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