396                         m->mothurOut("Sorting fastafile according to abundance..."); cout.flush();
1397                         priority = sortFastaFile(fastaFileNames[s], nameFile);
1398                         m->mothurOut("Done."); m->mothurOutEndLine();
1399
1400                         fileToPriority[fastaFileNames[s]] = priority;
1401                         fileGroup[fastaFileNames[s]] = "noGroup";
1402                 }else {
1403                         //Parse sequences by group
1404                         parser = new SequenceCountParser(nameFile, fastaFileNames[s]);
1405                         vector<string> groups = parser->getNamesOfGroups();
1406
1407                         for (int i = 0; i < groups.size(); i++) {
1408                                 vector<Sequence> thisGroupsSeqs = parser->getSeqs(groups[i]);
1409                                 map<string, int> thisGroupsMap = parser->getCountTable(groups[i]);
1410                                 string newFastaFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + groups[i] + "-sortedTemp.fasta";
1411                                 sortFastaFile(thisGroupsSeqs, thisGroupsMap, newFastaFile);
1412                                 fileToPriority[newFastaFile] = thisGroupsMap;
1413                                 fileGroup[newFastaFile] = groups[i];
1414                         }
1415                 }
1416
1417
1418                 return 0;
1419         }
1420         catch(exception& e) {
1421                 m->errorOut(e, "ChimeraSlayerCommand", "setUpForSelfReference");
1422                 exit(1);
1423         }
1424 }
1425 //**********************************************************************************************************************
1426 string ChimeraSlayerCommand::getNamesFile(string& inputFile){
1427         try {
1428                 string nameFile = "";
1429
1430                 m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine();
1431
1432                 //use unique.seqs to create new name and fastafile
1433                 string inputString = "fasta=" + inputFile;
1434                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
1435                 m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
1436                 m->mothurCalling = true;
1437
1438                 Command* uniqueCommand = new DeconvoluteCommand(inputString);
1439                 uniqueCommand->execute();
1440
1441                 map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
1442
1443                 delete uniqueCommand;
1444                 m->mothurCalling = false;
1445                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
1446
1447                 nameFile = filenames["name"][0];
1448                 inputFile = filenames["fasta"][0];
1449
1450                 return nameFile;
1451         }
1452         catch(exception& e) {
1453                 m->errorOut(e, "ChimeraSlayerCommand", "getNamesFile");
1454                 exit(1);
1455         }
1456 }
1457 //**********************************************************************************************************************
1458
1459 int ChimeraSlayerCommand::driverGroups(string outputFName, string accnos, string fasta, map<string, map<string, int> >& fileToPriority, map<string, string>& fileGroup, string countlist){
1460         try {
1461                 int totalSeqs = 0;
1462         ofstream outCountList;
1463
1464         if (hasCount && dups) { m->openOutputFile(countlist, outCountList); }
1465
1466                 for (map<string, map<string, int> >::iterator itFile = fileToPriority.begin(); itFile != fileToPriority.end(); itFile++) {
1467
1468                         if (m->control_pressed) {  return 0;  }
1469
1470                         int start = time(NULL);
1471                         string thisFastaName = itFile->first;
1472                         map<string, int> thisPriority = itFile->second;
1473                         string thisoutputFileName = outputDir + m->getRootName(m->getSimpleName(thisFastaName)) + fileGroup[thisFastaName] + "slayer.chimera";
1474                         string thisaccnosFileName = outputDir + m->getRootName(m->getSimpleName(thisFastaName)) + fileGroup[thisFastaName] + "slayer.accnos";
1475                         string thistrimFastaFileName = outputDir + m->getRootName(m->getSimpleName(thisFastaName)) + fileGroup[thisFastaName] + "slayer.fasta";
1476
1477                         m->mothurOutEndLine(); m->mothurOut("Checking sequences from group: " + fileGroup[thisFastaName] + "."); m->mothurOutEndLine();
1478
1479                         lines.clear();
1480 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1481                         int proc = 1;
1482                         vector<unsigned long long> positions = m->divideFile(thisFastaName, proc);
1483                         lines.push_back(linePair(positions[0], positions[1]));
1484 #else
1485                         lines.push_back(linePair(0, 1000));
1486 #endif
1487                         int numSeqs = driver(lines[0], thisoutputFileName, thisFastaName, thisaccnosFileName, thistrimFastaFileName, thisPriority);
1488
1489             //if we provided a count file with group info and set dereplicate=t, then we want to create a *.pick.count_table
1490             //This table will zero out group counts for seqs determined to be chimeric by that group.
1491             if (dups) {
1492                 if (!m->isBlank(thisaccnosFileName)) {
1493                     ifstream in;
1494                     m->openInputFile(thisaccnosFileName, in);
1495                     string name;
1496                     if (hasCount) {
1497                         while (!in.eof()) {
1498                             in >> name; m->gobble(in);
1499                             outCountList << name << '\t' << fileGroup[thisFastaName] << endl;
1500                         }
1501                         in.close();
1502                     }else {
1503                         map<string, map<string, string> >::iterator itGroupNameMap = group2NameMap.find(fileGroup[thisFastaName]);
1504                         if (itGroupNameMap != group2NameMap.end()) {
1505                             map<string, string> thisnamemap = itGroupNameMap->second;
1506                             map<string, string>::iterator itN;
1507                             ofstream out;
1508                             m->openOutputFile(thisaccnosFileName+".temp", out);
1509                             while (!in.eof()) {
1510                                 in >> name; m->gobble(in);
1511                                 itN = thisnamemap.find(name);
1512                                 if (itN != thisnamemap.end()) {
1513                                     vector<string> tempNames; m->splitAtComma(itN->second, tempNames);
1514                                     for (int j = 0; j < tempNames.size(); j++) { out << tempNames[j] << endl; }
1515
1516                                 }else { m->mothurOut("[ERROR]: parsing cannot find " + name + ".\n"); m->control_pressed = true; }
1517                             }
1518                             out.close();
1519                             in.close();
1520                             m->renameFile(thisaccnosFileName+".temp", thisaccnosFileName);
1521                         }else { m->mothurOut("[ERROR]: parsing cannot find " + fileGroup[thisFastaName] + ".\n"); m->control_pressed = true; }
1522                     }
1523
1524                 }
1525             }
1526
1527                         //append files
1528                         m->appendFiles(thisoutputFileName, outputFName); m->mothurRemove(thisoutputFileName);
1529                         m->appendFiles(thisaccnosFileName, accnos); m->mothurRemove(thisaccnosFileName);
1530                         if (trim) { m->appendFiles(thistrimFastaFileName, fasta); m->mothurRemove(thistrimFastaFileName); }
1531                         m->mothurRemove(thisFastaName);
1532
1533                         totalSeqs += numSeqs;
1534
1535                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences from group " + fileGroup[thisFastaName] + ".");     m->mothurOutEndLine();
1536                 }
1537
1538         if (hasCount && dups) { outCountList.close(); }
1539
1540                 return totalSeqs;
1541         }
1542         catch(exception& e) {
1543                 m->errorOut(e, "ChimeraSlayerCommand", "driverGroups");
1544                 exit(1);
1545         }
1546 }
1547 /**************************************************************************************************/
1548 int ChimeraSlayerCommand::createProcessesGroups(string outputFName, string accnos, string fasta, map<string, map<string, int> >& fileToPriority, map<string, string>& fileGroup, string countlist, string countFile) {
1549         try {
1550                 int process = 1;
1551                 int num = 0;
1552                 processIDS.clear();
1553
1554                 if (fileToPriority.size() < processors) { processors = fileToPriority.size(); }
1555
1556         CountTable newCount;
1557         if (hasCount && dups) { newCount.readTable(countFile); }
1558
1559                 int groupsPerProcessor = fileToPriority.size() / processors;
1560                 int remainder = fileToPriority.size() % processors;
1561
1562                 vector< map<string, map<string, int> > > breakUp;
1563
1564                 for (int i = 0; i < processors; i++) {
1565                         map<string, map<string, int> > thisFileToPriority;
1566                         map<string, map<string, int> >::iterator itFile;
1567                         int count = 0;
1568                         int enough = groupsPerProcessor;
1569                         if (i == 0) { enough = groupsPerProcessor + remainder; }
1570
1571                         for (itFile = fileToPriority.begin(); itFile != fileToPriority.end();) {
1572                                 thisFileToPriority[itFile->first] = itFile->second;
1573                                 fileToPriority.erase(itFile++);
1574                                 count++;
1575                                 if (count == enough) { break; }
1576                         }
1577                         breakUp.push_back(thisFileToPriority);
1578                 }
1579
1580 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1581                 //loop through and create all the processes you want
1582                 while (process != processors) {
1583                         int pid = fork();
1584
1585                         if (pid > 0) {
1586                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1587                                 process++;
1588                         }else if (pid == 0){
1589                                 num = driverGroups(outputFName + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp", breakUp[process], fileGroup, accnos + toString(getpid()) + ".byCount");
1590
1591                                 //pass numSeqs to parent
1592                                 ofstream out;
1593                                 string tempFile = outputFName + toString(getpid()) + ".num.temp";
1594                                 m->openOutputFile(tempFile, out);
1595                                 out << num << endl;
1596                                 out.close();
1597                                 exit(0);
1598                         }else {
1599                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1600                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1601                                 exit(0);
1602                         }
1603                 }
1604
1605                 num = driverGroups(outputFName, accnos, fasta, breakUp[0], fileGroup, accnos + ".byCount");
1606
1607                 //force parent to wait until all the processes are done
1608                 for (int i=0;i<processors;i++) {
1609                         int temp = processIDS[i];
1610                         wait(&temp);
1611                 }
1612
1613                 for (int i = 0; i < processIDS.size(); i++) {
1614                         ifstream in;
1615                         string tempFile =  outputFName + toString(processIDS[i]) + ".num.temp";
1616                         m->openInputFile(tempFile, in);
1617                         if (!in.eof()) { int tempNum = 0;  in >> tempNum; num += tempNum; }
1618                         in.close(); m->mothurRemove(tempFile);
1619                 }
1620 #else
1621
1622                 //////////////////////////////////////////////////////////////////////////////////////////////////////
1623                 //Windows version shared memory, so be careful when passing variables through the slayerData struct.
1624                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
1625                 //////////////////////////////////////////////////////////////////////////////////////////////////////
1626
1627                 vector<slayerData*> pDataArray;
1628                 DWORD   dwThreadIdArray[processors-1];
1629                 HANDLE  hThreadArray[processors-1];
1630
1631                 //Create processor worker threads.
1632                 for(int i=1; i<processors; i++ ){
1633                         string extension = toString(i) + ".temp";
1634                         slayerData* tempslayer = new slayerData(group2NameMap, hasCount, dups, (accnos + extension+".byCount"), (outputFName + extension), (fasta + extension), (accnos + extension), templatefile, search, blastlocation, trimera, trim, realign, m, breakUp[i], fileGroup, ksize, match, mismatch, window, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, divR, priority, i);
1635                         pDataArray.push_back(tempslayer);
1636                         processIDS.push_back(i);
1637
1638                         //MySlayerThreadFunction is in header. It must be global or static to work with the threads.
1639                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
1640                         hThreadArray[i-1] = CreateThread(NULL, 0, MySlayerGroupThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
1641                 }
1642
1643                 num = driverGroups(outputFName, accnos, fasta, breakUp[0], fileGroup, accnos + ".byCount");
1644
1645                 //Wait until all threads have terminated.
1646                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
1647
1648                 //Close all thread handles and free memory allocations.
1649                 for(int i=0; i < pDataArray.size(); i++){
1650             if (pDataArray[i]->fileToPriority.size() != pDataArray[i]->end) {
1651                 m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->end) + " of " + toString(pDataArray[i]->fileToPriority.size()) + " groups assigned to it, quitting. \n"); m->control_pressed = true;
1652             }
1653                         num += pDataArray[i]->count;
1654                         CloseHandle(hThreadArray[i]);
1655                         delete pDataArray[i];
1656                 }
1657 #endif
1658         //read my own
1659         if (hasCount && dups) {
1660             if (!m->isBlank(accnos + ".byCount")) {
1661                 ifstream in2;
1662                 m->openInputFile(accnos + ".byCount", in2);
1663
1664                 string name, group;
1665                 while (!in2.eof()) {
1666                     in2 >> name >> group; m->gobble(in2);
1667                     newCount.setAbund(name, group, 0);
1668                 }
1669                 in2.close();
1670             }
1671             m->mothurRemove(accnos + ".byCount");
1672         }
1673
1674
1675                 //append output files
1676                 for(int i=0;i<processIDS.size();i++){
1677                         m->appendFiles((outputFName + toString(processIDS[i]) + ".temp"), outputFName);
1678                         m->mothurRemove((outputFName + toString(processIDS[i]) + ".temp"));
1679
1680                         m->appendFiles((accnos + toString(processIDS[i]) + ".temp"), accnos);
1681                         m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));
1682
1683                         if (trim) {
1684                                 m->appendFiles((fasta + toString(processIDS[i]) + ".temp"), fasta);
1685                                 m->mothurRemove((fasta + toString(processIDS[i]) + ".temp"));
1686                         }
1687
1688             if (hasCount && dups) {
1689                 if (!m->isBlank(accnos + toString(processIDS[i]) + ".byCount")) {
1690                     ifstream in2;
1691                     m->openInputFile(accnos  + toString(processIDS[i]) + ".byCount", in2);
1692
1693                     string name, group;
1694                     while (!in2.eof()) {
1695                         in2 >> name >> group; m->gobble(in2);
1696                         newCount.setAbund(name, group, 0);
1697                     }
1698                     in2.close();
1699                 }
1700                 m->mothurRemove(accnos + toString(processIDS[i]) + ".byCount");
1701             }
1702
1703                 }
1704
1705         //print new *.pick.count_table
1706         if (hasCount && dups) {  newCount.printTable(countlist);   }
1707
1708                 return num;
1709         }
1710         catch(exception& e) {
1711                 m->errorOut(e, "ChimeraSlayerCommand", "createProcessesGroups");
1712                 exit(1);
1713         }
1714 }
1715 //**********************************************************************************************************************
1716
1717 int ChimeraSlayerCommand::driver(linePair filePos, string outputFName, string filename, string accnos, string fasta, map<string, int>& priority){
1718         try {
1719
1720                 Chimera* chimera;
1721                 if (templatefile != "self") { //you want to run slayer with a reference template
1722                         chimera = new ChimeraSlayer(filename, templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand());
1723                 }else {
1724                         chimera = new ChimeraSlayer(filename, templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand());
1725                 }
1726
1727                 if (m->control_pressed) { delete chimera; return 0; }
1728
1729                 if (chimera->getUnaligned()) { delete chimera; m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
1730                 templateSeqsLength = chimera->getLength();
1731
1732                 ofstream out;
1733                 m->openOutputFile(outputFName, out);
1734
1735                 ofstream out2;
1736                 m->openOutputFile(accnos, out2);
1737
1738                 ofstream out3;
1739                 if (trim) {  m->openOutputFile(fasta, out3); }
1740
1741                 ifstream inFASTA;
1742                 m->openInputFile(filename, inFASTA);
1743
1744                 inFASTA.seekg(filePos.start);
1745
1746                 if (filePos.start == 0) { chimera->printHeader(out); }
1747
1748                 bool done = false;
1749                 int count = 0;
1750
1751                 while (!done) {
1752
1753                         if (m->control_pressed) {       delete chimera; out.close(); out2.close(); if (trim) { out3.close(); } inFASTA.close(); return 1;       }
1754
1755                         Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
1756                         string candidateAligned = candidateSeq->getAligned();
1757
1758                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
1759                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
1760                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
1761                                 }else{
1762                                         //find chimeras
1763                                         chimera->getChimeras(candidateSeq);
1764
1765                                         if (m->control_pressed) {       delete chimera; delete candidateSeq; return 1;  }
1766
1767                                         //if you are not chimeric, then check each half
1768                                         data_results wholeResults = chimera->getResults();
1769
1770                                         //determine if we need to split
1771                                         bool isChimeric = false;
1772
1773                                         if (wholeResults.flag == "yes") {
1774                                                 string chimeraFlag = "no";
1775                                                 if(  (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
1776                                                    ||
1777                                                    (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
1778
1779
1780                                                 if (chimeraFlag == "yes") {
1781                                                         if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
1782                                                 }
1783                                         }
1784
1785                                         if ((!isChimeric) && trimera) {
1786
1787                                                 //split sequence in half by bases
1788                                                 string leftQuery, rightQuery;
1789                                                 Sequence tempSeq(candidateSeq->getName(), candidateAligned);
1790                                                 divideInHalf(tempSeq, leftQuery, rightQuery);
1791
1792                                                 //run chimeraSlayer on each piece
1793                                                 Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
1794                                                 Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
1795
1796                                                 //find chimeras
1797                                                 chimera->getChimeras(left);
1798                                                 data_results leftResults = chimera->getResults();
1799
1800                                                 chimera->getChimeras(right);
1801                                                 data_results rightResults = chimera->getResults();
1802
1803                                                 //if either piece is chimeric then report
1804                                                 Sequence trimmed = chimera->print(out, out2, leftResults, rightResults);
1805                                                 if (trim) { trimmed.printSequence(out3);  }
1806
1807                                                 delete left; delete right;
1808
1809                                         }else { //already chimeric
1810                                                 //print results
1811                                                 Sequence trimmed = chimera->print(out, out2);
1812                                                 if (trim) { trimmed.printSequence(out3);  }
1813                                         }
1814
1815
1816                                 }
1817                                 count++;
1818                         }
1819
1820                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1821                                 unsigned long long pos = inFASTA.tellg();
1822                                 if ((pos == -1) || (pos >= filePos.end)) { break; }
1823                         #else
1824                                 if (inFASTA.eof()) { break; }
1825                         #endif
1826
1827                         delete candidateSeq;
1828                         //report progress
1829                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1830                 }
1831                 //report progress
1832                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1833
1834                 int numNoParents = chimera->getNumNoParents();
1835                 if (numNoParents == count) { 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(); }
1836
1837                 out.close();
1838                 out2.close();
1839                 if (trim) { out3.close(); }
1840                 inFASTA.close();
1841                 delete chimera;
1842
1843                 return count;
1844
1845
1846         }
1847         catch(exception& e) {
1848                 m->errorOut(e, "ChimeraSlayerCommand", "driver");
1849                 exit(1);
1850         }
1851 }
1852 //**********************************************************************************************************************
1853 #ifdef USE_MPI
1854 int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, MPI_File& outFastaMPI, set<string>& cnames, vector<unsigned long long>& MPIPos, string filename, map<string, int>& priority, bool byGroup){
1855         try {
1856                 MPI_Status status;
1857                 int pid;
1858                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
1859
1860                 Chimera* chimera;
1861                 if (templatefile != "self") { //you want to run slayer with a reference template
1862                         chimera = new ChimeraSlayer(filename, templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand());
1863                 }else {
1864                         chimera = new ChimeraSlayer(filename, templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand(), byGroup);
1865                 }
1866
1867                 if (m->control_pressed) { delete chimera; return 0; }
1868
1869                 if (chimera->getUnaligned()) { delete chimera; m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
1870                 templateSeqsLength = chimera->getLength();
1871
1872                 for(int i=0;i<num;i++){
1873
1874                         if (m->control_pressed) {       delete chimera; return 1;       }
1875
1876                         //read next sequence
1877                         int length = MPIPos[start+i+1] - MPIPos[start+i];
1878
1879                         char* buf4 = new char[length];
1880                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
1881
1882                         string tempBuf = buf4;
1883                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
1884                         istringstream iss (tempBuf,istringstream::in);
1885
1886                         delete buf4;
1887
1888                         Sequence* candidateSeq = new Sequence(iss);  m->gobble(iss);
1889                         string candidateAligned = candidateSeq->getAligned();
1890
1891                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
1892
1893                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
1894                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
1895                                 }else{
1896
1897                                         //find chimeras
1898                                         chimera->getChimeras(candidateSeq);
1899
1900                                         if (m->control_pressed) {       delete chimera; delete candidateSeq; return 1;  }
1901
1902                                         //if you are not chimeric, then check each half
1903                                         data_results wholeResults = chimera->getResults();
1904
1905                                         //determine if we need to split
1906                                         bool isChimeric = false;
1907
1908                                         if (wholeResults.flag == "yes") {
1909                                                 string chimeraFlag = "no";
1910                                                 if(  (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
1911                                                    ||
1912                                                    (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
1913
1914
1915                                                 if (chimeraFlag == "yes") {
1916                                                         if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
1917                                                 }
1918                                         }
1919
1920                                         if ((!isChimeric) && trimera) {
1921                                                 //split sequence in half by bases
1922                                                 string leftQuery, rightQuery;
1923                                                 Sequence tempSeq(candidateSeq->getName(), candidateAligned);
1924                                                 divideInHalf(tempSeq, leftQuery, rightQuery);
1925
1926                                                 //run chimeraSlayer on each piece
1927                                                 Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
1928                                                 Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
1929
1930                                                 //find chimeras
1931                                                 chimera->getChimeras(left);
1932                                                 data_results leftResults = chimera->getResults();
1933
1934                                                 chimera->getChimeras(right);
1935                                                 data_results rightResults = chimera->getResults();
1936
1937                                                 //if either piece is chimeric then report
1938                         bool flag = false;
1939                                                 Sequence trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults, flag);
1940                         if (flag) { cnames.insert(candidateSeq->getName()); }
1941
1942                                                 if (trim) {
1943                                                         string outputString = ">" + trimmed.getName() + "\n" + trimmed.getAligned() + "\n";
1944
1945                                                         //write to accnos file
1946                                                         int length = outputString.length();
1947                                                         char* buf2 = new char[length];
1948                                                         memcpy(buf2, outputString.c_str(), length);
1949
1950                                                         MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
1951                                                         delete buf2;
1952                                                 }
1953
1954                                                 delete left; delete right;
1955
1956                                         }else {
1957                                                 //print results
1958                                                 Sequence trimmed = chimera->print(outMPI, outAccMPI);
1959                         cnames.insert(candidateSeq->getName());
1960
1961                                                 if (trim) {
1962                                                         string outputString = ">" + trimmed.getName() + "\n" + trimmed.getAligned() + "\n";
1963
1964                                                         //write to accnos file
1965                                                         int length = outputString.length();
1966                                                         char* buf2 = new char[length];
1967                                                         memcpy(buf2, outputString.c_str(), length);
1968
1969                                                         MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
1970                                                         delete buf2;
1971                                                 }
1972                                         }
1973
1974                                 }
1975                         }
1976                         delete candidateSeq;
1977
1978                         //report progress
1979                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
1980                 }
1981                 //report progress
1982                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
1983
1984                 int numNoParents = chimera->getNumNoParents();
1985                 if (numNoParents == num) { cout << "[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." << endl; }
1986
1987                 delete chimera;
1988                 return 0;
1989         }
1990         catch(exception& e) {
1991                 m->errorOut(e, "ChimeraSlayerCommand", "driverMPI");
1992                 exit(1);
1993         }
1994 }
1995 #endif
1996
1997 /**************************************************************************************************/
1998
1999 int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos, string fasta, map<string, int>& thisPriority) {
2000         try {
2001                 int process = 0;
2002                 int num = 0;
2003                 processIDS.clear();
2004
2005 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
2006                 //loop through and create all the processes you want
2007                 while (process != processors) {
2008                         int pid = fork();
2009
2010                         if (pid > 0) {
2011                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
2012                                 process++;
2013                         }else if (pid == 0){
2014                                 num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp", thisPriority);
2015
2016                                 //pass numSeqs to parent
2017                                 ofstream out;
2018                                 string tempFile = outputFileName + toString(getpid()) + ".num.temp";
2019                                 m->openOutputFile(tempFile, out);
2020                                 out << num << endl;
2021                                 out.close();
2022                                 exit(0);
2023                         }else {
2024                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
2025                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
2026                                 exit(0);
2027                         }
2028                 }
2029
2030                 //force parent to wait until all the processes are done
2031                 for (int i=0;i<processors;i++) {
2032                         int temp = processIDS[i];
2033                         wait(&temp);
2034                 }
2035
2036                 for (int i = 0; i < processIDS.size(); i++) {
2037                         ifstream in;
2038                         string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
2039                         m->openInputFile(tempFile, in);
2040                         if (!in.eof()) { int tempNum = 0;  in >> tempNum; num += tempNum; }
2041                         in.close(); m->mothurRemove(tempFile);
2042                 }
2043 #else
2044
2045                 //////////////////////////////////////////////////////////////////////////////////////////////////////
2046                 //Windows version shared memory, so be careful when passing variables through the slayerData struct.
2047                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
2048                 //////////////////////////////////////////////////////////////////////////////////////////////////////
2049
2050                 vector<slayerData*> pDataArray;
2051                 DWORD   dwThreadIdArray[processors];
2052                 HANDLE  hThreadArray[processors];
2053
2054                 //Create processor worker threads.
2055                 for( int i=0; i<processors; i++ ){
2056                         string extension = toString(i) + ".temp";
2057                         slayerData* tempslayer = new slayerData((outputFileName + extension), (fasta + extension), (accnos + extension), filename, templatefile, search, blastlocation, trimera, trim, realign, m, lines[i].start, lines[i].end, ksize, match, mismatch, window, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, divR, priority, i);
2058                         pDataArray.push_back(tempslayer);
2059                         processIDS.push_back(i);
2060
2061                         //MySlayerThreadFunction is in header. It must be global or static to work with the threads.
2062                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
2063                         hThreadArray[i] = CreateThread(NULL, 0, MySlayerThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
2064                 }
2065
2066                 //Wait until all threads have terminated.
2067                 WaitForMultipleObjects(processors, hThreadArray, TRUE, INFINITE);
2068
2069                 //Close all thread handles and free memory allocations.
2070                 for(int i=0; i < pDataArray.size(); i++){
2071                         num += pDataArray[i]->count;
2072                         CloseHandle(hThreadArray[i]);
2073                         delete pDataArray[i];
2074                 }
2075 #endif
2076
2077                 rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
2078                 rename((accnos + toString(processIDS[0]) + ".temp").c_str(), accnos.c_str());
2079                 if (trim) {  rename((fasta + toString(processIDS[0]) + ".temp").c_str(), fasta.c_str()); }
2080
2081                 //append output files
2082                 for(int i=1;i<processIDS.size();i++){
2083                         m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
2084                         m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp"));
2085
2086                         m->appendFiles((accnos + toString(processIDS[i]) + ".temp"), accnos);
2087                         m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));
2088
2089                         if (trim) {
2090                                 m->appendFiles((fasta + toString(processIDS[i]) + ".temp"), fasta);
2091                                 m->mothurRemove((fasta + toString(processIDS[i]) + ".temp"));
2092                         }
2093                 }
2094
2095
2096                 return num;
2097         }
2098         catch(exception& e) {
2099                 m->errorOut(e, "ChimeraSlayerCommand", "createProcesses");
2100                 exit(1);
2101         }
2102 }
2103
2104 /**************************************************************************************************/
2105
2106 int ChimeraSlayerCommand::divideInHalf(Sequence querySeq, string& leftQuery, string& rightQuery) {
2107         try {
2108
2109                 string queryUnAligned = querySeq.getUnaligned();
2110                 int numBases = int(queryUnAligned.length() * 0.5);
2111
2112                 string queryAligned = querySeq.getAligned();
2113                 leftQuery = querySeq.getAligned();
2114                 rightQuery = querySeq.getAligned();
2115
2116                 int baseCount = 0;
2117                 int leftSpot = 0;
2118                 for (int i = 0; i < queryAligned.length(); i++) {
2119                         //if you are a base
2120                         if (isalpha(queryAligned[i])) {
2121                                 baseCount++;
2122                         }
2123
2124                         //if you have half
2125                         if (baseCount >= numBases) {  leftSpot = i; break; } //first half
2126                 }
2127
2128                 //blank out right side
2129                 for (int i = leftSpot; i < leftQuery.length(); i++) { leftQuery[i] = '.'; }
2130
2131                 //blank out left side
2132                 for (int i = 0; i < leftSpot; i++) { rightQuery[i] = '.'; }
2133
2134                 return 0;
2135
2136         }
2137         catch(exception& e) {
2138                 m->errorOut(e, "ChimeraSlayerCommand", "divideInHalf");
2139                 exit(1);
2140         }
2141 }
2142 /**************************************************************************************************/
2143 map<string, int> ChimeraSlayerCommand::sortFastaFile(string fastaFile, string nameFile) {
2144         try {
2145                 map<string, int> nameAbund;
2146
2147                 //read through fastafile and store info
2148                 map<string, string> seqs;
2149                 ifstream in;
2150                 m->openInputFile(fastaFile, in);
2151
2152                 while (!in.eof()) {
2153
2154                         if (m->control_pressed) { in.close(); return nameAbund; }
2155
2156                         Sequence seq(in); m->gobble(in);
2157                         seqs[seq.getName()] = seq.getAligned();
2158                 }
2159
2160                 in.close();
2161
2162                 //read namefile or countfile
2163                 vector<seqPriorityNode> nameMapCount;
2164         int error;
2165         if (hasCount) {
2166             CountTable ct;
2167             ct.readTable(nameFile);
2168
2169             for(map<string, string>::iterator it = seqs.begin(); it != seqs.end(); it++) {
2170                 int num = ct.getNumSeqs(it->first);
2171                 if (num == 0) { error = 1; }
2172                 else {
2173                     seqPriorityNode temp(num, it->second, it->first);
2174                     nameMapCount.push_back(temp);
2175                 }
2176             }
2177         }else { error = m->readNames(nameFile, nameMapCount, seqs); }
2178
2179                 if (m->control_pressed) { return nameAbund; }
2180
2181                 if (error == 1) { m->control_pressed = true; return nameAbund; }
2182                 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; }
2183
2184                 sort(nameMapCount.begin(), nameMapCount.end(), compareSeqPriorityNodes);
2185
2186                 string newFasta = fastaFile + ".temp";
2187                 ofstream out;
2188                 m->openOutputFile(newFasta, out);
2189
2190                 //print new file in order of
2191                 for (int i = 0; i < nameMapCount.size(); i++) {
2192                         out << ">" << nameMapCount[i].name << endl << nameMapCount[i].seq << endl;
2193                         nameAbund[nameMapCount[i].name] = nameMapCount[i].numIdentical;
2194                 }
2195                 out.close();
2196
2197                 rename(newFasta.c_str(), fastaFile.c_str());
2198
2199                 return nameAbund;
2200
2201         }
2202         catch(exception& e) {
2203                 m->errorOut(e, "ChimeraSlayerCommand", "sortFastaFile");
2204                 exit(1);
2205         }
2206 }
2207 /**************************************************************************************************/
2208 map<string, int> ChimeraSlayerCommand::sortFastaFile(vector<Sequence>& thisseqs, map<string, string>& nameMap, string newFile) {
2209         try {
2210                 map<string, int> nameAbund;
2211                 vector<seqPriorityNode> nameVector;
2212
2213                 //read through fastafile and store info
2214                 map<string, string> seqs;
2215
2216                 for (int i = 0; i < thisseqs.size(); i++) {
2217
2218                         if (m->control_pressed) { return nameAbund; }
2219
2220                         map<string, string>::iterator itNameMap = nameMap.find(thisseqs[i].getName());
2221
2222                         if (itNameMap == nameMap.end()){
2223                                 m->control_pressed = true;
2224                                 m->mothurOut("[ERROR]: " + thisseqs[i].getName() + " is in your fastafile, but is not in your namesfile, please correct."); m->mothurOutEndLine();
2225                         }else {
2226                                 int num = m->getNumNames(itNameMap->second);
2227
2228                                 seqPriorityNode temp(num, thisseqs[i].getAligned(), thisseqs[i].getName());
2229                                 nameVector.push_back(temp);
2230                         }
2231                 }
2232
2233                 //sort by num represented
2234                 sort(nameVector.begin(), nameVector.end(), compareSeqPriorityNodes);
2235
2236                 if (m->control_pressed) { return nameAbund; }
2237
2238                 if (thisseqs.size() != nameVector.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; }
2239
2240                 ofstream out;
2241                 m->openOutputFile(newFile, out);
2242
2243                 //print new file in order of
2244                 for (int i = 0; i < nameVector.size(); i++) {
2245                         out << ">" << nameVector[i].name << endl << nameVector[i].seq << endl;
2246                         nameAbund[nameVector[i].name] = nameVector[i].numIdentical;
2247                 }
2248                 out.close();
2249
2250                 return nameAbund;
2251
2252         }
2253         catch(exception& e) {
2254                 m->errorOut(e, "ChimeraSlayerCommand", "sortFastaFile");
2255                 exit(1);
2256         }
2257 }
2258 /**************************************************************************************************/
2259 int ChimeraSlayerCommand::sortFastaFile(vector<Sequence>& thisseqs, map<string, int>& countMap, string newFile) {
2260         try {
2261                 vector<seqPriorityNode> nameVector;
2262
2263                 //read through fastafile and store info
2264                 map<string, string> seqs;
2265
2266                 for (int i = 0; i < thisseqs.size(); i++) {
2267
2268                         if (m->control_pressed) { return 0; }
2269
2270                         map<string, int>::iterator itCountMap = countMap.find(thisseqs[i].getName());
2271
2272                         if (itCountMap == countMap.end()){
2273                                 m->control_pressed = true;
2274                                 m->mothurOut("[ERROR]: " + thisseqs[i].getName() + " is in your fastafile, but is not in your count file, please correct."); m->mothurOutEndLine();
2275                         }else {
2276                 seqPriorityNode temp(itCountMap->second, thisseqs[i].getAligned(), thisseqs[i].getName());
2277                                 nameVector.push_back(temp);
2278                         }
2279                 }
2280
2281                 //sort by num represented
2282                 sort(nameVector.begin(), nameVector.end(), compareSeqPriorityNodes);
2283
2284                 if (m->control_pressed) { return 0; }
2285
2286                 if (thisseqs.size() != nameVector.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your count file, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
2287
2288                 ofstream out;
2289                 m->openOutputFile(newFile, out);
2290
2291                 //print new file in order of
2292                 for (int i = 0; i < nameVector.size(); i++) {
2293                         out << ">" << nameVector[i].name << endl << nameVector[i].seq << endl;
2294                 }
2295                 out.close();
2296
2297                 return 0;
2298
2299         }
2300         catch(exception& e) {
2301                 m->errorOut(e, "ChimeraSlayerCommand", "sortFastaFile");
2302                 exit(1);
2303         }
2304 }
2305 /**************************************************************************************************/
2306