chimeraperseuscommand.cpp

   1 /*
   2  *  chimeraperseuscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 10/26/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "chimeraperseuscommand.h"
  11 #include "deconvolutecommand.h"
  12 #include "sequence.hpp"
  13 #include "counttable.h"
  14 #include "sequencecountparser.h"
  15 //**********************************************************************************************************************
  16 vector<string> ChimeraPerseusCommand::setParameters(){
  17         try {
  18                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  19                 CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
  20         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
  21                 CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
  22                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  23                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  24                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  25                 CommandParameter pcutoff("cutoff", "Number", "", "0.5", "", "", "",false,false); parameters.push_back(pcutoff);
  26                 CommandParameter palpha("alpha", "Number", "", "-5.54", "", "", "",false,false); parameters.push_back(palpha);
  27                 CommandParameter pbeta("beta", "Number", "", "0.33", "", "", "",false,false); parameters.push_back(pbeta);
  28
  29                 vector<string> myArray;
  30                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  31                 return myArray;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "ChimeraPerseusCommand", "setParameters");
  35                 exit(1);
  36         }
  37 }
  38 //**********************************************************************************************************************
  39 string ChimeraPerseusCommand::getHelpString(){
  40         try {
  41                 string helpString = "";
  42                 helpString += "The chimera.perseus command reads a fastafile and namefile or countfile and outputs potentially chimeric sequences.\n";
  43                 helpString += "The chimera.perseus command parameters are fasta, name, group, cutoff, processors, alpha and beta.\n";
  44                 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";
  45                 helpString += "The name parameter allows you to provide a name file associated with your fasta file.\n";
  46         helpString += "The count parameter allows you to provide a count file associated with your fasta file. A count or name file is required. \n";
  47                 helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n";
  48                 helpString += "The group parameter allows you to provide a group file.  When checking sequences, only sequences from the same group as the query sequence will be used as the reference. \n";
  49                 helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
  50                 helpString += "The alpha parameter ....  The default is -5.54. \n";
  51                 helpString += "The beta parameter ....  The default is 0.33. \n";
  52                 helpString += "The cutoff parameter ....  The default is 0.50. \n";
  53                 helpString += "The chimera.perseus command should be in the following format: \n";
  54                 helpString += "chimera.perseus(fasta=yourFastaFile, name=yourNameFile) \n";
  55                 helpString += "Example: chimera.perseus(fasta=AD.align, name=AD.names) \n";
  56                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
  57                 return helpString;
  58         }
  59         catch(exception& e) {
  60                 m->errorOut(e, "ChimeraPerseusCommand", "getHelpString");
  61                 exit(1);
  62         }
  63 }
  64 //**********************************************************************************************************************
  65 string ChimeraPerseusCommand::getOutputFileNameTag(string type, string inputName=""){
  66         try {
  67         string outputFileName = "";
  68                 map<string, vector<string> >::iterator it;
  69
  70         //is this a type this command creates
  71         it = outputTypes.find(type);
  72         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  73         else {
  74             if (type == "chimera") {  outputFileName =  "perseus.chimeras"; }
  75             else if (type == "accnos") {  outputFileName =  "perseus.accnos"; }
  76             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  77         }
  78         return outputFileName;
  79         }
  80         catch(exception& e) {
  81                 m->errorOut(e, "ChimeraPerseusCommand", "getOutputFileNameTag");
  82                 exit(1);
  83         }
  84 }
  85 //**********************************************************************************************************************
  86 ChimeraPerseusCommand::ChimeraPerseusCommand(){
  87         try {
  88                 abort = true; calledHelp = true;
  89                 setParameters();
  90                 vector<string> tempOutNames;
  91                 outputTypes["chimera"] = tempOutNames;
  92                 outputTypes["accnos"] = tempOutNames;
  93         }
  94         catch(exception& e) {
  95                 m->errorOut(e, "ChimeraPerseusCommand", "ChimeraPerseusCommand");
  96                 exit(1);
  97         }
  98 }
  99 //***************************************************************************************************************
 100 ChimeraPerseusCommand::ChimeraPerseusCommand(string option)  {
 101         try {
 102                 abort = false; calledHelp = false;
 103         hasCount = false;
 104         hasName = false;
 105
 106                 //allow user to run help
 107                 if(option == "help") { help(); abort = true; calledHelp = true; }
 108                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 109
 110                 else {
 111                         vector<string> myArray = setParameters();
 112
 113                         OptionParser parser(option);
 114                         map<string,string> parameters = parser.getParameters();
 115
 116                         ValidParameters validParameter("chimera.perseus");
 117                         map<string,string>::iterator it;
 118
 119                         //check to make sure all parameters are valid for command
 120                         for (it = parameters.begin(); it != parameters.end(); it++) {
 121                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 122                         }
 123
 124                         vector<string> tempOutNames;
 125                         outputTypes["chimera"] = tempOutNames;
 126                         outputTypes["accnos"] = tempOutNames;
 127
 128                         //if the user changes the input directory command factory will send this info to us in the output parameter
 129                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 130                         if (inputDir == "not found"){   inputDir = "";          }
 131
 132                         //check for required parameters
 133                         fastafile = validParameter.validFile(parameters, "fasta", false);
 134                         if (fastafile == "not found") {
 135                                 //if there is a current fasta file, use it
 136                                 string filename = m->getFastaFile();
 137                                 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 138                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 139                         }else {
 140                                 m->splitAtDash(fastafile, fastaFileNames);
 141
 142                                 //go through files and make sure they are good, if not, then disregard them
 143                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 144
 145                                         bool ignore = false;
 146                                         if (fastaFileNames[i] == "current") {
 147                                                 fastaFileNames[i] = m->getFastaFile();
 148                                                 if (fastaFileNames[i] != "") {  m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 149                                                 else {
 150                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 151                                                         //erase from file list
 152                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 153                                                         i--;
 154                                                 }
 155                                         }
 156
 157                                         if (!ignore) {
 158
 159                                                 if (inputDir != "") {
 160                                                         string path = m->hasPath(fastaFileNames[i]);
 161                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 162                                                         if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 163                                                 }
 164
 165                                                 int ableToOpen;
 166                                                 ifstream in;
 167
 168                                                 ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 169
 170                                                 //if you can't open it, try default location
 171                                                 if (ableToOpen == 1) {
 172                                                         if (m->getDefaultPath() != "") { //default path is set
 173                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 174                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 175                                                                 ifstream in2;
 176                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 177                                                                 in2.close();
 178                                                                 fastaFileNames[i] = tryPath;
 179                                                         }
 180                                                 }
 181
 182                                                 if (ableToOpen == 1) {
 183                                                         if (m->getOutputDir() != "") { //default path is set
 184                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 185                                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 186                                                                 ifstream in2;
 187                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 188                                                                 in2.close();
 189                                                                 fastaFileNames[i] = tryPath;
 190                                                         }
 191                                                 }
 192
 193                                                 in.close();
 194
 195                                                 if (ableToOpen == 1) {
 196                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 197                                                         //erase from file list
 198                                                         fastaFileNames.erase(fastaFileNames.begin()+i);
 199                                                         i--;
 200                                                 }else {
 201                                                         m->setFastaFile(fastaFileNames[i]);
 202                                                 }
 203                                         }
 204                                 }
 205
 206                                 //make sure there is at least one valid file left
 207                                 if (fastaFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
 208                         }
 209
 210
 211                         //check for required parameters
 212                         namefile = validParameter.validFile(parameters, "name", false);
 213                         if (namefile == "not found") { namefile = "";   }
 214                         else {
 215                                 m->splitAtDash(namefile, nameFileNames);
 216
 217                                 //go through files and make sure they are good, if not, then disregard them
 218                                 for (int i = 0; i < nameFileNames.size(); i++) {
 219
 220                                         bool ignore = false;
 221                                         if (nameFileNames[i] == "current") {
 222                                                 nameFileNames[i] = m->getNameFile();
 223                                                 if (nameFileNames[i] != "") {  m->mothurOut("Using " + nameFileNames[i] + " as input file for the name parameter where you had given current."); m->mothurOutEndLine(); }
 224                                                 else {
 225                                                         m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 226                                                         //erase from file list
 227                                                         nameFileNames.erase(nameFileNames.begin()+i);
 228                                                         i--;
 229                                                 }
 230                                         }
 231
 232                                         if (!ignore) {
 233
 234                                                 if (inputDir != "") {
 235                                                         string path = m->hasPath(nameFileNames[i]);
 236                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 237                                                         if (path == "") {       nameFileNames[i] = inputDir + nameFileNames[i];         }
 238                                                 }
 239
 240                                                 int ableToOpen;
 241                                                 ifstream in;
 242
 243                                                 ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror");
 244
 245                                                 //if you can't open it, try default location
 246                                                 if (ableToOpen == 1) {
 247                                                         if (m->getDefaultPath() != "") { //default path is set
 248                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]);
 249                                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 250                                                                 ifstream in2;
 251                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 252                                                                 in2.close();
 253                                                                 nameFileNames[i] = tryPath;
 254                                                         }
 255                                                 }
 256
 257                                                 if (ableToOpen == 1) {
 258                                                         if (m->getOutputDir() != "") { //default path is set
 259                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]);
 260                                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 261                                                                 ifstream in2;
 262                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 263                                                                 in2.close();
 264                                                                 nameFileNames[i] = tryPath;
 265                                                         }
 266                                                 }
 267
 268                                                 in.close();
 269
 270                                                 if (ableToOpen == 1) {
 271                                                         m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 272                                                         //erase from file list
 273                                                         nameFileNames.erase(nameFileNames.begin()+i);
 274                                                         i--;
 275                                                 }else {
 276                                                         m->setNameFile(nameFileNames[i]);
 277                                                 }
 278                                         }
 279                                 }
 280                         }
 281
 282             if (nameFileNames.size() != 0) { hasName = true; }
 283
 284             //check for required parameters
 285             vector<string> countfileNames;
 286                         countfile = validParameter.validFile(parameters, "count", false);
 287                         if (countfile == "not found") {
 288                 countfile = "";
 289                         }else {
 290                                 m->splitAtDash(countfile, countfileNames);
 291
 292                                 //go through files and make sure they are good, if not, then disregard them
 293                                 for (int i = 0; i < countfileNames.size(); i++) {
 294
 295                                         bool ignore = false;
 296                                         if (countfileNames[i] == "current") {
 297                                                 countfileNames[i] = m->getCountTableFile();
 298                                                 if (nameFileNames[i] != "") {  m->mothurOut("Using " + countfileNames[i] + " as input file for the count parameter where you had given current."); m->mothurOutEndLine(); }
 299                                                 else {
 300                                                         m->mothurOut("You have no current count file, ignoring current."); m->mothurOutEndLine(); ignore=true;
 301                                                         //erase from file list
 302                                                         countfileNames.erase(countfileNames.begin()+i);
 303                                                         i--;
 304                                                 }
 305                                         }
 306
 307                                         if (!ignore) {
 308
 309                                                 if (inputDir != "") {
 310                                                         string path = m->hasPath(countfileNames[i]);
 311                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 312                                                         if (path == "") {       countfileNames[i] = inputDir + countfileNames[i];               }
 313                                                 }
 314
 315                                                 int ableToOpen;
 316                                                 ifstream in;
 317
 318                                                 ableToOpen = m->openInputFile(countfileNames[i], in, "noerror");
 319
 320                                                 //if you can't open it, try default location
 321                                                 if (ableToOpen == 1) {
 322                                                         if (m->getDefaultPath() != "") { //default path is set
 323                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(countfileNames[i]);
 324                                                                 m->mothurOut("Unable to open " + countfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 325                                                                 ifstream in2;
 326                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 327                                                                 in2.close();
 328                                                                 countfileNames[i] = tryPath;
 329                                                         }
 330                                                 }
 331
 332                                                 if (ableToOpen == 1) {
 333                                                         if (m->getOutputDir() != "") { //default path is set
 334                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(countfileNames[i]);
 335                                                                 m->mothurOut("Unable to open " + countfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 336                                                                 ifstream in2;
 337                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 338                                                                 in2.close();
 339                                                                 countfileNames[i] = tryPath;
 340                                                         }
 341                                                 }
 342
 343                                                 in.close();
 344
 345                                                 if (ableToOpen == 1) {
 346                                                         m->mothurOut("Unable to open " + countfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 347                                                         //erase from file list
 348                                                         countfileNames.erase(countfileNames.begin()+i);
 349                                                         i--;
 350                                                 }else {
 351                                                         m->setCountTableFile(countfileNames[i]);
 352                                                 }
 353                                         }
 354                                 }
 355                         }
 356
 357             if (countfileNames.size() != 0) { hasCount = true; }
 358
 359                         //make sure there is at least one valid file left
 360             if (hasName && hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
 361
 362             if (!hasName && !hasCount) {
 363                 //if there is a current name file, use it, else look for current count file
 364                                 string filename = m->getNameFile();
 365                                 if (filename != "") { hasName = true; nameFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the name parameter."); m->mothurOutEndLine(); }
 366                                 else {
 367                     filename = m->getCountTableFile();
 368                     if (filename != "") { hasCount = true; countfileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the count parameter."); m->mothurOutEndLine(); }
 369                     else { m->mothurOut("[ERROR]: You must provide a count or name file."); m->mothurOutEndLine(); abort = true;  }
 370                 }
 371             }
 372             if (!hasName && hasCount) { nameFileNames = countfileNames; }
 373
 374                         if (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; }
 375
 376                         bool hasGroup = true;
 377                         groupfile = validParameter.validFile(parameters, "group", false);
 378                         if (groupfile == "not found") { groupfile = "";  hasGroup = false; }
 379                         else {
 380                                 m->splitAtDash(groupfile, groupFileNames);
 381
 382                                 //go through files and make sure they are good, if not, then disregard them
 383                                 for (int i = 0; i < groupFileNames.size(); i++) {
 384
 385                                         bool ignore = false;
 386                                         if (groupFileNames[i] == "current") {
 387                                                 groupFileNames[i] = m->getGroupFile();
 388                                                 if (groupFileNames[i] != "") {  m->mothurOut("Using " + groupFileNames[i] + " as input file for the group parameter where you had given current."); m->mothurOutEndLine(); }
 389                                                 else {
 390                                                         m->mothurOut("You have no current namefile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 391                                                         //erase from file list
 392                                                         groupFileNames.erase(groupFileNames.begin()+i);
 393                                                         i--;
 394                                                 }
 395                                         }
 396
 397                                         if (!ignore) {
 398
 399                                                 if (inputDir != "") {
 400                                                         string path = m->hasPath(groupFileNames[i]);
 401                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 402                                                         if (path == "") {       groupFileNames[i] = inputDir + groupFileNames[i];               }
 403                                                 }
 404
 405                                                 int ableToOpen;
 406                                                 ifstream in;
 407
 408                                                 ableToOpen = m->openInputFile(groupFileNames[i], in, "noerror");
 409
 410                                                 //if you can't open it, try default location
 411                                                 if (ableToOpen == 1) {
 412                                                         if (m->getDefaultPath() != "") { //default path is set
 413                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(groupFileNames[i]);
 414                                                                 m->mothurOut("Unable to open " + groupFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 415                                                                 ifstream in2;
 416                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 417                                                                 in2.close();
 418                                                                 groupFileNames[i] = tryPath;
 419                                                         }
 420                                                 }
 421
 422                                                 if (ableToOpen == 1) {
 423                                                         if (m->getOutputDir() != "") { //default path is set
 424                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(groupFileNames[i]);
 425                                                                 m->mothurOut("Unable to open " + groupFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 426                                                                 ifstream in2;
 427                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 428                                                                 in2.close();
 429                                                                 groupFileNames[i] = tryPath;
 430                                                         }
 431                                                 }
 432
 433                                                 in.close();
 434
 435                                                 if (ableToOpen == 1) {
 436                                                         m->mothurOut("Unable to open " + groupFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 437                                                         //erase from file list
 438                                                         groupFileNames.erase(groupFileNames.begin()+i);
 439                                                         i--;
 440                                                 }else {
 441                                                         m->setGroupFile(groupFileNames[i]);
 442                                                 }
 443                                         }
 444                                 }
 445
 446                                 //make sure there is at least one valid file left
 447                                 if (groupFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid group files."); m->mothurOutEndLine(); abort = true; }
 448                         }
 449
 450                         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; }
 451
 452             if (hasGroup && hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or group."); m->mothurOutEndLine(); abort = true; }
 453
 454                         //if the user changes the output directory command factory will send this info to us in the output parameter
 455                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 456
 457                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 458                         m->setProcessors(temp);
 459                         m->mothurConvert(temp, processors);
 460
 461                         temp = validParameter.validFile(parameters, "cutoff", false);   if (temp == "not found"){       temp = "0.50";  }
 462                         m->mothurConvert(temp, cutoff);
 463
 464                         temp = validParameter.validFile(parameters, "alpha", false);    if (temp == "not found"){       temp = "-5.54"; }
 465                         m->mothurConvert(temp, alpha);
 466
 467                         temp = validParameter.validFile(parameters, "cutoff", false);   if (temp == "not found"){       temp = "0.33";  }
 468                         m->mothurConvert(temp, beta);
 469                 }
 470         }
 471         catch(exception& e) {
 472                 m->errorOut(e, "ChimeraPerseusCommand", "ChimeraPerseusCommand");
 473                 exit(1);
 474         }
 475 }
 476 //***************************************************************************************************************
 477
 478 int ChimeraPerseusCommand::execute(){
 479         try{
 480                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 481
 482
 483                 //process each file
 484                 for (int s = 0; s < fastaFileNames.size(); s++) {
 485
 486                         m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 487
 488                         int start = time(NULL);
 489                         if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it
 490                         string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera");
 491                         string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos");
 492
 493                         //string newFasta = m->getRootName(fastaFileNames[s]) + "temp";
 494
 495                         //you provided a groupfile
 496                         string groupFile = "";
 497                         if (groupFileNames.size() != 0) { groupFile = groupFileNames[s]; }
 498
 499                         string nameFile = "";
 500                         if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
 501                                 nameFile = nameFileNames[s];
 502                         }else { nameFile = getNamesFile(fastaFileNames[s]); }
 503
 504                         if (m->control_pressed) {  for (int j = 0; j < outputNames.size(); j++) {       m->mothurRemove(outputNames[j]);        } return 0;     }
 505
 506                         int numSeqs = 0;
 507                         int numChimeras = 0;
 508
 509             if (hasCount) {
 510                 CountTable* ct = new CountTable();
 511                 ct->readTable(nameFile);
 512
 513                 if (ct->hasGroupInfo()) {
 514                     cparser = new SequenceCountParser(fastaFileNames[s], *ct);
 515
 516                     vector<string> groups = cparser->getNamesOfGroups();
 517
 518                     if (m->control_pressed) { delete ct; delete cparser; for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]);        }  return 0; }
 519
 520                     //clears files
 521                     ofstream out, out1, out2;
 522                     m->openOutputFile(outputFileName, out); out.close();
 523                     m->openOutputFile(accnosFileName, out1); out1.close();
 524
 525                     if(processors == 1) {       numSeqs = driverGroups(outputFileName, accnosFileName, 0, groups.size(), groups);       }
 526                     else                                {       numSeqs = createProcessesGroups(outputFileName, accnosFileName, groups, groupFile, fastaFileNames[s], nameFile);                        }
 527
 528                     if (m->control_pressed) {  delete ct; delete cparser; for (int j = 0; j < outputNames.size(); j++) {        m->mothurRemove(outputNames[j]);        }  return 0;    }
 529                     map<string, string> uniqueNames = cparser->getAllSeqsMap();
 530                     numChimeras = deconvoluteResults(uniqueNames, outputFileName, accnosFileName);
 531                     delete cparser;
 532
 533                     m->mothurOut("The number of sequences checked may be larger than the number of unique sequences because some sequences are found in several samples."); m->mothurOutEndLine();
 534
 535                     if (m->control_pressed) {  delete ct; for (int j = 0; j < outputNames.size(); j++) {        m->mothurRemove(outputNames[j]);        }  return 0;  }
 536
 537                 }else {
 538                     if (processors != 1) { m->mothurOut("Your count file does not contain group information, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
 539
 540                     //read sequences and store sorted by frequency
 541                     vector<seqData> sequences = readFiles(fastaFileNames[s], ct);
 542
 543                     if (m->control_pressed) { delete ct; for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]);        } return 0; }
 544
 545                     numSeqs = driver(outputFileName, sequences, accnosFileName, numChimeras);
 546                 }
 547                 delete ct;
 548             }else {
 549                 if (groupFile != "") {
 550                     //Parse sequences by group
 551                     parser = new SequenceParser(groupFile, fastaFileNames[s], nameFile);
 552                     vector<string> groups = parser->getNamesOfGroups();
 553
 554                     if (m->control_pressed) { delete parser; for (int j = 0; j < outputNames.size(); j++) {     m->mothurRemove(outputNames[j]);        }  return 0; }
 555
 556                     //clears files
 557                     ofstream out, out1, out2;
 558                     m->openOutputFile(outputFileName, out); out.close();
 559                     m->openOutputFile(accnosFileName, out1); out1.close();
 560
 561                     if(processors == 1) {       numSeqs = driverGroups(outputFileName, accnosFileName, 0, groups.size(), groups);       }
 562                     else                                {       numSeqs = createProcessesGroups(outputFileName, accnosFileName, groups, groupFile, fastaFileNames[s], nameFile);                        }
 563
 564                     if (m->control_pressed) {  delete parser; for (int j = 0; j < outputNames.size(); j++) {    m->mothurRemove(outputNames[j]);        }  return 0;    }
 565                     map<string, string> uniqueNames = parser->getAllSeqsMap();
 566                     numChimeras = deconvoluteResults(uniqueNames, outputFileName, accnosFileName);
 567                     delete parser;
 568
 569                     m->mothurOut("The number of sequences checked may be larger than the number of unique sequences because some sequences are found in several samples."); m->mothurOutEndLine();
 570
 571                     if (m->control_pressed) {  for (int j = 0; j < outputNames.size(); j++) {   m->mothurRemove(outputNames[j]);        }  return 0;  }
 572                 }else{
 573                     if (processors != 1) { m->mothurOut("Without a groupfile, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
 574
 575                     //read sequences and store sorted by frequency
 576                     vector<seqData> sequences = readFiles(fastaFileNames[s], nameFile);
 577
 578                     if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) {    m->mothurRemove(outputNames[j]);        } return 0; }
 579
 580                     numSeqs = driver(outputFileName, sequences, accnosFileName, numChimeras);
 581                 }
 582                         }
 583
 584                         if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) {        m->mothurRemove(outputNames[j]);        } return 0; }
 585
 586                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences. " + toString(numChimeras) + " chimeras were found.");      m->mothurOutEndLine();
 587                         outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
 588                         outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
 589                 }
 590
 591                 //set accnos file as new current accnosfile
 592                 string current = "";
 593                 itTypes = outputTypes.find("accnos");
 594                 if (itTypes != outputTypes.end()) {
 595                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 596                 }
 597
 598                 m->mothurOutEndLine();
 599                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 600                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 601                 m->mothurOutEndLine();
 602
 603                 return 0;
 604
 605         }
 606         catch(exception& e) {
 607                 m->errorOut(e, "ChimeraPerseusCommand", "execute");
 608                 exit(1);
 609         }
 610 }
 611 //**********************************************************************************************************************
 612 string ChimeraPerseusCommand::getNamesFile(string& inputFile){
 613         try {
 614                 string nameFile = "";
 615
 616                 m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine();
 617
 618                 //use unique.seqs to create new name and fastafile
 619                 string inputString = "fasta=" + inputFile;
 620                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 621                 m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
 622                 m->mothurCalling = true;
 623
 624                 Command* uniqueCommand = new DeconvoluteCommand(inputString);
 625                 uniqueCommand->execute();
 626
 627                 map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 628
 629                 delete uniqueCommand;
 630                 m->mothurCalling = false;
 631                 m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 632
 633                 nameFile = filenames["name"][0];
 634                 inputFile = filenames["fasta"][0];
 635
 636                 return nameFile;
 637         }
 638         catch(exception& e) {
 639                 m->errorOut(e, "ChimeraPerseusCommand", "getNamesFile");
 640                 exit(1);
 641         }
 642 }
 643 //**********************************************************************************************************************
 644 int ChimeraPerseusCommand::driverGroups(string outputFName, string accnos, int start, int end, vector<string> groups){
 645         try {
 646
 647                 int totalSeqs = 0;
 648                 int numChimeras = 0;
 649
 650                 for (int i = start; i < end; i++) {
 651
 652                         m->mothurOutEndLine(); m->mothurOut("Checking sequences from group " + groups[i] + "...");      m->mothurOutEndLine();
 653
 654                         int start = time(NULL);  if (m->control_pressed) {  return 0; }
 655
 656                         vector<seqData> sequences = loadSequences(groups[i]);
 657
 658                         if (m->control_pressed) { return 0; }
 659
 660                         int numSeqs = driver((outputFName + groups[i]), sequences, (accnos+groups[i]), numChimeras);
 661                         totalSeqs += numSeqs;
 662
 663                         if (m->control_pressed) { return 0; }
 664
 665                         //append files
 666                         m->appendFiles((outputFName+groups[i]), outputFName); m->mothurRemove((outputFName+groups[i]));
 667                         m->appendFiles((accnos+groups[i]), accnos); m->mothurRemove((accnos+groups[i]));
 668
 669                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences from group " + groups[i] + ".");    m->mothurOutEndLine();
 670                 }
 671
 672                 return totalSeqs;
 673
 674         }
 675         catch(exception& e) {
 676                 m->errorOut(e, "ChimeraPerseusCommand", "driverGroups");
 677                 exit(1);
 678         }
 679 }
 680 //**********************************************************************************************************************
 681 vector<seqData> ChimeraPerseusCommand::loadSequences(string group){
 682         try {
 683         bool error = false;
 684                 alignLength = 0;
 685         vector<seqData> sequences;
 686         if (hasCount) {
 687             vector<Sequence> thisGroupsSeqs = cparser->getSeqs(group);
 688             map<string, int> counts = cparser->getCountTable(group);
 689             map<string, int>::iterator it;
 690
 691             for (int i = 0; i < thisGroupsSeqs.size(); i++) {
 692
 693                 if (m->control_pressed) {  return sequences; }
 694
 695                 it = counts.find(thisGroupsSeqs[i].getName());
 696                 if (it == counts.end()) { error = true; m->mothurOut("[ERROR]: " + thisGroupsSeqs[i].getName() + " is in your fasta file and not in your count file, please correct."); m->mothurOutEndLine(); }
 697                 else {
 698                     sequences.push_back(seqData(thisGroupsSeqs[i].getName(), thisGroupsSeqs[i].getUnaligned(), it->second));
 699                     if (thisGroupsSeqs[i].getUnaligned().length() > alignLength) { alignLength = thisGroupsSeqs[i].getUnaligned().length(); }
 700                 }
 701             }
 702         }else{
 703             vector<Sequence> thisGroupsSeqs = parser->getSeqs(group);
 704             map<string, string> nameMap = parser->getNameMap(group);
 705             map<string, string>::iterator it;
 706
 707             for (int i = 0; i < thisGroupsSeqs.size(); i++) {
 708
 709                 if (m->control_pressed) {  return sequences; }
 710
 711                 it = nameMap.find(thisGroupsSeqs[i].getName());
 712                 if (it == nameMap.end()) { error = true; m->mothurOut("[ERROR]: " + thisGroupsSeqs[i].getName() + " is in your fasta file and not in your namefile, please correct."); m->mothurOutEndLine(); }
 713                 else {
 714                     int num = m->getNumNames(it->second);
 715                     sequences.push_back(seqData(thisGroupsSeqs[i].getName(), thisGroupsSeqs[i].getUnaligned(), num));
 716                     if (thisGroupsSeqs[i].getUnaligned().length() > alignLength) { alignLength = thisGroupsSeqs[i].getUnaligned().length(); }
 717                 }
 718             }
 719
 720                 }
 721
 722         if (error) { m->control_pressed = true; }
 723                 //sort by frequency
 724                 sort(sequences.rbegin(), sequences.rend());
 725
 726                 return sequences;
 727         }
 728         catch(exception& e) {
 729                 m->errorOut(e, "ChimeraPerseusCommand", "loadSequences");
 730                 exit(1);
 731         }
 732 }
 733
 734 //**********************************************************************************************************************
 735 vector<seqData> ChimeraPerseusCommand::readFiles(string inputFile, string name){
 736         try {
 737                 map<string, int>::iterator it;
 738                 map<string, int> nameMap = m->readNames(name);
 739
 740                 //read fasta file and create sequenceData structure - checking for file mismatches
 741                 vector<seqData> sequences;
 742                 bool error = false;
 743                 ifstream in;
 744                 m->openInputFile(inputFile, in);
 745                 alignLength = 0;
 746
 747                 while (!in.eof()) {
 748
 749                         if (m->control_pressed) { in.close(); return sequences; }
 750
 751                         Sequence temp(in); m->gobble(in);
 752
 753                         it = nameMap.find(temp.getName());
 754                         if (it == nameMap.end()) { error = true; m->mothurOut("[ERROR]: " + temp.getName() + " is in your fasta file and not in your namefile, please correct."); m->mothurOutEndLine(); }
 755                         else {
 756                                 sequences.push_back(seqData(temp.getName(), temp.getUnaligned(), it->second));
 757                 if (temp.getUnaligned().length() > alignLength) { alignLength = temp.getUnaligned().length(); }
 758                         }
 759                 }
 760                 in.close();
 761
 762                 if (error) { m->control_pressed = true; }
 763
 764                 //sort by frequency
 765                 sort(sequences.rbegin(), sequences.rend());
 766
 767                 return sequences;
 768         }
 769         catch(exception& e) {
 770                 m->errorOut(e, "ChimeraPerseusCommand", "readFiles");
 771                 exit(1);
 772         }
 773 }
 774 //**********************************************************************************************************************
 775 vector<seqData> ChimeraPerseusCommand::readFiles(string inputFile, CountTable* ct){
 776         try {
 777                 //read fasta file and create sequenceData structure - checking for file mismatches
 778                 vector<seqData> sequences;
 779                 ifstream in;
 780                 m->openInputFile(inputFile, in);
 781                 alignLength = 0;
 782
 783                 while (!in.eof()) {
 784             Sequence temp(in); m->gobble(in);
 785
 786                         int count = ct->getNumSeqs(temp.getName());
 787                         if (m->control_pressed) { break; }
 788                         else {
 789                                 sequences.push_back(seqData(temp.getName(), temp.getUnaligned(), count));
 790                 if (temp.getUnaligned().length() > alignLength) { alignLength = temp.getUnaligned().length(); }
 791                         }
 792                 }
 793                 in.close();
 794
 795                 //sort by frequency
 796                 sort(sequences.rbegin(), sequences.rend());
 797
 798                 return sequences;
 799         }
 800         catch(exception& e) {
 801                 m->errorOut(e, "ChimeraPerseusCommand", "getNamesFile");
 802                 exit(1);
 803         }
 804 }
 805 //**********************************************************************************************************************
 806 int ChimeraPerseusCommand::driver(string chimeraFileName, vector<seqData>& sequences, string accnosFileName, int& numChimeras){
 807         try {
 808
 809                 vector<vector<double> > correctModel(4);        //could be an option in the future to input own model matrix
 810                 for(int i=0;i<4;i++){   correctModel[i].resize(4);      }
 811
 812                 correctModel[0][0] = 0.000000;  //AA
 813                 correctModel[1][0] = 11.619259; //CA
 814                 correctModel[2][0] = 11.694004; //TA
 815                 correctModel[3][0] = 7.748623;  //GA
 816
 817                 correctModel[1][1] = 0.000000;  //CC
 818                 correctModel[2][1] = 7.619657;  //TC
 819                 correctModel[3][1] = 12.852562; //GC
 820
 821                 correctModel[2][2] = 0.000000;  //TT
 822                 correctModel[3][2] = 10.964048; //TG
 823
 824                 correctModel[3][3] = 0.000000;  //GG
 825
 826                 for(int i=0;i<4;i++){
 827                         for(int j=0;j<i;j++){
 828                                 correctModel[j][i] = correctModel[i][j];
 829                         }
 830                 }
 831
 832                 int numSeqs = sequences.size();
 833                 //int alignLength = sequences[0].sequence.size();
 834
 835                 ofstream chimeraFile;
 836                 ofstream accnosFile;
 837                 m->openOutputFile(chimeraFileName, chimeraFile);
 838                 m->openOutputFile(accnosFileName, accnosFile);
 839
 840                 Perseus myPerseus;
 841                 vector<vector<double> > binMatrix = myPerseus.binomial(alignLength);
 842
 843                 chimeraFile << "SequenceIndex\tName\tDiffsToBestMatch\tBestMatchIndex\tBestMatchName\tDiffstToChimera\tIndexofLeftParent\tIndexOfRightParent\tNameOfLeftParent\tNameOfRightParent\tDistanceToBestMatch\tcIndex\t(cIndex - singleDist)\tloonIndex\tMismatchesToChimera\tMismatchToTrimera\tChimeraBreakPoint\tLogisticProbability\tTypeOfSequence\n";
 844
 845                 vector<bool> chimeras(numSeqs, 0);
 846
 847                 for(int i=0;i<numSeqs;i++){
 848                         if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
 849
 850                         vector<bool> restricted = chimeras;
 851
 852                         vector<vector<int> > leftDiffs(numSeqs);
 853                         vector<vector<int> > leftMaps(numSeqs);
 854                         vector<vector<int> > rightDiffs(numSeqs);
 855                         vector<vector<int> > rightMaps(numSeqs);
 856
 857                         vector<int> singleLeft, bestLeft;
 858                         vector<int> singleRight, bestRight;
 859
 860                         int bestSingleIndex, bestSingleDiff;
 861                         vector<pwAlign> alignments(numSeqs);
 862
 863                         int comparisons = myPerseus.getAlignments(i, sequences, alignments, leftDiffs, leftMaps, rightDiffs, rightMaps, bestSingleIndex, bestSingleDiff, restricted);
 864                         if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
 865
 866                         int minMismatchToChimera, leftParentBi, rightParentBi, breakPointBi;
 867
 868                         string dummyA, dummyB;
 869
 870             if (sequences[i].sequence.size() < 3) {
 871                 chimeraFile << i << '\t' << sequences[i].seqName << "\t0\t0\tNull\t0\t0\t0\tNull\tNull\t0.0\t0.0\t0.0\t0\t0\t0\t0.0\t0.0\tgood" << endl;
 872             }else if(comparisons >= 2){
 873                                 minMismatchToChimera = myPerseus.getChimera(sequences, leftDiffs, rightDiffs, leftParentBi, rightParentBi, breakPointBi, singleLeft, bestLeft, singleRight, bestRight, restricted);
 874                                 if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
 875
 876                                 int minMismatchToTrimera = numeric_limits<int>::max();
 877                                 int leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB;
 878
 879                                 if(minMismatchToChimera >= 3 && comparisons >= 3){
 880                                         minMismatchToTrimera = myPerseus.getTrimera(sequences, leftDiffs, leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB, singleLeft, bestLeft, singleRight, bestRight, restricted);
 881                                         if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
 882                                 }
 883
 884                                 double singleDist = myPerseus.modeledPairwiseAlignSeqs(sequences[i].sequence, sequences[bestSingleIndex].sequence, dummyA, dummyB, correctModel);
 885
 886                                 if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
 887
 888                                 string type;
 889                                 string chimeraRefSeq;
 890
 891                                 if(minMismatchToChimera - minMismatchToTrimera >= 3){
 892                                         type = "trimera";
 893                                         chimeraRefSeq = myPerseus.stitchTrimera(alignments, leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB, leftMaps, rightMaps);
 894                                 }
 895                                 else{
 896                                         type = "chimera";
 897                                         chimeraRefSeq = myPerseus.stitchBimera(alignments, leftParentBi, rightParentBi, breakPointBi, leftMaps, rightMaps);
 898                                 }
 899                                 ;
 900                                 if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
 901
 902                                 double chimeraDist = myPerseus.modeledPairwiseAlignSeqs(sequences[i].sequence, chimeraRefSeq, dummyA, dummyB, correctModel);
 903
 904                                 if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
 905
 906                                 double cIndex = chimeraDist;//modeledPairwiseAlignSeqs(sequences[i].sequence, chimeraRefSeq);
 907                                 double loonIndex = myPerseus.calcLoonIndex(sequences[i].sequence, sequences[leftParentBi].sequence, sequences[rightParentBi].sequence, breakPointBi, binMatrix);
 908
 909                                 if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
 910
 911                                 chimeraFile << i << '\t' << sequences[i].seqName << '\t' << bestSingleDiff << '\t' << bestSingleIndex << '\t' << sequences[bestSingleIndex].seqName << '\t';
 912                                 chimeraFile << minMismatchToChimera << '\t' << leftParentBi << '\t' << rightParentBi << '\t' << sequences[leftParentBi].seqName << '\t' << sequences[rightParentBi].seqName << '\t';
 913                                 chimeraFile << singleDist << '\t' << cIndex << '\t' << (cIndex - singleDist) << '\t' << loonIndex << '\t';
 914                                 chimeraFile << minMismatchToChimera << '\t' << minMismatchToTrimera << '\t' << breakPointBi << '\t';
 915
 916                                 double probability = myPerseus.classifyChimera(singleDist, cIndex, loonIndex, alpha, beta);
 917
 918                                 chimeraFile << probability << '\t';
 919
 920                                 if(probability > cutoff){
 921                                         chimeraFile << type << endl;
 922                                         accnosFile << sequences[i].seqName << endl;
 923                                         chimeras[i] = 1;
 924                                         numChimeras++;
 925                                 }
 926                                 else{
 927                                         chimeraFile << "good" << endl;
 928                                 }
 929
 930                         }
 931                         else{
 932                                 chimeraFile << i << '\t' << sequences[i].seqName << "\t0\t0\tNull\t0\t0\t0\tNull\tNull\t0.0\t0.0\t0.0\t0\t0\t0\t0.0\t0.0\tgood" << endl;
 933                         }
 934
 935                         //report progress
 936                         if((i+1) % 100 == 0){   m->mothurOut("Processing sequence: " + toString(i+1) + "\n");           }
 937                 }
 938
 939                 if((numSeqs) % 100 != 0){       m->mothurOut("Processing sequence: " + toString(numSeqs) + "\n");               }
 940
 941                 chimeraFile.close();
 942                 accnosFile.close();
 943
 944                 return numSeqs;
 945         }
 946         catch(exception& e) {
 947                 m->errorOut(e, "ChimeraPerseusCommand", "driver");
 948                 exit(1);
 949         }
 950 }
 951 /**************************************************************************************************/
 952 int ChimeraPerseusCommand::createProcessesGroups(string outputFName, string accnos, vector<string> groups, string group, string fasta, string name) {
 953         try {
 954
 955                 vector<int> processIDS;
 956                 int process = 1;
 957                 int num = 0;
 958
 959                 //sanity check
 960                 if (groups.size() < processors) { processors = groups.size(); }
 961
 962                 //divide the groups between the processors
 963                 vector<linePair> lines;
 964                 int numGroupsPerProcessor = groups.size() / processors;
 965                 for (int i = 0; i < processors; i++) {
 966                         int startIndex =  i * numGroupsPerProcessor;
 967                         int endIndex = (i+1) * numGroupsPerProcessor;
 968                         if(i == (processors - 1)){      endIndex = groups.size();       }
 969                         lines.push_back(linePair(startIndex, endIndex));
 970                 }
 971
 972 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 973
 974                 //loop through and create all the processes you want
 975                 while (process != processors) {
 976                         int pid = fork();
 977
 978                         if (pid > 0) {
 979                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 980                                 process++;
 981                         }else if (pid == 0){
 982                                 num = driverGroups(outputFName + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", lines[process].start, lines[process].end, groups);
 983
 984                                 //pass numSeqs to parent
 985                                 ofstream out;
 986                                 string tempFile = outputFName + toString(getpid()) + ".num.temp";
 987                                 m->openOutputFile(tempFile, out);
 988                                 out << num << endl;
 989                                 out.close();
 990
 991                                 exit(0);
 992                         }else {
 993                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 994                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 995                                 exit(0);
 996                         }
 997                 }
 998
 999                 //do my part
1000                 num = driverGroups(outputFName, accnos, lines[0].start, lines[0].end, groups);
1001
1002                 //force parent to wait until all the processes are done
1003                 for (int i=0;i<processIDS.size();i++) {
1004                         int temp = processIDS[i];
1005                         wait(&temp);
1006                 }
1007
1008                 for (int i = 0; i < processIDS.size(); i++) {
1009                         ifstream in;
1010                         string tempFile =  outputFName + toString(processIDS[i]) + ".num.temp";
1011                         m->openInputFile(tempFile, in);
1012                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
1013                         in.close(); m->mothurRemove(tempFile);
1014                 }
1015
1016 #else
1017                 //////////////////////////////////////////////////////////////////////////////////////////////////////
1018                 //Windows version shared memory, so be careful when passing variables through the preClusterData struct.
1019                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
1020                 //////////////////////////////////////////////////////////////////////////////////////////////////////
1021
1022                 vector<perseusData*> pDataArray;
1023                 DWORD   dwThreadIdArray[processors-1];
1024                 HANDLE  hThreadArray[processors-1];
1025
1026                 //Create processor worker threads.
1027                 for( int i=1; i<processors; i++ ){
1028                         // Allocate memory for thread data.
1029                         string extension = toString(i) + ".temp";
1030
1031                         perseusData* tempPerseus = new perseusData(hasName, hasCount, alpha, beta, cutoff, outputFName+extension, fasta, name, group, accnos+extension, groups, m, lines[i].start, lines[i].end, i);
1032
1033                         pDataArray.push_back(tempPerseus);
1034                         processIDS.push_back(i);
1035
1036                         //MyPerseusThreadFunction is in header. It must be global or static to work with the threads.
1037                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
1038                         hThreadArray[i-1] = CreateThread(NULL, 0, MyPerseusThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
1039                 }
1040
1041
1042                 //using the main process as a worker saves time and memory
1043                 num = driverGroups(outputFName, accnos, lines[0].start, lines[0].end, groups);
1044
1045                 //Wait until all threads have terminated.
1046                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
1047
1048                 //Close all thread handles and free memory allocations.
1049                 for(int i=0; i < pDataArray.size(); i++){
1050                         num += pDataArray[i]->count;
1051                         CloseHandle(hThreadArray[i]);
1052                         delete pDataArray[i];
1053                 }
1054 #endif
1055
1056
1057                 //append output files
1058                 for(int i=0;i<processIDS.size();i++){
1059                         m->appendFiles((outputFName + toString(processIDS[i]) + ".temp"), outputFName);
1060                         m->mothurRemove((outputFName + toString(processIDS[i]) + ".temp"));
1061
1062                         m->appendFiles((accnos + toString(processIDS[i]) + ".temp"), accnos);
1063                         m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));
1064                 }
1065
1066                 return num;
1067
1068         }
1069         catch(exception& e) {
1070                 m->errorOut(e, "ChimeraPerseusCommand", "createProcessesGroups");
1071                 exit(1);
1072         }
1073 }
1074 //**********************************************************************************************************************
1075 int ChimeraPerseusCommand::deconvoluteResults(map<string, string>& uniqueNames, string outputFileName, string accnosFileName){
1076         try {
1077                 map<string, string>::iterator itUnique;
1078                 int total = 0;
1079
1080                 //edit accnos file
1081                 ifstream in2;
1082                 m->openInputFile(accnosFileName, in2);
1083
1084                 ofstream out2;
1085                 m->openOutputFile(accnosFileName+".temp", out2);
1086
1087                 string name;
1088                 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
1089                 set<string>::iterator itNames;
1090                 set<string> chimerasInFile;
1091                 set<string>::iterator itChimeras;
1092
1093
1094                 while (!in2.eof()) {
1095                         if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; }
1096
1097                         in2 >> name; m->gobble(in2);
1098
1099                         //find unique name
1100                         itUnique = uniqueNames.find(name);
1101
1102                         if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
1103                         else {
1104                                 itChimeras = chimerasInFile.find((itUnique->second));
1105
1106                                 if (itChimeras == chimerasInFile.end()) {
1107                                         out2 << itUnique->second << endl;
1108                                         chimerasInFile.insert((itUnique->second));
1109                                         total++;
1110                                 }
1111                         }
1112                 }
1113                 in2.close();
1114                 out2.close();
1115
1116                 m->mothurRemove(accnosFileName);
1117                 rename((accnosFileName+".temp").c_str(), accnosFileName.c_str());
1118
1119                 //edit chimera file
1120                 ifstream in;
1121                 m->openInputFile(outputFileName, in);
1122
1123                 ofstream out;
1124                 m->openOutputFile(outputFileName+".temp", out); out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
1125
1126                 int DiffsToBestMatch, BestMatchIndex, DiffstToChimera, IndexofLeftParent, IndexOfRightParent;
1127                 float temp1,temp2, temp3, temp4, temp5, temp6, temp7, temp8;
1128                 string index, BestMatchName, parent1, parent2, flag;
1129                 name = "";
1130                 namesInFile.clear();
1131                 //assumptions - in file each read will always look like
1132                 /*
1133                  SequenceIndex  Name    DiffsToBestMatch        BestMatchIndex  BestMatchName   DiffstToChimera IndexofLeftParent       IndexOfRightParent      NameOfLeftParent        NameOfRightParent       DistanceToBestMatch     cIndex  (cIndex - singleDist)   loonIndex       MismatchesToChimera     MismatchToTrimera       ChimeraBreakPoint       LogisticProbability     TypeOfSequence
1134                  0      F01QG4L02JVBQY  0       0       Null    0       0       0       Null    Null    0.0     0.0     0.0     0.0     0       0       0       0.0     0.0     good
1135                  1      F01QG4L02ICTC6  0       0       Null    0       0       0       Null    Null    0.0     0.0     0.0     0.0     0       0       0       0.0     0.0     good
1136                  2      F01QG4L02JZOEC  48      0       F01QG4L02JVBQY  47      0       0       F01QG4L02JVBQY  F01QG4L02JVBQY  2.0449  2.03545 -0.00944493     0       47      2147483647      138     0       good
1137                  3      F01QG4L02G7JEC  42      0       F01QG4L02JVBQY  40      1       0       F01QG4L02ICTC6  F01QG4L02JVBQY  1.87477 1.81113 -0.0636404      5.80145 40      2147483647      25      0       good
1138                  */
1139
1140                 //get and print headers
1141                 BestMatchName = m->getline(in); m->gobble(in);
1142                 out << BestMatchName << endl;
1143
1144                 while (!in.eof()) {
1145
1146                         if (m->control_pressed) { in.close(); out.close(); m->mothurRemove((outputFileName+".temp")); return 0; }
1147
1148                         bool print = false;
1149                         in >> index;    m->gobble(in);
1150
1151                         if (index != "SequenceIndex") { //if you are not a header line, there will be a header line for each group if group file is given
1152                                 in >> name;             m->gobble(in);
1153                                 in >> DiffsToBestMatch; m->gobble(in);
1154                                 in >> BestMatchIndex; m->gobble(in);
1155                                 in >> BestMatchName; m->gobble(in);
1156                                 in >> DiffstToChimera; m->gobble(in);
1157                                 in >> IndexofLeftParent; m->gobble(in);
1158                                 in >> IndexOfRightParent; m->gobble(in);
1159                                 in >> parent1;  m->gobble(in);
1160                                 in >> parent2;  m->gobble(in);
1161                                 in >> temp1 >> temp2 >> temp3 >> temp4 >> temp5 >> temp6 >> temp7 >> temp8 >> flag; m->gobble(in);
1162
1163                                 //find unique name
1164                                 itUnique = uniqueNames.find(name);
1165
1166                                 if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find "+ name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
1167                                 else {
1168                                         name = itUnique->second;
1169                                         //is this name already in the file
1170                                         itNames = namesInFile.find((name));
1171
1172                                         if (itNames == namesInFile.end()) { //no not in file
1173                                                 if (flag == "good") { //are you really a no??
1174                                                         //is this sequence really not chimeric??
1175                                                         itChimeras = chimerasInFile.find(name);
1176
1177                                                         //then you really are a no so print, otherwise skip
1178                                                         if (itChimeras == chimerasInFile.end()) { print = true; }
1179                                                 }else{ print = true; }
1180                                         }
1181                                 }
1182
1183                                 if (print) {
1184                                         out << index << '\t' << name  << '\t' << DiffsToBestMatch << '\t' << BestMatchIndex << '\t';
1185                                         namesInFile.insert(name);
1186
1187                                         if (BestMatchName != "Null") {
1188                                                 itUnique = uniqueNames.find(BestMatchName);
1189                                                 if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find BestMatchName "+ BestMatchName + "."); m->mothurOutEndLine(); m->control_pressed = true; }
1190                                                 else {  out << itUnique->second << '\t';        }
1191                                         }else { out << "Null" << '\t'; }
1192
1193                                         out << DiffstToChimera << '\t' << IndexofLeftParent << '\t' << IndexOfRightParent << '\t';
1194
1195                                         if (parent1 != "Null") {
1196                                                 itUnique = uniqueNames.find(parent1);
1197                                                 if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parent1 "+ parent1 + "."); m->mothurOutEndLine(); m->control_pressed = true; }
1198                                                 else {  out << itUnique->second << '\t';        }
1199                                         }else { out << "Null" << '\t'; }
1200
1201                                         if (parent1 != "Null") {
1202                                                 itUnique = uniqueNames.find(parent2);
1203                                                 if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing chimera results. Cannot find parent2 "+ parent2 + "."); m->mothurOutEndLine(); m->control_pressed = true; }
1204                                                 else {  out << itUnique->second << '\t';        }
1205                                         }else { out << "Null" << '\t'; }
1206
1207                                         out << temp1 << '\t' << temp2 << '\t' << temp3 << '\t' << temp4 << '\t' << temp5 << '\t' << temp6 << '\t' << temp7 << '\t' << temp8 << '\t' << flag << endl;
1208                                 }
1209                         }else { index = m->getline(in); m->gobble(in); }
1210                 }
1211                 in.close();
1212                 out.close();
1213
1214                 m->mothurRemove(outputFileName);
1215                 rename((outputFileName+".temp").c_str(), outputFileName.c_str());
1216
1217                 return total;
1218         }
1219         catch(exception& e) {
1220                 m->errorOut(e, "ChimeraPerseusCommand", "deconvoluteResults");
1221                 exit(1);
1222         }
1223 }
1224 //**********************************************************************************************************************
1225
1226