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") { temp = "false";                      }
 607                         dups = m->isTrue(temp);
 608
 609                         blastlocation = validParameter.validFile(parameters, "blastlocation", false);
 610                         if (blastlocation == "not found") { blastlocation = ""; }
 611                         else {
 612                                 //add / to name if needed
 613                                 string lastChar = blastlocation.substr(blastlocation.length()-1);
 614 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 615                                 if (lastChar != "/") { blastlocation += "/"; }
 616 #else
 617                                 if (lastChar != "\\") { blastlocation += "\\"; }
 618 #endif
 619                                 blastlocation = m->getFullPathName(blastlocation);
 620                                 string formatdbCommand = "";
 621 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 622                                 formatdbCommand = blastlocation + "formatdb";
 623 #else
 624                                 formatdbCommand = blastlocation + "formatdb.exe";
 625 #endif
 626
 627                                 //test to make sure formatdb exists
 628                                 ifstream in;
 629                                 formatdbCommand = m->getFullPathName(formatdbCommand);
 630                                 int ableToOpen = m->openInputFile(formatdbCommand, in, "no error"); in.close();
 631                                 if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe to run chimera.slayer."); m->mothurOutEndLine(); abort = true; }
 632
 633                                 string blastCommand = "";
 634 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 635                                 blastCommand = blastlocation + "megablast";
 636 #else
 637                                 blastCommand = blastlocation + "megablast.exe";
 638 #endif
 639                                 //test to make sure formatdb exists
 640                                 ifstream in2;
 641                                 blastCommand = m->getFullPathName(blastCommand);
 642                                 ableToOpen = m->openInputFile(blastCommand, in2, "no error"); in2.close();
 643                                 if(ableToOpen == 1) {   m->mothurOut("[ERROR]: " + blastCommand + " file does not exist. mothur requires blastall.exe to run chimera.slayer."); m->mothurOutEndLine(); abort = true; }
 644                         }
 645
 646                         if ((search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true;  }
 647
 648                         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; }
 649                         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; }
 650
 651                         //until we resolve the issue 10-18-11
 652 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 653 #else
 654                         //processors=1;
 655 #endif
 656                 }
 657         }
 658         catch(exception& e) {
 659                 m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
 660                 exit(1);
 661         }
 662 }
 663 //***************************************************************************************************************
 664
 665 int ChimeraSlayerCommand::execute(){
 666         try{
 667                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 668
 669                 for (int s = 0; s < fastaFileNames.size(); s++) {
 670
 671                         m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 672
 673                         int start = time(NULL);
 674                         if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it
 675                         map<string, string> variables;
 676             variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]));
 677                         string outputFileName = getOutputFileName("chimera", variables);
 678                         string accnosFileName = getOutputFileName("accnos", variables);
 679                         string trimFastaFileName = getOutputFileName("fasta", variables);
 680             string newCountFile = "";
 681
 682                         //clears files
 683                         ofstream out, out1, out2;
 684                         m->openOutputFile(outputFileName, out); out.close();
 685                         m->openOutputFile(accnosFileName, out1); out1.close();
 686                         if (trim) { m->openOutputFile(trimFastaFileName, out2); out2.close(); }
 687                         outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
 688                         outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
 689                         if (trim) {  outputNames.push_back(trimFastaFileName); outputTypes["fasta"].push_back(trimFastaFileName); }
 690
 691                         //maps a filename to priority map.
 692                         //if no groupfile this is fastafileNames[s] -> prioirity
 693                         //if groupfile then this is each groups seqs -> priority
 694                         map<string, map<string, int> > fileToPriority;
 695                         map<string, map<string, int> >::iterator itFile;
 696                         map<string, string> fileGroup;
 697                         fileToPriority[fastaFileNames[s]] = priority; //default
 698                         fileGroup[fastaFileNames[s]] = "noGroup";
 699             map<string, string> uniqueNames;
 700                         int totalChimeras = 0;
 701                         lines.clear();
 702
 703                         if (templatefile == "self") {
 704                 if (hasCount) {
 705                     SequenceCountParser* parser = NULL;
 706                     setUpForSelfReference(parser, fileGroup, fileToPriority, s);
 707                     if (parser != NULL) { uniqueNames = parser->getAllSeqsMap(); delete parser; }
 708                 }else {
 709                     SequenceParser* parser = NULL;
 710                     setUpForSelfReference(parser, fileGroup, fileToPriority, s);
 711                     if (parser != NULL) { uniqueNames = parser->getAllSeqsMap(); delete parser; }
 712                 }
 713             }
 714
 715                         if (m->control_pressed) {   for (int j = 0; j < outputNames.size(); j++) {      m->mothurRemove(outputNames[j]);        }  return 0;    }
 716
 717                         if (fileToPriority.size() == 1) { //you running without a groupfile
 718                                 itFile = fileToPriority.begin();
 719                                 string thisFastaName = itFile->first;
 720                                 map<string, int> thisPriority = itFile->second;
 721 #ifdef USE_MPI
 722                                 MPIExecute(thisFastaName, outputFileName, accnosFileName, trimFastaFileName, thisPriority);
 723 #else
 724                                 //break up file
 725                                 vector<unsigned long long> positions;
 726 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 727                                 positions = m->divideFile(thisFastaName, processors);
 728                                 for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(linePair(positions[i], positions[(i+1)]));      }
 729 #else
 730                                 if (processors == 1) {  lines.push_back(linePair(0, 1000)); }
 731                                 else {
 732                                         positions = m->setFilePosFasta(thisFastaName, numSeqs);
 733                     if (positions.size() < processors) { processors = positions.size(); }
 734
 735                                         //figure out how many sequences you have to process
 736                                         int numSeqsPerProcessor = numSeqs / processors;
 737                                         for (int i = 0; i < processors; i++) {
 738                                                 int startIndex =  i * numSeqsPerProcessor;
 739                                                 if(i == (processors - 1)){      numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;        }
 740                                                 lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
 741                                         }
 742                                 }
 743 #endif
 744                                 if(processors == 1){ numSeqs = driver(lines[0], outputFileName, thisFastaName, accnosFileName, trimFastaFileName, thisPriority);  }
 745                                 else{ numSeqs = createProcesses(outputFileName, thisFastaName, accnosFileName, trimFastaFileName, thisPriority); }
 746
 747                                 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; }
 748 #endif
 749                         }else { //you have provided a groupfile
 750                 string countFile = "";
 751                 if (hasCount) {
 752                     countFile = nameFileNames[s];
 753                     variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(nameFileNames[s]));
 754                     newCountFile = getOutputFileName("count", variables);
 755                 }
 756 #ifdef USE_MPI
 757                                 MPIExecuteGroups(outputFileName, accnosFileName, trimFastaFileName, fileToPriority, fileGroup, newCountFile, countFile);
 758 #else
 759                                 if (processors == 1) {
 760                     numSeqs = driverGroups(outputFileName, accnosFileName, trimFastaFileName, fileToPriority, fileGroup, newCountFile);
 761                     if (hasCount && dups) {
 762                         CountTable c; c.readTable(nameFileNames[s], true);
 763                         if (!m->isBlank(newCountFile)) {
 764                             ifstream in2;
 765                             m->openInputFile(newCountFile, in2);
 766
 767                             string name, group;
 768                             while (!in2.eof()) {
 769                                 in2 >> name >> group; m->gobble(in2);
 770                                 c.setAbund(name, group, 0);
 771                             }
 772                             in2.close();
 773                         }
 774                         m->mothurRemove(newCountFile);
 775                         c.printTable(newCountFile);
 776                     }
 777
 778                 }
 779                                 else {  numSeqs = createProcessesGroups(outputFileName, accnosFileName, trimFastaFileName, fileToPriority, fileGroup, newCountFile, countFile);                 } //destroys fileToPriority
 780 #endif
 781
 782 #ifdef USE_MPI
 783                                 int pid;
 784                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 785
 786                                 if (pid == 0) {
 787 #endif
 788                     if (!dups) {
 789                         totalChimeras = deconvoluteResults(uniqueNames, outputFileName, accnosFileName, trimFastaFileName);
 790                         m->mothurOutEndLine(); m->mothurOut(toString(totalChimeras) + " chimera found."); m->mothurOutEndLine();
 791                     }else {
 792                         if (hasCount) {
 793                             set<string> doNotRemove;
 794                             CountTable c; c.readTable(newCountFile, true);
 795                             vector<string> namesInTable = c.getNamesOfSeqs();
 796                             for (int i = 0; i < namesInTable.size(); i++) {
 797                                 int temp = c.getNumSeqs(namesInTable[i]);
 798                                 if (temp == 0) {  c.remove(namesInTable[i]);  }
 799                                 else { doNotRemove.insert((namesInTable[i])); }
 800                             }
 801                             //remove names we want to keep from accnos file.
 802                             set<string> accnosNames = m->readAccnos(accnosFileName);
 803                             ofstream out2;
 804                             m->openOutputFile(accnosFileName, out2);
 805                             for (set<string>::iterator it = accnosNames.begin(); it != accnosNames.end(); it++) {
 806                                 if (doNotRemove.count(*it) == 0) {  out2 << (*it) << endl; }
 807                             }
 808                             out2.close();
 809                             c.printTable(newCountFile);
 810                             outputNames.push_back(newCountFile); outputTypes["count"].push_back(newCountFile);
 811                         }
 812                     }
 813
 814 #ifdef USE_MPI
 815                                 }
 816                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait
 817 #endif
 818                         }
 819
 820             m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences.");    m->mothurOutEndLine();
 821                 }
 822
 823                 //set accnos file as new current accnosfile
 824                 string current = "";
 825                 itTypes = outputTypes.find("accnos");
 826                 if (itTypes != outputTypes.end()) {
 827                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 828                 }
 829
 830                 if (trim) {
 831                         itTypes = outputTypes.find("fasta");
 832                         if (itTypes != outputTypes.end()) {
 833                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 834                         }
 835                 }
 836
 837         itTypes = outputTypes.find("count");
 838                 if (itTypes != outputTypes.end()) {
 839                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 840                 }
 841
 842                 m->mothurOutEndLine();
 843                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 844                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 845                 m->mothurOutEndLine();
 846
 847                 return 0;
 848
 849         }
 850         catch(exception& e) {
 851                 m->errorOut(e, "ChimeraSlayerCommand", "execute");
 852                 exit(1);
 853         }
 854 }
 855 //**********************************************************************************************************************
 856 int ChimeraSlayerCommand::MPIExecuteGroups(string outputFileName, string accnosFileName, string trimFastaFileName, map<string, map<string, int> >& fileToPriority, map<string, string>& fileGroup, string countlist, string countfile){
 857         try {
 858 #ifdef USE_MPI
 859                 int pid;
 860                 int tag = 2001;
 861
 862                 MPI_Status status;
 863                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 864                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 865
 866                 //put filenames in a vector, then pass each process a starting and ending point in the vector
 867                 //all processes already have the fileToPriority and fileGroup, they just need to know which files to process
 868                 map<string, map<string, int> >::iterator itFile;
 869                 vector<string> filenames;
 870                 for(itFile = fileToPriority.begin(); itFile != fileToPriority.end(); itFile++) { filenames.push_back(itFile->first); }
 871
 872                 int numGroupsPerProcessor = filenames.size() / processors;
 873                 int startIndex =  pid * numGroupsPerProcessor;
 874                 int endIndex = (pid+1) * numGroupsPerProcessor;
 875                 if(pid == (processors - 1)){    endIndex = filenames.size();    }
 876
 877                 vector<unsigned long long> MPIPos;
 878
 879                 MPI_File outMPI;
 880                 MPI_File outMPIAccnos;
 881                 MPI_File outMPIFasta;
 882         MPI_File outMPICount;
 883
 884                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 885                 int inMode=MPI_MODE_RDONLY;
 886
 887                 char outFilename[1024];
 888                 strcpy(outFilename, outputFileName.c_str());
 889
 890                 char outAccnosFilename[1024];
 891                 strcpy(outAccnosFilename, accnosFileName.c_str());
 892
 893                 char outFastaFilename[1024];
 894                 strcpy(outFastaFilename, trimFastaFileName.c_str());
 895
 896         char outCountFilename[1024];
 897                 strcpy(outCountFilename, countlist.c_str());
 898
 899                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 900                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 901                 if (trim) { MPI_File_open(MPI_COMM_WORLD, outFastaFilename, outMode, MPI_INFO_NULL, &outMPIFasta); }
 902         if (hasCount && dups) {  MPI_File_open(MPI_COMM_WORLD, outCountFilename, outMode, MPI_INFO_NULL, &outMPICount); }
 903
 904                 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;  }
 905
 906                 //print headers
 907                 if (pid == 0) { //you are the root process
 908                         m->mothurOutEndLine();
 909                         m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
 910                         m->mothurOutEndLine();
 911
 912                         string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
 913
 914                         //print header
 915                         int length = outTemp.length();
 916                         char* buf2 = new char[length];
 917                         memcpy(buf2, outTemp.c_str(), length);
 918
 919                         MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
 920                         delete buf2;
 921                 }
 922                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait
 923
 924                 for (int i = startIndex; i < endIndex; i++) {
 925
 926                         int start = time(NULL);
 927                         int num = 0;
 928                         string thisFastaName = filenames[i];
 929                         map<string, int> thisPriority = fileToPriority[thisFastaName];
 930
 931                         char inFileName[1024];
 932                         strcpy(inFileName, thisFastaName.c_str());
 933                         MPI_File inMPI;
 934                         MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 935
 936                         MPIPos = m->setFilePosFasta(thisFastaName, num); //fills MPIPos, returns numSeqs
 937
 938                         cout << endl << "Checking sequences from group: " << fileGroup[thisFastaName] << "." << endl;
 939
 940             set<string> cnames;
 941                         driverMPI(0, num, inMPI, outMPI, outMPIAccnos, outMPIFasta, cnames, MPIPos, thisFastaName, thisPriority, true);
 942                         numSeqs += num;
 943
 944                         MPI_File_close(&inMPI);
 945                         m->mothurRemove(thisFastaName);
 946
 947             if (dups) {
 948                 if (cnames.size() != 0) {
 949                     if (hasCount) {
 950                         for (set<string>::iterator it = cnames.begin(); it != cnames.end(); it++) {
 951                             string outputString = (*it) + "\t" + fileGroup[thisFastaName] + "\n";
 952                             int length = outputString.length();
 953                             char* buf2 = new char[length];
 954                             memcpy(buf2, outputString.c_str(), length);
 955                             MPI_File_write_shared(outMPICount, buf2, length, MPI_CHAR, &status);
 956                             delete buf2;
 957                         }
 958                     }else {
 959                         map<string, map<string, string> >::iterator itGroupNameMap = group2NameMap.find(fileGroup[thisFastaName]);
 960                         if (itGroupNameMap != group2NameMap.end()) {
 961                             map<string, string> thisnamemap = itGroupNameMap->second;
 962                             map<string, string>::iterator itN;
 963                             for (set<string>::iterator it = cnames.begin(); it != cnames.end(); it++) {
 964                                 itN = thisnamemap.find(*it);
 965                                 if (itN != thisnamemap.end()) {
 966                                     vector<string> tempNames; m->splitAtComma(itN->second, tempNames);
 967                                     for (int j = 0; j < tempNames.size(); j++) { //write to accnos file
 968                                         string outputString = tempNames[j] + "\n";
 969                                         int length = outputString.length();
 970                                         char* buf2 = new char[length];
 971                                         memcpy(buf2, outputString.c_str(), length);
 972
 973                                         MPI_File_write_shared(outMPIAccnos, buf2, length, MPI_CHAR, &status);
 974                                         delete buf2;
 975                                     }
 976
 977                                 }else { m->mothurOut("[ERROR]: parsing cannot find " + *it + ".\n"); m->control_pressed = true; }
 978                             }
 979                         }else { m->mothurOut("[ERROR]: parsing cannot find " + fileGroup[thisFastaName] + ".\n"); m->control_pressed = true; }
 980                     }
 981
 982                 }
 983             }
 984
 985                         cout << endl << "It took " << toString(time(NULL) - start) << " secs to check " + toString(num) + " sequences from group " << fileGroup[thisFastaName] << "." << endl;
 986                 }
 987
 988                 if (pid == 0) {
 989                         for(int i = 1; i < processors; i++) {
 990                                 int temp = 0;
 991                                 MPI_Recv(&temp, 1, MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 992                                 numSeqs += temp;
 993                         }
 994                 }else{ MPI_Send(&numSeqs, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD); }
 995
 996                 MPI_File_close(&outMPI);
 997                 MPI_File_close(&outMPIAccnos);
 998                 if (trim) { MPI_File_close(&outMPIFasta); }
 999         if (hasCount && dups) { MPI_File_close(&outMPICount); }
1000
1001                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait
1002 #endif
1003                 return 0;
1004
1005         }catch(exception& e) {
1006                 m->errorOut(e, "ChimeraSlayerCommand", "MPIExecuteGroups");
1007                 exit(1);
1008         }
1009 }
1010 //**********************************************************************************************************************
1011 int ChimeraSlayerCommand::MPIExecute(string inputFile, string outputFileName, string accnosFileName, string trimFastaFileName, map<string, int>& priority){
1012         try {
1013
1014 #ifdef USE_MPI
1015                 int pid, numSeqsPerProcessor;
1016                 int tag = 2001;
1017                 vector<unsigned long long> MPIPos;
1018
1019                 MPI_Status status;
1020                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
1021                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
1022
1023                 MPI_File inMPI;
1024                 MPI_File outMPI;
1025                 MPI_File outMPIAccnos;
1026                 MPI_File outMPIFasta;
1027
1028                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
1029                 int inMode=MPI_MODE_RDONLY;
1030
1031                 char outFilename[1024];
1032                 strcpy(outFilename, outputFileName.c_str());
1033
1034                 char outAccnosFilename[1024];
1035                 strcpy(outAccnosFilename, accnosFileName.c_str());
1036
1037                 char outFastaFilename[1024];
1038                 strcpy(outFastaFilename, trimFastaFileName.c_str());
1039
1040                 char inFileName[1024];
1041                 strcpy(inFileName, inputFile.c_str());
1042
1043                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
1044                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
1045                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
1046                 if (trim) { MPI_File_open(MPI_COMM_WORLD, outFastaFilename, outMode, MPI_INFO_NULL, &outMPIFasta); }
1047
1048                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) {  MPI_File_close(&outMPIFasta);  } MPI_File_close(&outMPIAccnos);  return 0;  }
1049
1050                 if (pid == 0) { //you are the root process
1051                         m->mothurOutEndLine();
1052                         m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
1053                         m->mothurOutEndLine();
1054
1055                         string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
1056
1057                         //print header
1058                         int length = outTemp.length();
1059                         char* buf2 = new char[length];
1060                         memcpy(buf2, outTemp.c_str(), length);
1061
1062                         MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
1063                         delete buf2;
1064
1065                         MPIPos = m->setFilePosFasta(inputFile, numSeqs); //fills MPIPos, returns numSeqs
1066
1067                         if (templatefile != "self") { //if template=self we can only use 1 processor
1068                                 //send file positions to all processes
1069                                 for(int i = 1; i < processors; i++) {
1070                                         MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
1071                                         MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
1072                                 }
1073                         }
1074                         //figure out how many sequences you have to align
1075                         numSeqsPerProcessor = numSeqs / processors;
1076                         int startIndex =  pid * numSeqsPerProcessor;
1077                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
1078
1079                         if (templatefile == "self") { //if template=self we can only use 1 processor
1080                                 startIndex = 0;
1081                                 numSeqsPerProcessor = numSeqs;
1082                         }
1083
1084                         //do your part
1085             set<string> cnames;
1086                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, cnames, MPIPos, inputFile, priority, false);
1087
1088                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); }  MPI_File_close(&outMPIAccnos);   return 0;  }
1089
1090                 }else{ //you are a child process
1091                         if (templatefile != "self") { //if template=self we can only use 1 processor
1092                                 MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
1093                                 MPIPos.resize(numSeqs+1);
1094                                 MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
1095
1096                                 //figure out how many sequences you have to align
1097                                 numSeqsPerProcessor = numSeqs / processors;
1098                                 int startIndex =  pid * numSeqsPerProcessor;
1099                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
1100
1101                                 //do your part
1102                 set<string> cnames;
1103                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, cnames, MPIPos, inputFile, priority, false);
1104
1105                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); }  MPI_File_close(&outMPIAccnos);  return 0;  }
1106
1107                         }
1108                 }
1109
1110                 //close files
1111                 MPI_File_close(&inMPI);
1112                 MPI_File_close(&outMPI);
1113                 MPI_File_close(&outMPIAccnos);
1114                 if (trim) { MPI_File_close(&outMPIFasta); }
1115                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
1116
1117
1118 #endif
1119                 return numSeqs;
1120         }
1121         catch(exception& e) {
1122                 m->errorOut(e, "ChimeraSlayerCommand", "MPIExecute");
1123                 exit(1);
1124         }
1125 }
1126 //**********************************************************************************************************************
1127 int ChimeraSlayerCommand::deconvoluteResults(map<string, string>& uniqueNames, string outputFileName, string accnosFileName, string trimFileName){
1128         try {
1129                 map<string, string>::iterator itUnique;
1130                 int total = 0;
1131
1132         if (trimera) { //add in more potential uniqueNames
1133             map<string, string> newUniqueNames = uniqueNames;
1134             for (map<string, string>::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) {
1135                 newUniqueNames[(it->first)+"_LEFT"] = (it->first)+"_LEFT";
1136                 newUniqueNames[(it->first)+"_RIGHT"] = (it->first)+"_RIGHT";
1137             }
1138             uniqueNames = newUniqueNames;
1139             newUniqueNames.clear();
1140         }
1141
1142                 //edit accnos file
1143                 ifstream in2;
1144                 m->openInputFile(accnosFileName, in2, "no error");
1145
1146                 ofstream out2;
1147                 m->openOutputFile(accnosFileName+".temp", out2);
1148
1149                 string name; name = "";
1150                 set<string> chimerasInFile;
1151                 set<string>::iterator itChimeras;
1152
1153                 while (!in2.eof()) {
1154                         if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; }
1155
1156                         in2 >> name; m->gobble(in2);
1157
1158                         //find unique name
1159                         itUnique = uniqueNames.find(name);
1160
1161                         if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
1162                         else {
1163                                 itChimeras = chimerasInFile.find((itUnique->second));
1164
1165                                 if (itChimeras == chimerasInFile.end()) {
1166                                         out2 << itUnique->second << endl;
1167                                         chimerasInFile.insert((itUnique->second));
1168                                         total++;
1169                                 }
1170                         }
1171                 }
1172                 in2.close();
1173                 out2.close();
1174
1175                 m->mothurRemove(accnosFileName);
1176                 rename((accnosFileName+".temp").c_str(), accnosFileName.c_str());
1177
1178
1179                 //edit chimera file
1180                 ifstream in;
1181                 m->openInputFile(outputFileName, in);
1182
1183                 ofstream out;
1184                 m->openOutputFile(outputFileName+".temp", out); out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
1185
1186                 string rest, parent1, parent2, line;
1187                 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
1188                 set<string>::iterator itNames;
1189
1190                 //assumptions - in file each read will always look like...
1191                 /*
1192                  F11Fcsw_92754  no
1193                  F11Fcsw_63104  F11Fcsw_33372   F11Fcsw_37007   0.89441 80.4469 0.2     1.03727 93.2961 52.2    no      0-241   243-369
1194                  */
1195
1196                 //get header line
1197                 if (!in.eof()) {
1198                         line = m->getline(in); m->gobble(in);
1199                         out << line << endl;
1200                 }
1201
1202                 //for the chimera file, we want to make sure if any group finds a sequence to be chimeric then all groups do,
1203                 //so if this is a report that did not find it to be chimeric, but it appears in the accnos file,
1204                 //then ignore this report and continue until we find the report that found it to be chimeric
1205
1206                 while (!in.eof()) {
1207
1208                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove((outputFileName+".temp")); return 0; }
1209
1210                         in >> name;             m->gobble(in);
1211                         in >> parent1;  m->gobble(in);
1212
1213                         if (name == "Name") { //name = "Name" because we append the header line each time we add results from the groups
1214                                 line = m->getline(in); m->gobble(in);
1215                         }else {
1216                                 if (parent1 == "no") {
1217                                         //find unique name
1218                                         itUnique = uniqueNames.find(name);
1219
1220                                         if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
1221                                         else {
1222                                                 //is this sequence really not chimeric??
1223                                                 itChimeras = chimerasInFile.find(itUnique->second);
1224
1225                                                 if (itChimeras == chimerasInFile.end()) {
1226                                                         //is this sequence not already in the file
1227                                                         itNames = namesInFile.find((itUnique->second));
1228
1229                                                         if (itNames == namesInFile.end()) { out << itUnique->second << '\t' << "no" << endl; namesInFile.insert(itUnique->second); }
1230                                                 }
1231                                         }
1232                                 }else { //read the rest of the line
1233                                         double DivQLAQRB,PerIDQLAQRB,BootStrapA,DivQLBQRA,PerIDQLBQRA,BootStrapB;
1234                                         string flag, range1, range2;
1235                                         bool print = false;
1236                                         in >> parent2 >> DivQLAQRB >> PerIDQLAQRB >> BootStrapA >> DivQLBQRA >> PerIDQLBQRA >> BootStrapB >> flag >> range1 >> range2;  m->gobble(in);
1237
1238                                         //find unique name
1239                                         itUnique = uniqueNames.find(name);
1240
1241                                         if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
1242                                         else {
1243                                                 name = itUnique->second;
1244                                                 //is this name already in the file
1245                                                 itNames = namesInFile.find((name));
1246
1247                                                 if (itNames == namesInFile.end()) { //no not in file
1248                                                         if (flag == "no") { //are you really a no??
1249                                                                 //is this sequence really not chimeric??
1250                                                                 itChimeras = chimerasInFile.find(name);
1251
1252                                                                 //then you really are a no so print, otherwise skip
1253                                                                 if (itChimeras == chimerasInFile.end()) { print = true; }
1254
1255                                                         }else{ print = true; }
1256                                                 }
1257                                         }
1258
1259                                         if (print) {
1260                                                 out << name << '\t';
1261
1262                                                 namesInFile.insert(name);
1263
1264                                                 //output parent1's name
1265                                                 itUnique = uniqueNames.find(parent1);
1266                                                 if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parentA "+ parent1 + "."); m->mothurOutEndLine(); m->control_pressed = true; }
1267                                                 else { out << itUnique->second << '\t'; }
1268
1269                                                 //output parent2's name
1270                                                 itUnique = uniqueNames.find(parent2);
1271                                                 if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parentA "+ parent2 + "."); m->mothurOutEndLine(); m->control_pressed = true; }
1272                                                 else { out << itUnique->second << '\t'; }
1273
1274                                                 out << DivQLAQRB << '\t' << PerIDQLAQRB << '\t' << BootStrapA << '\t' << DivQLBQRA << '\t' << PerIDQLBQRA << '\t' << BootStrapB << '\t' << flag << '\t' << range1 << '\t' << range2 << endl;
1275                                         }
1276                                 }
1277                         }
1278                 }
1279                 in.close();
1280                 out.close();
1281
1282                 m->mothurRemove(outputFileName);
1283                 rename((outputFileName+".temp").c_str(), outputFileName.c_str());
1284
1285                 //edit fasta file
1286                 if (trim) {
1287                         ifstream in3;
1288                         m->openInputFile(trimFileName, in3);
1289
1290                         ofstream out3;
1291                         m->openOutputFile(trimFileName+".temp", out3);
1292
1293                         namesInFile.clear();
1294
1295                         while (!in3.eof()) {
1296                                 if (m->control_pressed) { in3.close(); out3.close(); m->mothurRemove(outputFileName); m->mothurRemove(accnosFileName); m->mothurRemove((trimFileName+".temp")); return 0; }
1297
1298                                 Sequence seq(in3); m->gobble(in3);
1299
1300                                 if (seq.getName() != "") {
1301                                         //find unique name
1302                                         itUnique = uniqueNames.find(seq.getName());
1303
1304                                         if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find "+ seq.getName() + "."); m->mothurOutEndLine(); m->control_pressed = true; }
1305                                         else {
1306                                                 itNames = namesInFile.find((itUnique->second));
1307
1308                                                 if (itNames == namesInFile.end()) {
1309                                                         seq.printSequence(out3);
1310                                                 }
1311                                         }
1312                                 }
1313                         }
1314                         in3.close();
1315                         out3.close();
1316
1317                         m->mothurRemove(trimFileName);
1318                         rename((trimFileName+".temp").c_str(), trimFileName.c_str());
1319                 }
1320
1321                 return total;
1322         }
1323         catch(exception& e) {
1324                 m->errorOut(e, "ChimeraSlayerCommand", "deconvoluteResults");
1325                 exit(1);
1326         }
1327 }
1328 //**********************************************************************************************************************
1329 int ChimeraSlayerCommand::setUpForSelfReference(SequenceParser*& parser, map<string, string>& fileGroup, map<string, map<string, int> >& fileToPriority, int s){
1330         try {
1331                 fileGroup.clear();
1332                 fileToPriority.clear();
1333
1334                 string nameFile = "";
1335                 if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
1336                         nameFile = nameFileNames[s];
1337                 }else {  nameFile = getNamesFile(fastaFileNames[s]); }
1338
1339                 //you provided a groupfile
1340                 string groupFile = "";
1341                 if (groupFileNames.size() != 0) { groupFile = groupFileNames[s]; }
1342
1343                 if (groupFile == "") {
1344                         if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
1345
1346                         //sort fastafile by abundance, returns new sorted fastafile name
1347                         m->mothurOut("Sorting fastafile according to abundance..."); cout.flush();
1348                         priority = sortFastaFile(fastaFileNames[s], nameFile);
1349                         m->mothurOut("Done."); m->mothurOutEndLine();
1350
1351                         fileToPriority[fastaFileNames[s]] = priority;
1352                         fileGroup[fastaFileNames[s]] = "noGroup";
1353                 }else {
1354                         //Parse sequences by group
1355                         parser = new SequenceParser(groupFile, fastaFileNames[s], nameFile);
1356                         vector<string> groups = parser->getNamesOfGroups();
1357
1358                         for (int i = 0; i < groups.size(); i++) {
1359                                 vector<Sequence> thisGroupsSeqs = parser->getSeqs(groups[i]);
1360                                 map<string, string> thisGroupsMap = parser->getNameMap(groups[i]);
1361                 group2NameMap[groups[i]] = thisGroupsMap;
1362                                 string newFastaFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + groups[i] + "-sortedTemp.fasta";
1363                                 priority = sortFastaFile(thisGroupsSeqs, thisGroupsMap, newFastaFile);
1364                                 fileToPriority[newFastaFile] = priority;
1365                                 fileGroup[newFastaFile] = groups[i];
1366                         }
1367                 }
1368
1369
1370                 return 0;
1371         }
1372         catch(exception& e) {
1373                 m->errorOut(e, "ChimeraSlayerCommand", "setUpForSelfReference");
1374                 exit(1);
1375         }
1376 }
1377 //**********************************************************************************************************************
1378 int ChimeraSlayerCommand::setUpForSelfReference(SequenceCountParser*& parser, map<string, string>& fileGroup, map<string, map<string, int> >& fileToPriority, int s){
1379         try {
1380                 fileGroup.clear();
1381                 fileToPriority.clear();
1382
1383                 string nameFile = "";
1384                 if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
1385                         nameFile = nameFileNames[s];
1386                 }else {  m->control_pressed = true; return 0; }
1387
1388                 CountTable ct;
1389                 if (!ct.testGroups(nameFile)) {
1390                         if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
1391
1392                         //sort fastafile by abundance, returns new sorted fastafile name
1393                         m->mothurOut("Sorting fastafile according to abundance..."); cout.flush();
1394                         priority = sortFastaFile(fastaFileNames[s], nameFile);
1395                         m->mothurOut("Done."); m->mothurOutEndLine();
1396
1397                         fileToPriority[fastaFileNames[s]] = priority;
1398                         fileGroup[fastaFileNames[s]] = "noGroup";
1399                 }else {
1400                         //Parse sequences by group
1401                         parser = new SequenceCountParser(nameFile, fastaFileNames[s]);
1402                         vector<string> groups = parser->getNamesOfGroups();
1403
1404                         for (int i = 0; i < groups.size(); i++) {
1405                                 vector<Sequence> thisGroupsSeqs = parser->getSeqs(groups[i]);
1406                                 map<string, int> thisGroupsMap = parser->getCountTable(groups[i]);
1407                                 string newFastaFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + groups[i] + "-sortedTemp.fasta";
1408                                 sortFastaFile(thisGroupsSeqs, thisGroupsMap, newFastaFile);
1409                                 fileToPriority[newFastaFile] = thisGroupsMap;
1410                                 fileGroup[newFastaFile] = groups[i];
1411                         }
1412                 }
1413
1414
1415                 return 0;
1416         }
1417         catch(exception& e) {
1418                 m->errorOut(e, "ChimeraSlayerCommand", "setUpForSelfReference");
1419                 exit(1);
1420         }
1421 }
1422 //**********************************************************************************************************************
1423 string ChimeraSlayerCommand::getNamesFile(string& inputFile){
1424         try {
1425                 string nameFile = "";
1426
1427                 m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine();
1428
1429                 //use unique.seqs to create new name and fastafile
1430                 string inputString = "fasta=" + inputFile;
1431                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
1432                 m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
1433                 m->mothurCalling = true;
1434
1435                 Command* uniqueCommand = new DeconvoluteCommand(inputString);
1436                 uniqueCommand->execute();
1437
1438                 map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
1439
1440                 delete uniqueCommand;
1441                 m->mothurCalling = false;
1442                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
1443
1444                 nameFile = filenames["name"][0];
1445                 inputFile = filenames["fasta"][0];
1446
1447                 return nameFile;
1448         }
1449         catch(exception& e) {
1450                 m->errorOut(e, "ChimeraSlayerCommand", "getNamesFile");
1451                 exit(1);
1452         }
1453 }
1454 //**********************************************************************************************************************
1455
1456 int ChimeraSlayerCommand::driverGroups(string outputFName, string accnos, string fasta, map<string, map<string, int> >& fileToPriority, map<string, string>& fileGroup, string countlist){
1457         try {
1458                 int totalSeqs = 0;
1459         ofstream outCountList;
1460
1461         if (hasCount && dups) { m->openOutputFile(countlist, outCountList); }
1462
1463                 for (map<string, map<string, int> >::iterator itFile = fileToPriority.begin(); itFile != fileToPriority.end(); itFile++) {
1464
1465                         if (m->control_pressed) {  return 0;  }
1466
1467                         int start = time(NULL);
1468                         string thisFastaName = itFile->first;
1469                         map<string, int> thisPriority = itFile->second;
1470                         string thisoutputFileName = outputDir + m->getRootName(m->getSimpleName(thisFastaName)) + fileGroup[thisFastaName] + "slayer.chimera";
1471                         string thisaccnosFileName = outputDir + m->getRootName(m->getSimpleName(thisFastaName)) + fileGroup[thisFastaName] + "slayer.accnos";
1472                         string thistrimFastaFileName = outputDir + m->getRootName(m->getSimpleName(thisFastaName)) + fileGroup[thisFastaName] + "slayer.fasta";
1473
1474                         m->mothurOutEndLine(); m->mothurOut("Checking sequences from group: " + fileGroup[thisFastaName] + "."); m->mothurOutEndLine();
1475
1476                         lines.clear();
1477 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1478                         int proc = 1;
1479                         vector<unsigned long long> positions = m->divideFile(thisFastaName, proc);
1480                         lines.push_back(linePair(positions[0], positions[1]));
1481 #else
1482                         lines.push_back(linePair(0, 1000));
1483 #endif
1484                         int numSeqs = driver(lines[0], thisoutputFileName, thisFastaName, thisaccnosFileName, thistrimFastaFileName, thisPriority);
1485
1486             //if we provided a count file with group info and set dereplicate=t, then we want to create a *.pick.count_table
1487             //This table will zero out group counts for seqs determined to be chimeric by that group.
1488             if (dups) {
1489                 if (!m->isBlank(thisaccnosFileName)) {
1490                     ifstream in;
1491                     m->openInputFile(thisaccnosFileName, in);
1492                     string name;
1493                     if (hasCount) {
1494                         while (!in.eof()) {
1495                             in >> name; m->gobble(in);
1496                             outCountList << name << '\t' << fileGroup[thisFastaName] << endl;
1497                         }
1498                         in.close();
1499                     }else {
1500                         map<string, map<string, string> >::iterator itGroupNameMap = group2NameMap.find(fileGroup[thisFastaName]);
1501                         if (itGroupNameMap != group2NameMap.end()) {
1502                             map<string, string> thisnamemap = itGroupNameMap->second;
1503                             map<string, string>::iterator itN;
1504                             ofstream out;
1505                             m->openOutputFile(thisaccnosFileName+".temp", out);
1506                             while (!in.eof()) {
1507                                 in >> name; m->gobble(in);
1508                                 itN = thisnamemap.find(name);
1509                                 if (itN != thisnamemap.end()) {
1510                                     vector<string> tempNames; m->splitAtComma(itN->second, tempNames);
1511                                     for (int j = 0; j < tempNames.size(); j++) { out << tempNames[j] << endl; }
1512
1513                                 }else { m->mothurOut("[ERROR]: parsing cannot find " + name + ".\n"); m->control_pressed = true; }
1514                             }
1515                             out.close();
1516                             in.close();
1517                             m->renameFile(thisaccnosFileName+".temp", thisaccnosFileName);
1518                         }else { m->mothurOut("[ERROR]: parsing cannot find " + fileGroup[thisFastaName] + ".\n"); m->control_pressed = true; }
1519                     }
1520
1521                 }
1522             }
1523
1524                         //append files
1525                         m->appendFiles(thisoutputFileName, outputFName); m->mothurRemove(thisoutputFileName);
1526                         m->appendFiles(thisaccnosFileName, accnos); m->mothurRemove(thisaccnosFileName);
1527                         if (trim) { m->appendFiles(thistrimFastaFileName, fasta); m->mothurRemove(thistrimFastaFileName); }
1528                         m->mothurRemove(thisFastaName);
1529
1530                         totalSeqs += numSeqs;
1531
1532                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences from group " + fileGroup[thisFastaName] + ".");     m->mothurOutEndLine();
1533                 }
1534
1535         if (hasCount && dups) { outCountList.close(); }
1536
1537                 return totalSeqs;
1538         }
1539         catch(exception& e) {
1540                 m->errorOut(e, "ChimeraSlayerCommand", "driverGroups");
1541                 exit(1);
1542         }
1543 }
1544 /**************************************************************************************************/
1545 int ChimeraSlayerCommand::createProcessesGroups(string outputFName, string accnos, string fasta, map<string, map<string, int> >& fileToPriority, map<string, string>& fileGroup, string countlist, string countFile) {
1546         try {
1547                 int process = 1;
1548                 int num = 0;
1549                 processIDS.clear();
1550
1551                 if (fileToPriority.size() < processors) { processors = fileToPriority.size(); }
1552
1553         CountTable newCount;
1554         if (hasCount && dups) { newCount.readTable(countFile, true); }
1555
1556                 int groupsPerProcessor = fileToPriority.size() / processors;
1557                 int remainder = fileToPriority.size() % processors;
1558
1559                 vector< map<string, map<string, int> > > breakUp;
1560
1561                 for (int i = 0; i < processors; i++) {
1562                         map<string, map<string, int> > thisFileToPriority;
1563                         map<string, map<string, int> >::iterator itFile;
1564                         int count = 0;
1565                         int enough = groupsPerProcessor;
1566                         if (i == 0) { enough = groupsPerProcessor + remainder; }
1567
1568                         for (itFile = fileToPriority.begin(); itFile != fileToPriority.end();) {
1569                                 thisFileToPriority[itFile->first] = itFile->second;
1570                                 fileToPriority.erase(itFile++);
1571                                 count++;
1572                                 if (count == enough) { break; }
1573                         }
1574                         breakUp.push_back(thisFileToPriority);
1575                 }
1576
1577 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1578                 //loop through and create all the processes you want
1579                 while (process != processors) {
1580                         int pid = fork();
1581
1582                         if (pid > 0) {
1583                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1584                                 process++;
1585                         }else if (pid == 0){
1586                                 num = driverGroups(outputFName + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp", breakUp[process], fileGroup, accnos + toString(getpid()) + ".byCount");
1587
1588                                 //pass numSeqs to parent
1589                                 ofstream out;
1590                                 string tempFile = outputFName + toString(getpid()) + ".num.temp";
1591                                 m->openOutputFile(tempFile, out);
1592                                 out << num << endl;
1593                                 out.close();
1594                                 exit(0);
1595                         }else {
1596                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1597                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1598                                 exit(0);
1599                         }
1600                 }
1601
1602                 num = driverGroups(outputFName, accnos, fasta, breakUp[0], fileGroup, accnos + ".byCount");
1603
1604                 //force parent to wait until all the processes are done
1605                 for (int i=0;i<processors;i++) {
1606                         int temp = processIDS[i];
1607                         wait(&temp);
1608                 }
1609
1610                 for (int i = 0; i < processIDS.size(); i++) {
1611                         ifstream in;
1612                         string tempFile =  outputFName + toString(processIDS[i]) + ".num.temp";
1613                         m->openInputFile(tempFile, in);
1614                         if (!in.eof()) { int tempNum = 0;  in >> tempNum; num += tempNum; }
1615                         in.close(); m->mothurRemove(tempFile);
1616                 }
1617 #else
1618
1619                 //////////////////////////////////////////////////////////////////////////////////////////////////////
1620                 //Windows version shared memory, so be careful when passing variables through the slayerData struct.
1621                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
1622                 //////////////////////////////////////////////////////////////////////////////////////////////////////
1623
1624                 vector<slayerData*> pDataArray;
1625                 DWORD   dwThreadIdArray[processors-1];
1626                 HANDLE  hThreadArray[processors-1];
1627
1628                 //Create processor worker threads.
1629                 for(int i=1; i<processors; i++ ){
1630                         string extension = toString(i) + ".temp";
1631                         slayerData* tempslayer = new slayerData(group2NameMap, hasCount, dups, (accnos + toString(i) +".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);
1632                         pDataArray.push_back(tempslayer);
1633                         processIDS.push_back(i);
1634
1635                         //MySlayerThreadFunction is in header. It must be global or static to work with the threads.
1636                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
1637                         hThreadArray[i-1] = CreateThread(NULL, 0, MySlayerGroupThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
1638                 }
1639
1640                 num = driverGroups(outputFName, accnos, fasta, breakUp[0], fileGroup, accnos + ".byCount");
1641
1642                 //Wait until all threads have terminated.
1643                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
1644
1645                 //Close all thread handles and free memory allocations.
1646                 for(int i=0; i < pDataArray.size(); i++){
1647             if (pDataArray[i]->fileToPriority.size() != pDataArray[i]->end) {
1648                 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;
1649             }
1650                         num += pDataArray[i]->count;
1651                         CloseHandle(hThreadArray[i]);
1652                         delete pDataArray[i];
1653                 }
1654 #endif
1655         //read my own
1656         if (hasCount && dups) {
1657             if (!m->isBlank(accnos + ".byCount")) {
1658                 ifstream in2;
1659                 m->openInputFile(accnos + ".byCount", in2);
1660
1661                 string name, group;
1662                 while (!in2.eof()) {
1663                     in2 >> name >> group; m->gobble(in2);
1664                     newCount.setAbund(name, group, 0);
1665                 }
1666                 in2.close();
1667             }
1668             m->mothurRemove(accnos + ".byCount");
1669         }
1670
1671
1672                 //append output files
1673                 for(int i=0;i<processIDS.size();i++){
1674                         m->appendFiles((outputFName + toString(processIDS[i]) + ".temp"), outputFName);
1675                         m->mothurRemove((outputFName + toString(processIDS[i]) + ".temp"));
1676
1677                         m->appendFiles((accnos + toString(processIDS[i]) + ".temp"), accnos);
1678                         m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));
1679
1680                         if (trim) {
1681                                 m->appendFiles((fasta + toString(processIDS[i]) + ".temp"), fasta);
1682                                 m->mothurRemove((fasta + toString(processIDS[i]) + ".temp"));
1683                         }
1684
1685             if (hasCount && dups) {
1686                 if (!m->isBlank(accnos + toString(processIDS[i]) + ".byCount")) {
1687                     ifstream in2;
1688                     m->openInputFile(accnos  + toString(processIDS[i]) + ".byCount", in2);
1689
1690                     string name, group;
1691                     while (!in2.eof()) {
1692                         in2 >> name >> group; m->gobble(in2);
1693                         newCount.setAbund(name, group, 0);
1694                     }
1695                     in2.close();
1696                 }
1697                 m->mothurRemove(accnos + toString(processIDS[i]) + ".byCount");
1698             }
1699
1700                 }
1701
1702         //print new *.pick.count_table
1703         if (hasCount && dups) {  newCount.printTable(countlist);   }
1704
1705                 return num;
1706         }
1707         catch(exception& e) {
1708                 m->errorOut(e, "ChimeraSlayerCommand", "createProcessesGroups");
1709                 exit(1);
1710         }
1711 }
1712 //**********************************************************************************************************************
1713
1714 int ChimeraSlayerCommand::driver(linePair filePos, string outputFName, string filename, string accnos, string fasta, map<string, int>& priority){
1715         try {
1716
1717                 Chimera* chimera;
1718                 if (templatefile != "self") { //you want to run slayer with a reference template
1719                         chimera = new ChimeraSlayer(filename, templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand());
1720                 }else {
1721                         chimera = new ChimeraSlayer(filename, templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand());
1722                 }
1723
1724                 if (m->control_pressed) { delete chimera; return 0; }
1725
1726                 if (chimera->getUnaligned()) { delete chimera; m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
1727                 templateSeqsLength = chimera->getLength();
1728
1729                 ofstream out;
1730                 m->openOutputFile(outputFName, out);
1731
1732                 ofstream out2;
1733                 m->openOutputFile(accnos, out2);
1734
1735                 ofstream out3;
1736                 if (trim) {  m->openOutputFile(fasta, out3); }
1737
1738                 ifstream inFASTA;
1739                 m->openInputFile(filename, inFASTA);
1740
1741                 inFASTA.seekg(filePos.start);
1742
1743                 if (filePos.start == 0) { chimera->printHeader(out); }
1744
1745                 bool done = false;
1746                 int count = 0;
1747
1748                 while (!done) {
1749
1750                         if (m->control_pressed) {       delete chimera; out.close(); out2.close(); if (trim) { out3.close(); } inFASTA.close(); return 1;       }
1751
1752                         Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
1753                         string candidateAligned = candidateSeq->getAligned();
1754
1755                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
1756                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
1757                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
1758                                 }else{
1759                                         //find chimeras
1760                                         chimera->getChimeras(candidateSeq);
1761
1762                                         if (m->control_pressed) {       delete chimera; delete candidateSeq; return 1;  }
1763
1764                                         //if you are not chimeric, then check each half
1765                                         data_results wholeResults = chimera->getResults();
1766
1767                                         //determine if we need to split
1768                                         bool isChimeric = false;
1769
1770                                         if (wholeResults.flag == "yes") {
1771                                                 string chimeraFlag = "no";
1772                                                 if(  (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
1773                                                    ||
1774                                                    (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
1775
1776
1777                                                 if (chimeraFlag == "yes") {
1778                                                         if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
1779                                                 }
1780                                         }
1781
1782                                         if ((!isChimeric) && trimera) {
1783
1784                                                 //split sequence in half by bases
1785                                                 string leftQuery, rightQuery;
1786                                                 Sequence tempSeq(candidateSeq->getName(), candidateAligned);
1787                                                 divideInHalf(tempSeq, leftQuery, rightQuery);
1788
1789                                                 //run chimeraSlayer on each piece
1790                                                 Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
1791                                                 Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
1792
1793                                                 //find chimeras
1794                                                 chimera->getChimeras(left);
1795                                                 data_results leftResults = chimera->getResults();
1796
1797                                                 chimera->getChimeras(right);
1798                                                 data_results rightResults = chimera->getResults();
1799
1800                                                 //if either piece is chimeric then report
1801                                                 Sequence trimmed = chimera->print(out, out2, leftResults, rightResults);
1802                                                 if (trim) { trimmed.printSequence(out3);  }
1803
1804                                                 delete left; delete right;
1805
1806                                         }else { //already chimeric
1807                                                 //print results
1808                                                 Sequence trimmed = chimera->print(out, out2);
1809                                                 if (trim) { trimmed.printSequence(out3);  }
1810                                         }
1811
1812
1813                                 }
1814                                 count++;
1815                         }
1816
1817                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1818                                 unsigned long long pos = inFASTA.tellg();
1819                                 if ((pos == -1) || (pos >= filePos.end)) { break; }
1820                         #else
1821                                 if (inFASTA.eof()) { break; }
1822                         #endif
1823
1824                         delete candidateSeq;
1825                         //report progress
1826                         if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");             }
1827                 }
1828                 //report progress
1829                 if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count)+ "\n");              }
1830
1831                 int numNoParents = chimera->getNumNoParents();
1832                 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(); }
1833
1834                 out.close();
1835                 out2.close();
1836                 if (trim) { out3.close(); }
1837                 inFASTA.close();
1838                 delete chimera;
1839
1840                 return count;
1841
1842
1843         }
1844         catch(exception& e) {
1845                 m->errorOut(e, "ChimeraSlayerCommand", "driver");
1846                 exit(1);
1847         }
1848 }
1849 //**********************************************************************************************************************
1850 #ifdef USE_MPI
1851 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){
1852         try {
1853                 MPI_Status status;
1854                 int pid;
1855                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
1856
1857                 Chimera* chimera;
1858                 if (templatefile != "self") { //you want to run slayer with a reference template
1859                         chimera = new ChimeraSlayer(filename, templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand());
1860                 }else {
1861                         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);
1862                 }
1863
1864                 if (m->control_pressed) { delete chimera; return 0; }
1865
1866                 if (chimera->getUnaligned()) { delete chimera; m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
1867                 templateSeqsLength = chimera->getLength();
1868
1869                 for(int i=0;i<num;i++){
1870
1871                         if (m->control_pressed) {       delete chimera; return 1;       }
1872
1873                         //read next sequence
1874                         int length = MPIPos[start+i+1] - MPIPos[start+i];
1875
1876                         char* buf4 = new char[length];
1877                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
1878
1879                         string tempBuf = buf4;
1880                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
1881                         istringstream iss (tempBuf,istringstream::in);
1882
1883                         delete buf4;
1884
1885                         Sequence* candidateSeq = new Sequence(iss);  m->gobble(iss);
1886                         string candidateAligned = candidateSeq->getAligned();
1887
1888                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
1889
1890                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
1891                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
1892                                 }else{
1893
1894                                         //find chimeras
1895                                         chimera->getChimeras(candidateSeq);
1896
1897                                         if (m->control_pressed) {       delete chimera; delete candidateSeq; return 1;  }
1898
1899                                         //if you are not chimeric, then check each half
1900                                         data_results wholeResults = chimera->getResults();
1901
1902                                         //determine if we need to split
1903                                         bool isChimeric = false;
1904
1905                                         if (wholeResults.flag == "yes") {
1906                                                 string chimeraFlag = "no";
1907                                                 if(  (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
1908                                                    ||
1909                                                    (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
1910
1911
1912                                                 if (chimeraFlag == "yes") {
1913                                                         if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
1914                                                 }
1915                                         }
1916
1917                                         if ((!isChimeric) && trimera) {
1918                                                 //split sequence in half by bases
1919                                                 string leftQuery, rightQuery;
1920                                                 Sequence tempSeq(candidateSeq->getName(), candidateAligned);
1921                                                 divideInHalf(tempSeq, leftQuery, rightQuery);
1922
1923                                                 //run chimeraSlayer on each piece
1924                                                 Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
1925                                                 Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
1926
1927                                                 //find chimeras
1928                                                 chimera->getChimeras(left);
1929                                                 data_results leftResults = chimera->getResults();
1930
1931                                                 chimera->getChimeras(right);
1932                                                 data_results rightResults = chimera->getResults();
1933
1934                                                 //if either piece is chimeric then report
1935                         bool flag = false;
1936                                                 Sequence trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults, flag);
1937                         if (flag) { cnames.insert(candidateSeq->getName()); }
1938
1939                                                 if (trim) {
1940                                                         string outputString = ">" + trimmed.getName() + "\n" + trimmed.getAligned() + "\n";
1941
1942                                                         //write to accnos file
1943                                                         int length = outputString.length();
1944                                                         char* buf2 = new char[length];
1945                                                         memcpy(buf2, outputString.c_str(), length);
1946
1947                                                         MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
1948                                                         delete buf2;
1949                                                 }
1950
1951                                                 delete left; delete right;
1952
1953                                         }else {
1954                                                 //print results
1955                                                 Sequence trimmed = chimera->print(outMPI, outAccMPI);
1956                         cnames.insert(candidateSeq->getName());
1957
1958                                                 if (trim) {
1959                                                         string outputString = ">" + trimmed.getName() + "\n" + trimmed.getAligned() + "\n";
1960
1961                                                         //write to accnos file
1962                                                         int length = outputString.length();
1963                                                         char* buf2 = new char[length];
1964                                                         memcpy(buf2, outputString.c_str(), length);
1965
1966                                                         MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
1967                                                         delete buf2;
1968                                                 }
1969                                         }
1970
1971                                 }
1972                         }
1973                         delete candidateSeq;
1974
1975                         //report progress
1976                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;                }
1977                 }
1978                 //report progress
1979                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl;         }
1980
1981                 int numNoParents = chimera->getNumNoParents();
1982                 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; }
1983
1984                 delete chimera;
1985                 return 0;
1986         }
1987         catch(exception& e) {
1988                 m->errorOut(e, "ChimeraSlayerCommand", "driverMPI");
1989                 exit(1);
1990         }
1991 }
1992 #endif
1993
1994 /**************************************************************************************************/
1995
1996 int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos, string fasta, map<string, int>& thisPriority) {
1997         try {
1998                 int process = 0;
1999                 int num = 0;
2000                 processIDS.clear();
2001
2002 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
2003                 //loop through and create all the processes you want
2004                 while (process != processors) {
2005                         int pid = fork();
2006
2007                         if (pid > 0) {
2008                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
2009                                 process++;
2010                         }else if (pid == 0){
2011                                 num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp", thisPriority);
2012
2013                                 //pass numSeqs to parent
2014                                 ofstream out;
2015                                 string tempFile = outputFileName + toString(getpid()) + ".num.temp";
2016                                 m->openOutputFile(tempFile, out);
2017                                 out << num << endl;
2018                                 out.close();
2019                                 exit(0);
2020                         }else {
2021                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
2022                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
2023                                 exit(0);
2024                         }
2025                 }
2026
2027                 //force parent to wait until all the processes are done
2028                 for (int i=0;i<processors;i++) {
2029                         int temp = processIDS[i];
2030                         wait(&temp);
2031                 }
2032
2033                 for (int i = 0; i < processIDS.size(); i++) {
2034                         ifstream in;
2035                         string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
2036                         m->openInputFile(tempFile, in);
2037                         if (!in.eof()) { int tempNum = 0;  in >> tempNum; num += tempNum; }
2038                         in.close(); m->mothurRemove(tempFile);
2039                 }
2040 #else
2041
2042                 //////////////////////////////////////////////////////////////////////////////////////////////////////
2043                 //Windows version shared memory, so be careful when passing variables through the slayerData struct.
2044                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
2045                 //////////////////////////////////////////////////////////////////////////////////////////////////////
2046
2047                 vector<slayerData*> pDataArray;
2048                 DWORD   dwThreadIdArray[processors];
2049                 HANDLE  hThreadArray[processors];
2050
2051                 //Create processor worker threads.
2052                 for( int i=0; i<processors; i++ ){
2053                         string extension = toString(i) + ".temp";
2054                         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);
2055                         pDataArray.push_back(tempslayer);
2056                         processIDS.push_back(i);
2057
2058                         //MySlayerThreadFunction is in header. It must be global or static to work with the threads.
2059                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
2060                         hThreadArray[i] = CreateThread(NULL, 0, MySlayerThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
2061                 }
2062
2063                 //Wait until all threads have terminated.
2064                 WaitForMultipleObjects(processors, hThreadArray, TRUE, INFINITE);
2065
2066                 //Close all thread handles and free memory allocations.
2067                 for(int i=0; i < pDataArray.size(); i++){
2068                         num += pDataArray[i]->count;
2069                         CloseHandle(hThreadArray[i]);
2070                         delete pDataArray[i];
2071                 }
2072 #endif
2073
2074                 rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
2075                 rename((accnos + toString(processIDS[0]) + ".temp").c_str(), accnos.c_str());
2076                 if (trim) {  rename((fasta + toString(processIDS[0]) + ".temp").c_str(), fasta.c_str()); }
2077
2078                 //append output files
2079                 for(int i=1;i<processIDS.size();i++){
2080                         m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
2081                         m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp"));
2082
2083                         m->appendFiles((accnos + toString(processIDS[i]) + ".temp"), accnos);
2084                         m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));
2085
2086                         if (trim) {
2087                                 m->appendFiles((fasta + toString(processIDS[i]) + ".temp"), fasta);
2088                                 m->mothurRemove((fasta + toString(processIDS[i]) + ".temp"));
2089                         }
2090                 }
2091
2092
2093                 return num;
2094         }
2095         catch(exception& e) {
2096                 m->errorOut(e, "ChimeraSlayerCommand", "createProcesses");
2097                 exit(1);
2098         }
2099 }
2100
2101 /**************************************************************************************************/
2102
2103 int ChimeraSlayerCommand::divideInHalf(Sequence querySeq, string& leftQuery, string& rightQuery) {
2104         try {
2105
2106                 string queryUnAligned = querySeq.getUnaligned();
2107                 int numBases = int(queryUnAligned.length() * 0.5);
2108
2109                 string queryAligned = querySeq.getAligned();
2110                 leftQuery = querySeq.getAligned();
2111                 rightQuery = querySeq.getAligned();
2112
2113                 int baseCount = 0;
2114                 int leftSpot = 0;
2115                 for (int i = 0; i < queryAligned.length(); i++) {
2116                         //if you are a base
2117                         if (isalpha(queryAligned[i])) {
2118                                 baseCount++;
2119                         }
2120
2121                         //if you have half
2122                         if (baseCount >= numBases) {  leftSpot = i; break; } //first half
2123                 }
2124
2125                 //blank out right side
2126                 for (int i = leftSpot; i < leftQuery.length(); i++) { leftQuery[i] = '.'; }
2127
2128                 //blank out left side
2129                 for (int i = 0; i < leftSpot; i++) { rightQuery[i] = '.'; }
2130
2131                 return 0;
2132
2133         }
2134         catch(exception& e) {
2135                 m->errorOut(e, "ChimeraSlayerCommand", "divideInHalf");
2136                 exit(1);
2137         }
2138 }
2139 /**************************************************************************************************/
2140 map<string, int> ChimeraSlayerCommand::sortFastaFile(string fastaFile, string nameFile) {
2141         try {
2142                 map<string, int> nameAbund;
2143
2144                 //read through fastafile and store info
2145                 map<string, string> seqs;
2146                 ifstream in;
2147                 m->openInputFile(fastaFile, in);
2148
2149                 while (!in.eof()) {
2150
2151                         if (m->control_pressed) { in.close(); return nameAbund; }
2152
2153                         Sequence seq(in); m->gobble(in);
2154                         seqs[seq.getName()] = seq.getAligned();
2155                 }
2156
2157                 in.close();
2158
2159                 //read namefile or countfile
2160                 vector<seqPriorityNode> nameMapCount;
2161         int error;
2162         if (hasCount) {
2163             CountTable ct;
2164             ct.readTable(nameFile, true);
2165
2166             for(map<string, string>::iterator it = seqs.begin(); it != seqs.end(); it++) {
2167                 int num = ct.getNumSeqs(it->first);
2168                 if (num == 0) { error = 1; }
2169                 else {
2170                     seqPriorityNode temp(num, it->second, it->first);
2171                     nameMapCount.push_back(temp);
2172                 }
2173             }
2174         }else { error = m->readNames(nameFile, nameMapCount, seqs); }
2175
2176                 if (m->control_pressed) { return nameAbund; }
2177
2178                 if (error == 1) { m->control_pressed = true; return nameAbund; }
2179                 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; }
2180
2181                 sort(nameMapCount.begin(), nameMapCount.end(), compareSeqPriorityNodes);
2182
2183                 string newFasta = fastaFile + ".temp";
2184                 ofstream out;
2185                 m->openOutputFile(newFasta, out);
2186
2187                 //print new file in order of
2188                 for (int i = 0; i < nameMapCount.size(); i++) {
2189                         out << ">" << nameMapCount[i].name << endl << nameMapCount[i].seq << endl;
2190                         nameAbund[nameMapCount[i].name] = nameMapCount[i].numIdentical;
2191                 }
2192                 out.close();
2193
2194                 rename(newFasta.c_str(), fastaFile.c_str());
2195
2196                 return nameAbund;
2197
2198         }
2199         catch(exception& e) {
2200                 m->errorOut(e, "ChimeraSlayerCommand", "sortFastaFile");
2201                 exit(1);
2202         }
2203 }
2204 /**************************************************************************************************/
2205 map<string, int> ChimeraSlayerCommand::sortFastaFile(vector<Sequence>& thisseqs, map<string, string>& nameMap, string newFile) {
2206         try {
2207                 map<string, int> nameAbund;
2208                 vector<seqPriorityNode> nameVector;
2209
2210                 //read through fastafile and store info
2211                 map<string, string> seqs;
2212
2213                 for (int i = 0; i < thisseqs.size(); i++) {
2214
2215                         if (m->control_pressed) { return nameAbund; }
2216
2217                         map<string, string>::iterator itNameMap = nameMap.find(thisseqs[i].getName());
2218
2219                         if (itNameMap == nameMap.end()){
2220                                 m->control_pressed = true;
2221                                 m->mothurOut("[ERROR]: " + thisseqs[i].getName() + " is in your fastafile, but is not in your namesfile, please correct."); m->mothurOutEndLine();
2222                         }else {
2223                                 int num = m->getNumNames(itNameMap->second);
2224
2225                                 seqPriorityNode temp(num, thisseqs[i].getAligned(), thisseqs[i].getName());
2226                                 nameVector.push_back(temp);
2227                         }
2228                 }
2229
2230                 //sort by num represented
2231                 sort(nameVector.begin(), nameVector.end(), compareSeqPriorityNodes);
2232
2233                 if (m->control_pressed) { return nameAbund; }
2234
2235                 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; }
2236
2237                 ofstream out;
2238                 m->openOutputFile(newFile, out);
2239
2240                 //print new file in order of
2241                 for (int i = 0; i < nameVector.size(); i++) {
2242                         out << ">" << nameVector[i].name << endl << nameVector[i].seq << endl;
2243                         nameAbund[nameVector[i].name] = nameVector[i].numIdentical;
2244                 }
2245                 out.close();
2246
2247                 return nameAbund;
2248
2249         }
2250         catch(exception& e) {
2251                 m->errorOut(e, "ChimeraSlayerCommand", "sortFastaFile");
2252                 exit(1);
2253         }
2254 }
2255 /**************************************************************************************************/
2256 int ChimeraSlayerCommand::sortFastaFile(vector<Sequence>& thisseqs, map<string, int>& countMap, string newFile) {
2257         try {
2258                 vector<seqPriorityNode> nameVector;
2259
2260                 //read through fastafile and store info
2261                 map<string, string> seqs;
2262
2263                 for (int i = 0; i < thisseqs.size(); i++) {
2264
2265                         if (m->control_pressed) { return 0; }
2266
2267                         map<string, int>::iterator itCountMap = countMap.find(thisseqs[i].getName());
2268
2269                         if (itCountMap == countMap.end()){
2270                                 m->control_pressed = true;
2271                                 m->mothurOut("[ERROR]: " + thisseqs[i].getName() + " is in your fastafile, but is not in your count file, please correct."); m->mothurOutEndLine();
2272                         }else {
2273                 seqPriorityNode temp(itCountMap->second, thisseqs[i].getAligned(), thisseqs[i].getName());
2274                                 nameVector.push_back(temp);
2275                         }
2276                 }
2277
2278                 //sort by num represented
2279                 sort(nameVector.begin(), nameVector.end(), compareSeqPriorityNodes);
2280
2281                 if (m->control_pressed) { return 0; }
2282
2283                 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; }
2284
2285                 ofstream out;
2286                 m->openOutputFile(newFile, out);
2287
2288                 //print new file in order of
2289                 for (int i = 0; i < nameVector.size(); i++) {
2290                         out << ">" << nameVector[i].name << endl << nameVector[i].seq << endl;
2291                 }
2292                 out.close();
2293
2294                 return 0;
2295
2296         }
2297         catch(exception& e) {
2298                 m->errorOut(e, "ChimeraSlayerCommand", "sortFastaFile");
2299                 exit(1);
2300         }
2301 }
2302 /**************************************************************************************************/
2303