chopseqscommand.cpp

   1 /*
   2  *  chopseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 5/10/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "chopseqscommand.h"
  11 #include "sequence.hpp"
  12
  13 //**********************************************************************************************************************
  14 vector<string> ChopSeqsCommand::setParameters(){
  15         try {
  16                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
  17                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
  18         CommandParameter pnumbases("numbases", "Number", "", "0", "", "", "","",false,true,true); parameters.push_back(pnumbases);
  19                 CommandParameter pcountgaps("countgaps", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pcountgaps);
  20                 CommandParameter pshort("short", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pshort);
  21                 CommandParameter pkeep("keep", "Multiple", "front-back", "front", "", "", "","",false,false); parameters.push_back(pkeep);
  22                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  23                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  24
  25                 vector<string> myArray;
  26                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  27                 return myArray;
  28         }
  29         catch(exception& e) {
  30                 m->errorOut(e, "ChopSeqsCommand", "setParameters");
  31                 exit(1);
  32         }
  33 }
  34 //**********************************************************************************************************************
  35 string ChopSeqsCommand::getHelpString(){
  36         try {
  37                 string helpString = "";
  38                 helpString += "The chop.seqs command reads a fasta file and outputs a .chop.fasta containing the trimmed sequences. Note: If a sequence is completely 'chopped', an accnos file will be created with the names of the sequences removed. \n";
  39                 helpString += "The chop.seqs command parameters are fasta, numbases, countgaps and keep. fasta is required unless you have a valid current fasta file. numbases is required.\n";
  40                 helpString += "The chop.seqs command should be in the following format: chop.seqs(fasta=yourFasta, numbases=yourNum, keep=yourKeep).\n";
  41                 helpString += "The numbases parameter allows you to specify the number of bases you want to keep.\n";
  42                 helpString += "The keep parameter allows you to specify whether you want to keep the front or the back of your sequence, default=front.\n";
  43                 helpString += "The countgaps parameter allows you to specify whether you want to count gaps as bases, default=false.\n";
  44                 helpString += "The short parameter allows you to specify you want to keep sequences that are too short to chop, default=false.\n";
  45                 helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
  46         helpString += "For example, if you ran chop.seqs with numbases=200 and short=t, if a sequence had 100 bases mothur would keep the sequence rather than eliminate it.\n";
  47                 helpString += "Example chop.seqs(fasta=amazon.fasta, numbases=200, keep=front).\n";
  48                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  49                 return helpString;
  50         }
  51         catch(exception& e) {
  52                 m->errorOut(e, "ChopSeqsCommand", "getHelpString");
  53                 exit(1);
  54         }
  55 }
  56 //**********************************************************************************************************************
  57 string ChopSeqsCommand::getOutputPattern(string type) {
  58     try {
  59         string pattern = "";
  60
  61         if (type == "fasta") {  pattern = "[filename],chop.fasta"; }
  62         else if (type == "accnos") {  pattern = "[filename],chop.accnos"; }
  63         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  64
  65         return pattern;
  66     }
  67     catch(exception& e) {
  68         m->errorOut(e, "ChopSeqsCommand", "getOutputPattern");
  69         exit(1);
  70     }
  71 }
  72 //**********************************************************************************************************************
  73 ChopSeqsCommand::ChopSeqsCommand(){
  74         try {
  75                 abort = true; calledHelp = true;
  76                 setParameters();
  77                 vector<string> tempOutNames;
  78                 outputTypes["fasta"] = tempOutNames;
  79                 outputTypes["accnos"] = tempOutNames;
  80         }
  81         catch(exception& e) {
  82                 m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
  83                 exit(1);
  84         }
  85 }
  86 //**********************************************************************************************************************
  87 ChopSeqsCommand::ChopSeqsCommand(string option)  {
  88         try {
  89                 abort = false; calledHelp = false;
  90
  91                 //allow user to run help
  92                 if(option == "help") { help(); abort = true; calledHelp = true; }
  93                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  94
  95                 else {
  96                         vector<string> myArray = setParameters();
  97
  98                         OptionParser parser(option);
  99                         map<string,string> parameters = parser.getParameters();
 100
 101                         ValidParameters validParameter;
 102                         map<string,string>::iterator it;
 103
 104                         //check to make sure all parameters are valid for command
 105                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 106                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 107                         }
 108
 109                         //initialize outputTypes
 110                         vector<string> tempOutNames;
 111                         outputTypes["fasta"] = tempOutNames;
 112                         outputTypes["accnos"] = tempOutNames;
 113
 114                         //if the user changes the input directory command factory will send this info to us in the output parameter
 115                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 116                         if (inputDir == "not found"){   inputDir = "";          }
 117                         else {
 118                                 string path;
 119                                 it = parameters.find("fasta");
 120                                 //user has given a template file
 121                                 if(it != parameters.end()){
 122                                         path = m->hasPath(it->second);
 123                                         //if the user has not given a path then, add inputdir. else leave path alone.
 124                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 125                                 }
 126                         }
 127
 128                         //check for required parameters
 129                         fastafile = validParameter.validFile(parameters, "fasta", true);
 130                         if (fastafile == "not open") { abort = true; }
 131                         else if (fastafile == "not found") {                            //if there is a current fasta file, use it
 132                                 fastafile = m->getFastaFile();
 133                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 134                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 135                         }else { m->setFastaFile(fastafile); }
 136
 137                         //if the user changes the output directory command factory will send this info to us in the output parameter
 138                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);      }
 139
 140                         string temp = validParameter.validFile(parameters, "numbases", false);  if (temp == "not found") { temp = "0"; }
 141                         m->mothurConvert(temp, numbases);
 142
 143             temp = validParameter.validFile(parameters, "processors", false);   if (temp == "not found"){       temp = m->getProcessors();      }
 144                         m->setProcessors(temp);
 145                         m->mothurConvert(temp, processors);
 146
 147                         temp = validParameter.validFile(parameters, "countgaps", false);        if (temp == "not found") { temp = "f"; }
 148                         countGaps = m->isTrue(temp);
 149
 150                         temp = validParameter.validFile(parameters, "short", false);    if (temp == "not found") { temp = "f"; }
 151                         Short = m->isTrue(temp);
 152
 153                         keep = validParameter.validFile(parameters, "keep", false);             if (keep == "not found") { keep = "front"; }
 154
 155                         if (numbases == 0)  { m->mothurOut("You must provide the number of bases you want to keep for the chops.seqs command."); m->mothurOutEndLine(); abort = true;  }
 156                 }
 157
 158         }
 159         catch(exception& e) {
 160                 m->errorOut(e, "ChopSeqsCommand", "ChopSeqsCommand");
 161                 exit(1);
 162         }
 163 }
 164 //**********************************************************************************************************************
 165
 166 int ChopSeqsCommand::execute(){
 167         try {
 168
 169                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 170
 171         map<string, string> variables;
 172         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
 173         string outputFileName = getOutputFileName("fasta", variables);
 174         string outputFileNameAccnos = getOutputFileName("accnos", variables);
 175
 176         vector<unsigned long long> positions;
 177         vector<linePair> lines;
 178 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 179         positions = m->divideFile(fastafile, processors);
 180         for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(linePair(positions[i], positions[(i+1)]));      }
 181 #else
 182         int numSeqs = 0;
 183         positions = m->setFilePosFasta(fastafile, numSeqs);
 184         if (positions.size() < processors) { processors = positions.size(); }
 185
 186         //figure out how many sequences you have to process
 187         int numSeqsPerProcessor = numSeqs / processors;
 188         for (int i = 0; i < processors; i++) {
 189             int startIndex =  i * numSeqsPerProcessor;
 190             if(i == (processors - 1)){  numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;        }
 191             lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
 192         }
 193 #endif
 194
 195         bool wroteAccnos = false;
 196         if(processors == 1) {   wroteAccnos = driver(lines[0], fastafile, outputFileName, outputFileNameAccnos);        }
 197         else                {   wroteAccnos = createProcesses(lines, fastafile, outputFileName, outputFileNameAccnos);  }
 198
 199         if (m->control_pressed) {  return 0; }
 200
 201                 m->mothurOutEndLine();
 202                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 203                 m->mothurOut(outputFileName); m->mothurOutEndLine();    outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
 204
 205                 if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine(); outputNames.push_back(outputFileNameAccnos); outputTypes["accnos"].push_back(outputFileNameAccnos); }
 206                 else {  m->mothurRemove(outputFileNameAccnos);  }
 207
 208                 m->mothurOutEndLine();
 209
 210                 //set fasta file as new current fastafile
 211                 string current = "";
 212                 itTypes = outputTypes.find("fasta");
 213                 if (itTypes != outputTypes.end()) {
 214                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 215                 }
 216
 217                 if (wroteAccnos) { //set accnos file as new current accnosfile
 218                         itTypes = outputTypes.find("accnos");
 219                         if (itTypes != outputTypes.end()) {
 220                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 221                         }
 222                 }
 223
 224
 225                 return 0;
 226         }
 227
 228         catch(exception& e) {
 229                 m->errorOut(e, "ChopSeqsCommand", "execute");
 230                 exit(1);
 231         }
 232 }
 233 /**************************************************************************************************/
 234 bool ChopSeqsCommand::createProcesses(vector<linePair> lines, string filename, string outFasta, string outAccnos) {
 235         try {
 236                 int process = 1;
 237                 bool wroteAccnos = false;
 238                 vector<int> processIDS;
 239         vector<string> nonBlankAccnosFiles;
 240
 241 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 242
 243                 //loop through and create all the processes you want
 244                 while (process != processors) {
 245                         int pid = fork();
 246
 247                         if (pid > 0) {
 248                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 249                                 process++;
 250                         }else if (pid == 0){
 251                                 wroteAccnos = driver(lines[process], filename, outFasta + toString(getpid()) + ".temp", outAccnos + toString(getpid()) + ".temp");
 252
 253                                 //pass numSeqs to parent
 254                                 ofstream out;
 255                                 string tempFile = fastafile + toString(getpid()) + ".bool.temp";
 256                                 m->openOutputFile(tempFile, out);
 257                                 out << wroteAccnos << endl;
 258                                 out.close();
 259
 260                                 exit(0);
 261                         }else {
 262                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 263                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 264                                 exit(0);
 265                         }
 266                 }
 267
 268                 //do your part
 269                 wroteAccnos = driver(lines[0], filename, outFasta, outAccnos);
 270
 271                 //force parent to wait until all the processes are done
 272                 for (int i=0;i<processIDS.size();i++) {
 273                         int temp = processIDS[i];
 274                         wait(&temp);
 275                 }
 276
 277
 278                 if (wroteAccnos) { nonBlankAccnosFiles.push_back(outAccnos); }
 279                 else { m->mothurRemove(outAccnos); } //remove so other files can be renamed to it
 280
 281                 //parent reads in and combine Filter info
 282                 for (int i = 0; i < processIDS.size(); i++) {
 283                         string tempFilename = fastafile + toString(processIDS[i]) + ".bool.temp";
 284                         ifstream in;
 285                         m->openInputFile(tempFilename, in);
 286
 287                         bool temp;
 288                         in >> temp; m->gobble(in);
 289             if (temp) { wroteAccnos = temp; nonBlankAccnosFiles.push_back(outAccnos + toString(processIDS[i]) + ".temp");  }
 290                         else { m->mothurRemove((outAccnos + toString(processIDS[i]) + ".temp"));  }
 291
 292                         in.close();
 293                         m->mothurRemove(tempFilename);
 294                 }
 295 #else
 296                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 297                 //Windows version shared memory, so be careful when passing variables through the seqSumData struct.
 298                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 299                 //Taking advantage of shared memory to allow both threads to add info to vectors.
 300                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 301
 302                 vector<chopData*> pDataArray;
 303                 DWORD   dwThreadIdArray[processors-1];
 304                 HANDLE  hThreadArray[processors-1];
 305
 306                 //Create processor worker threads.
 307                 for( int i=0; i<processors-1; i++ ){
 308
 309             string extension = "";
 310             if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
 311                         // Allocate memory for thread data.
 312                         chopData* tempChop = new chopData(filename, (outFasta+extension), (outAccnos+extension), m, lines[i].start, lines[i].end, keep, countGaps, numbases, Short);
 313                         pDataArray.push_back(tempChop);
 314
 315                         //MyChopThreadFunction is in header. It must be global or static to work with the threads.
 316                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 317                         hThreadArray[i] = CreateThread(NULL, 0, MyChopThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 318                 }
 319
 320         //do your part
 321                 wroteAccnos = driver(lines[processors-1], filename, (outFasta + toString(processors-1) + ".temp"), (outAccnos + toString(processors-1) + ".temp"));
 322         processIDS.push_back(processors-1);
 323
 324                 //Wait until all threads have terminated.
 325                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 326
 327         if (wroteAccnos) { nonBlankAccnosFiles.push_back(outAccnos); }
 328                 else { m->mothurRemove(outAccnos); } //remove so other files can be renamed to it
 329
 330                 //Close all thread handles and free memory allocations.
 331                 for(int i=0; i < pDataArray.size(); i++){
 332             if (pDataArray[i]->wroteAccnos) { wroteAccnos = pDataArray[i]->wroteAccnos; nonBlankAccnosFiles.push_back(outAccnos + toString(processIDS[i]) + ".temp");  }
 333                         else { m->mothurRemove((outAccnos + toString(processIDS[i]) + ".temp"));  }
 334             //check to make sure the process finished
 335             if (pDataArray[i]->count != pDataArray[i]->end) {
 336                 m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true;
 337             }
 338                         CloseHandle(hThreadArray[i]);
 339                         delete pDataArray[i];
 340                 }
 341 #endif
 342
 343                 for (int i = 0; i < processIDS.size(); i++) {
 344                         m->appendFiles((outFasta + toString(processIDS[i]) + ".temp"), outFasta);
 345                         m->mothurRemove((outFasta + toString(processIDS[i]) + ".temp"));
 346                 }
 347
 348         if (nonBlankAccnosFiles.size() != 0) {
 349                         m->renameFile(nonBlankAccnosFiles[0], outAccnos);
 350
 351                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 352                                 m->appendFiles(nonBlankAccnosFiles[h], outAccnos);
 353                                 m->mothurRemove(nonBlankAccnosFiles[h]);
 354                         }
 355                 }else { //recreate the accnosfile if needed
 356                         ofstream out;
 357                         m->openOutputFile(outAccnos, out);
 358                         out.close();
 359                 }
 360
 361                 return wroteAccnos;
 362         }
 363         catch(exception& e) {
 364                 m->errorOut(e, "ChopSeqsCommand", "createProcesses");
 365                 exit(1);
 366         }
 367 }
 368 /**************************************************************************************/
 369 bool ChopSeqsCommand::driver(linePair filePos, string filename, string outFasta, string outAccnos) {
 370         try {
 371
 372                 ofstream out;
 373                 m->openOutputFile(outFasta, out);
 374
 375         ofstream outAcc;
 376                 m->openOutputFile(outAccnos, outAcc);
 377
 378                 ifstream in;
 379                 m->openInputFile(filename, in);
 380
 381                 in.seekg(filePos.start);
 382
 383                 bool done = false;
 384         bool wroteAccnos = false;
 385                 int count = 0;
 386
 387                 while (!done) {
 388
 389                         if (m->control_pressed) { in.close(); out.close(); return 1; }
 390
 391                         Sequence seq(in); m->gobble(in);
 392
 393                         if (m->control_pressed) {  in.close(); out.close(); outAcc.close(); m->mothurRemove(outFasta); m->mothurRemove(outAccnos); return 0;  }
 394
 395                         if (seq.getName() != "") {
 396                                 string newSeqString = getChopped(seq);
 397
 398                                 //output trimmed sequence
 399                                 if (newSeqString != "") {
 400                                         out << ">" << seq.getName() << endl << newSeqString << endl;
 401                                 }else{
 402                                         outAcc << seq.getName() << endl;
 403                                         wroteAccnos = true;
 404                                 }
 405                 count++;
 406                         }
 407
 408 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 409             unsigned long long pos = in.tellg();
 410             if ((pos == -1) || (pos >= filePos.end)) { break; }
 411 #else
 412             if (in.eof()) { break; }
 413 #endif
 414             //report progress
 415                         if((count) % 1000 == 0){        m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 416
 417                 }
 418                 //report progress
 419                 if((count) % 1000 != 0){        m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 420
 421
 422                 in.close();
 423         out.close();
 424         outAcc.close();
 425
 426                 return wroteAccnos;
 427         }
 428         catch(exception& e) {
 429                 m->errorOut(e, "ChopSeqsCommand", "driver");
 430                 exit(1);
 431         }
 432 }
 433 //**********************************************************************************************************************
 434 string ChopSeqsCommand::getChopped(Sequence seq) {
 435         try {
 436                 string temp = seq.getAligned();
 437                 string tempUnaligned = seq.getUnaligned();
 438
 439                 if (countGaps) {
 440                         //if needed trim sequence
 441                         if (keep == "front") {//you want to keep the beginning
 442                                 int tempLength = temp.length();
 443
 444                                 if (tempLength > numbases) { //you have enough bases to remove some
 445
 446                                         int stopSpot = 0;
 447                                         int numBasesCounted = 0;
 448
 449                                         for (int i = 0; i < temp.length(); i++) {
 450                                                 //eliminate N's
 451                                                 if (toupper(temp[i]) == 'N') { temp[i] = '.'; }
 452
 453                                                 numBasesCounted++;
 454
 455                                                 if (numBasesCounted >= numbases) { stopSpot = i; break; }
 456                                         }
 457
 458                                         if (stopSpot == 0) { temp = ""; }
 459                                         else {  temp = temp.substr(0, stopSpot+1);  }
 460
 461                                 }else {
 462                                         if (!Short) { temp = ""; } //sequence too short
 463                                 }
 464                         }else { //you are keeping the back
 465                                 int tempLength = temp.length();
 466                                 if (tempLength > numbases) { //you have enough bases to remove some
 467
 468                                         int stopSpot = 0;
 469                                         int numBasesCounted = 0;
 470
 471                                         for (int i = (temp.length()-1); i >= 0; i--) {
 472                                                 //eliminate N's
 473                                                 if (toupper(temp[i]) == 'N') { temp[i] = '.'; }
 474
 475                                                 numBasesCounted++;
 476
 477                                                 if (numBasesCounted >= numbases) { stopSpot = i; break; }
 478                                         }
 479
 480                                         if (stopSpot == 0) { temp = ""; }
 481                                         else {  temp = temp.substr(stopSpot+1);  }
 482                                 }else {
 483                                         if (!Short) { temp = ""; } //sequence too short
 484                                 }
 485                         }
 486
 487                 }else{
 488
 489                         //if needed trim sequence
 490                         if (keep == "front") {//you want to keep the beginning
 491                                 int tempLength = tempUnaligned.length();
 492
 493                                 if (tempLength > numbases) { //you have enough bases to remove some
 494
 495                                         int stopSpot = 0;
 496                                         int numBasesCounted = 0;
 497
 498                                         for (int i = 0; i < temp.length(); i++) {
 499                                                 //eliminate N's
 500                                                 if (toupper(temp[i]) == 'N') {
 501                                                         temp[i] = '.';
 502                                                         tempLength--;
 503                                                         if (tempLength < numbases) { stopSpot = 0; break; }
 504                                                 }
 505
 506                                                 if(isalpha(temp[i])) { numBasesCounted++; }
 507
 508                                                 if (numBasesCounted >= numbases) { stopSpot = i; break; }
 509                                         }
 510
 511                                         if (stopSpot == 0) { temp = ""; }
 512                                         else {  temp = temp.substr(0, stopSpot+1);  }
 513
 514                                 }else {
 515                                         if (!Short) { temp = ""; } //sequence too short
 516                                 }
 517                         }else { //you are keeping the back
 518                                 int tempLength = tempUnaligned.length();
 519                                 if (tempLength > numbases) { //you have enough bases to remove some
 520
 521                                         int stopSpot = 0;
 522                                         int numBasesCounted = 0;
 523
 524                                         for (int i = (temp.length()-1); i >= 0; i--) {
 525                                                 //eliminate N's
 526                                                 if (toupper(temp[i]) == 'N') {
 527                                                         temp[i] = '.';
 528                                                         tempLength--;
 529                                                         if (tempLength < numbases) { stopSpot = 0; break; }
 530                                                 }
 531
 532                                                 if(isalpha(temp[i])) { numBasesCounted++; }
 533
 534                                                 if (numBasesCounted >= numbases) { stopSpot = i; break; }
 535                                         }
 536
 537                                         if (stopSpot == 0) { temp = ""; }
 538                                         else {  temp = temp.substr(stopSpot);  }
 539                                 }else {
 540                                         if (!Short) { temp = ""; } //sequence too short
 541                                 }
 542                         }
 543                 }
 544
 545                 return temp;
 546         }
 547         catch(exception& e) {
 548                 m->errorOut(e, "ChopSeqsCommand", "getChopped");
 549                 exit(1);
 550         }
 551 }
 552 //**********************************************************************************************************************
 553
 554