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