sffinfocommand.cpp

   1 /*
   2  *  sffinfocommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 7/7/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "sffinfocommand.h"
  11 #include "endiannessmacros.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> SffInfoCommand::getValidParameters(){
  15         try {
  16                 string Array[] =  {"sff","qfile","fasta","flow","trim","accnos","sfftxt","outputdir","inputdir", "outputdir"};
  17                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "SffInfoCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 SffInfoCommand::SffInfoCommand(){
  27         try {
  28                 abort = true;
  29                 //initialize outputTypes
  30                 vector<string> tempOutNames;
  31                 outputTypes["fasta"] = tempOutNames;
  32                 outputTypes["flow"] = tempOutNames;
  33                 outputTypes["sfftxt"] = tempOutNames;
  34                 outputTypes["qual"] = tempOutNames;
  35         }
  36         catch(exception& e) {
  37                 m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
  38                 exit(1);
  39         }
  40 }
  41 //**********************************************************************************************************************
  42 vector<string> SffInfoCommand::getRequiredParameters(){
  43         try {
  44                 string Array[] =  {"sff", "sfftxt", "or"};
  45                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  46                 return myArray;
  47         }
  48         catch(exception& e) {
  49                 m->errorOut(e, "SffInfoCommand", "getRequiredParameters");
  50                 exit(1);
  51         }
  52 }
  53 //**********************************************************************************************************************
  54 vector<string> SffInfoCommand::getRequiredFiles(){
  55         try {
  56                 vector<string> myArray;
  57                 return myArray;
  58         }
  59         catch(exception& e) {
  60                 m->errorOut(e, "SffInfoCommand", "getRequiredFiles");
  61                 exit(1);
  62         }
  63 }
  64 //**********************************************************************************************************************
  65
  66 SffInfoCommand::SffInfoCommand(string option)  {
  67         try {
  68                 abort = false;
  69                 hasAccnos = false;
  70
  71                 //allow user to run help
  72                 if(option == "help") { help(); abort = true; }
  73
  74                 else {
  75                         //valid paramters for this command
  76                         string Array[] =  {"sff","qfile","fasta","flow","trim","accnos","sfftxt","outputdir","inputdir", "outputdir"};
  77                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  78
  79                         OptionParser parser(option);
  80                         map<string, string> parameters = parser.getParameters();
  81
  82                         ValidParameters validParameter;
  83                         //check to make sure all parameters are valid for command
  84                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  85                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  86                         }
  87
  88                         //initialize outputTypes
  89                         vector<string> tempOutNames;
  90                         outputTypes["fasta"] = tempOutNames;
  91                         outputTypes["flow"] = tempOutNames;
  92                         outputTypes["sfftxt"] = tempOutNames;
  93                         outputTypes["qual"] = tempOutNames;
  94
  95                         //if the user changes the output directory command factory will send this info to us in the output parameter
  96                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
  97
  98                         //if the user changes the input directory command factory will send this info to us in the output parameter
  99                         string inputDir = validParameter.validFile(parameters, "inputdir", false);        if (inputDir == "not found"){ inputDir = "";          }
 100
 101                         sffFilename = validParameter.validFile(parameters, "sff", false);
 102                         if (sffFilename == "not found") { sffFilename = "";  }
 103                         else {
 104                                 m->splitAtDash(sffFilename, filenames);
 105
 106                                 //go through files and make sure they are good, if not, then disregard them
 107                                 for (int i = 0; i < filenames.size(); i++) {
 108                                         if (inputDir != "") {
 109                                                 string path = m->hasPath(filenames[i]);
 110                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 111                                                 if (path == "") {       filenames[i] = inputDir + filenames[i];         }
 112                                         }
 113
 114                                         ifstream in;
 115                                         int ableToOpen = m->openInputFile(filenames[i], in, "noerror");
 116
 117                                         //if you can't open it, try default location
 118                                         if (ableToOpen == 1) {
 119                                                 if (m->getDefaultPath() != "") { //default path is set
 120                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(filenames[i]);
 121                                                         m->mothurOut("Unable to open " + filenames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 122                                                         ifstream in2;
 123                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 124                                                         in2.close();
 125                                                         filenames[i] = tryPath;
 126                                                 }
 127                                         }
 128
 129                                         //if you can't open it, try default location
 130                                         if (ableToOpen == 1) {
 131                                                 if (m->getOutputDir() != "") { //default path is set
 132                                                         string tryPath = m->getOutputDir() + m->getSimpleName(filenames[i]);
 133                                                         m->mothurOut("Unable to open " + filenames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 134                                                         ifstream in2;
 135                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 136                                                         in2.close();
 137                                                         filenames[i] = tryPath;
 138                                                 }
 139                                         }
 140
 141                                         in.close();
 142
 143                                         if (ableToOpen == 1) {
 144                                                 m->mothurOut("Unable to open " + filenames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 145                                                 //erase from file list
 146                                                 filenames.erase(filenames.begin()+i);
 147                                                 i--;
 148                                         }
 149                                 }
 150
 151                                 //make sure there is at least one valid file left
 152                                 if (filenames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 153                         }
 154
 155                         accnosName = validParameter.validFile(parameters, "accnos", false);
 156                         if (accnosName == "not found") { accnosName = "";  }
 157                         else {
 158                                 hasAccnos = true;
 159                                 m->splitAtDash(accnosName, accnosFileNames);
 160
 161                                 //go through files and make sure they are good, if not, then disregard them
 162                                 for (int i = 0; i < accnosFileNames.size(); i++) {
 163                                         if (inputDir != "") {
 164                                                 string path = m->hasPath(accnosFileNames[i]);
 165                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 166                                                 if (path == "") {       accnosFileNames[i] = inputDir + accnosFileNames[i];             }
 167                                         }
 168
 169                                         ifstream in;
 170                                         int ableToOpen = m->openInputFile(accnosFileNames[i], in, "noerror");
 171
 172                                         //if you can't open it, try default location
 173                                         if (ableToOpen == 1) {
 174                                                 if (m->getDefaultPath() != "") { //default path is set
 175                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(accnosFileNames[i]);
 176                                                         m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 177                                                         ifstream in2;
 178                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 179                                                         in2.close();
 180                                                         accnosFileNames[i] = tryPath;
 181                                                 }
 182                                         }
 183                                         //if you can't open it, try default location
 184                                         if (ableToOpen == 1) {
 185                                                 if (m->getOutputDir() != "") { //default path is set
 186                                                         string tryPath = m->getOutputDir() + m->getSimpleName(accnosFileNames[i]);
 187                                                         m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 188                                                         ifstream in2;
 189                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 190                                                         in2.close();
 191                                                         accnosFileNames[i] = tryPath;
 192                                                 }
 193                                         }
 194                                         in.close();
 195
 196                                         if (ableToOpen == 1) {
 197                                                 m->mothurOut("Unable to open " + accnosFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 198                                                 //erase from file list
 199                                                 accnosFileNames.erase(accnosFileNames.begin()+i);
 200                                                 i--;
 201                                         }
 202                                 }
 203
 204                                 //make sure there is at least one valid file left
 205                                 if (accnosFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 206                         }
 207
 208                         if (hasAccnos) {
 209                                 if (accnosFileNames.size() != filenames.size()) { abort = true; m->mothurOut("If you provide a accnos file, you must have one for each sff file."); m->mothurOutEndLine(); }
 210                         }
 211
 212                         string temp = validParameter.validFile(parameters, "qfile", false);                     if (temp == "not found"){       temp = "T";                             }
 213                         qual = m->isTrue(temp);
 214
 215                         temp = validParameter.validFile(parameters, "fasta", false);                            if (temp == "not found"){       temp = "T";                             }
 216                         fasta = m->isTrue(temp);
 217
 218                         temp = validParameter.validFile(parameters, "flow", false);                                     if (temp == "not found"){       temp = "F";                             }
 219                         flow = m->isTrue(temp);
 220
 221                         temp = validParameter.validFile(parameters, "trim", false);                                     if (temp == "not found"){       temp = "T";                             }
 222                         trim = m->isTrue(temp);
 223
 224                         temp = validParameter.validFile(parameters, "sfftxt", false);
 225                         if (temp == "not found")        {       temp = "F";      sfftxt = false; sfftxtFilename = "";           }
 226                         else if (m->isTrue(temp))       {       sfftxt = true;          sfftxtFilename = "";                            }
 227                         else {
 228                                 //you are a filename
 229                                 if (inputDir != "") {
 230                                         map<string,string>::iterator it = parameters.find("sfftxt");
 231                                         //user has given a template file
 232                                         if(it != parameters.end()){
 233                                                 string path = m->hasPath(it->second);
 234                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 235                                                 if (path == "") {       parameters["sfftxt"] = inputDir + it->second;           }
 236                                         }
 237                                 }
 238
 239                                 sfftxtFilename = validParameter.validFile(parameters, "sfftxt", true);
 240                                 if (sfftxtFilename == "not found") { sfftxtFilename = "";  }
 241                                 else if (sfftxtFilename == "not open") { sfftxtFilename = "";  }
 242                         }
 243
 244                         if ((sfftxtFilename == "") && (filenames.size() == 0)) {  m->mothurOut("[ERROR]: you must provide a valid sff or sfftxt file."); m->mothurOutEndLine(); abort=true; }
 245                 }
 246         }
 247         catch(exception& e) {
 248                 m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
 249                 exit(1);
 250         }
 251 }
 252 //**********************************************************************************************************************
 253
 254 void SffInfoCommand::help(){
 255         try {
 256                 m->mothurOut("The sffinfo command reads a sff file and extracts the sequence data, or you can use it to parse a sfftxt file..\n");
 257                 m->mothurOut("The sffinfo command parameters are sff, fasta, qfile, accnos, flow, sfftxt, and trim. sff is required. \n");
 258                 m->mothurOut("The sff parameter allows you to enter the sff file you would like to extract data from.  You may enter multiple files by separating them by -'s.\n");
 259                 m->mothurOut("The fasta parameter allows you to indicate if you would like a fasta formatted file generated.  Default=True. \n");
 260                 m->mothurOut("The qfile parameter allows you to indicate if you would like a quality file generated.  Default=True. \n");
 261                 m->mothurOut("The flow parameter allows you to indicate if you would like a flowgram file generated.  Default=False. \n");
 262                 m->mothurOut("The sfftxt parameter allows you to indicate if you would like a sff.txt file generated.  Default=False. \n");
 263                 m->mothurOut("If you want to parse an existing sfftxt file into flow, fasta and quality file, enter the file name using the sfftxt parameter. \n");
 264                 m->mothurOut("The trim parameter allows you to indicate if you would like a sequences and quality scores trimmed to the clipQualLeft and clipQualRight values.  Default=True. \n");
 265                 m->mothurOut("The accnos parameter allows you to provide a accnos file containing the names of the sequences you would like extracted. You may enter multiple files by separating them by -'s. \n");
 266                 m->mothurOut("Example sffinfo(sff=mySffFile.sff, trim=F).\n");
 267                 m->mothurOut("Note: No spaces between parameter labels (i.e. sff), '=' and parameters (i.e.yourSffFileName).\n\n");
 268         }
 269         catch(exception& e) {
 270                 m->errorOut(e, "SffInfoCommand", "help");
 271                 exit(1);
 272         }
 273 }
 274 //**********************************************************************************************************************
 275
 276 SffInfoCommand::~SffInfoCommand(){}
 277
 278 //**********************************************************************************************************************
 279 int SffInfoCommand::execute(){
 280         try {
 281
 282                 if (abort == true) { return 0; }
 283
 284                 for (int s = 0; s < filenames.size(); s++) {
 285
 286                         if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         } return 0; }
 287
 288                         int start = time(NULL);
 289
 290                         m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
 291
 292                         string accnos = "";
 293                         if (hasAccnos) { accnos = accnosFileNames[s]; }
 294
 295                         int numReads = extractSffInfo(filenames[s], accnos);
 296
 297                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to extract " + toString(numReads) + ".");
 298                 }
 299
 300                 if (sfftxtFilename != "") {  parseSffTxt(); }
 301
 302                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         } return 0; }
 303
 304                 //report output filenames
 305                 m->mothurOutEndLine();
 306                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 307                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 308                 m->mothurOutEndLine();
 309
 310                 return 0;
 311         }
 312         catch(exception& e) {
 313                 m->errorOut(e, "SffInfoCommand", "execute");
 314                 exit(1);
 315         }
 316 }
 317 //**********************************************************************************************************************
 318 int SffInfoCommand::extractSffInfo(string input, string accnos){
 319         try {
 320
 321                 if (outputDir == "") {  outputDir += m->hasPath(input); }
 322
 323                 if (accnos != "")       {  readAccnosFile(accnos);  }
 324                 else                            {       seqNames.clear();               }
 325
 326                 ofstream outSfftxt, outFasta, outQual, outFlow;
 327                 string outFastaFileName, outQualFileName;
 328                 string sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "sff.txt";
 329                 string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "flow";
 330                 if (trim) {
 331                         outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "fasta";
 332                         outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "qual";
 333                 }else{
 334                         outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.fasta";
 335                         outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.qual";
 336                 }
 337
 338                 if (sfftxt) { m->openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint);  outputNames.push_back(sfftxtFileName);  outputTypes["sfftxt"].push_back(sfftxtFileName); }
 339                 if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
 340                 if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qual"].push_back(outQualFileName);  }
 341                 if (flow)       { m->openOutputFile(outFlowFileName, outFlow);          outputNames.push_back(outFlowFileName);  outFlow.setf(ios::fixed, ios::floatfield); outFlow.setf(ios::showpoint); outputTypes["flow"].push_back(outFlowFileName);  }
 342
 343                 ifstream in;
 344                 in.open(input.c_str(), ios::binary);
 345
 346                 CommonHeader header;
 347                 readCommonHeader(in, header);
 348
 349                 int count = 0;
 350
 351                 //check magic number and version
 352                 if (header.magicNumber != 779314790) { m->mothurOut("Magic Number is not correct, not a valid .sff file"); m->mothurOutEndLine(); return count; }
 353                 if (header.version != "0001") { m->mothurOut("Version is not supported, only support version 0001."); m->mothurOutEndLine(); return count; }
 354
 355                 //print common header
 356                 if (sfftxt) {   printCommonHeader(outSfftxt, header);           }
 357                 if (flow)       {       outFlow << header.numFlowsPerRead << endl;      }
 358
 359                 //read through the sff file
 360                 while (!in.eof()) {
 361
 362                         bool print = true;
 363
 364                         //read header
 365                         Header readheader;
 366                         readHeader(in, readheader);
 367
 368                         //read data
 369                         seqRead read;
 370                         readSeqData(in, read, header.numFlowsPerRead, readheader.numBases);
 371
 372                         //if you have provided an accosfile and this seq is not in it, then dont print
 373                         if (seqNames.size() != 0) {   if (seqNames.count(readheader.name) == 0) { print = false; }  }
 374
 375                         //print
 376                         if (print) {
 377                                 if (sfftxt) { printHeader(outSfftxt, readheader); printSffTxtSeqData(outSfftxt, read, readheader); }
 378                                 if (fasta)      {       printFastaSeqData(outFasta, read, readheader);  }
 379                                 if (qual)       {       printQualSeqData(outQual, read, readheader);    }
 380                                 if (flow)       {       printFlowSeqData(outFlow, read, readheader);    }
 381                         }
 382
 383                         count++;
 384
 385                         //report progress
 386                         if((count+1) % 10000 == 0){     m->mothurOut(toString(count+1)); m->mothurOutEndLine();         }
 387
 388                         if (m->control_pressed) { count = 0; break;   }
 389
 390                         if (count >= header.numReads) { break; }
 391                 }
 392
 393                 //report progress
 394                 if (!m->control_pressed) {   if((count) % 10000 != 0){  m->mothurOut(toString(count)); m->mothurOutEndLine();           }  }
 395
 396                 in.close();
 397
 398                 if (sfftxt) {  outSfftxt.close();       }
 399                 if (fasta)      {  outFasta.close();    }
 400                 if (qual)       {  outQual.close();             }
 401                 if (flow)       {  outFlow.close();             }
 402
 403                 return count;
 404         }
 405         catch(exception& e) {
 406                 m->errorOut(e, "SffInfoCommand", "extractSffInfo");
 407                 exit(1);
 408         }
 409 }
 410 //**********************************************************************************************************************
 411 int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
 412         try {
 413
 414                 if (!in.eof()) {
 415
 416                         //read magic number
 417                         char buffer[4];
 418                         in.read(buffer, 4);
 419                         header.magicNumber = be_int4(*(unsigned int *)(&buffer));
 420
 421                         //read version
 422                         char buffer9[4];
 423                         in.read(buffer9, 4);
 424                         header.version = "";
 425                         for (int i = 0; i < 4; i++) {  header.version += toString((int)(buffer9[i])); }
 426
 427                         //read offset
 428                         char buffer2 [8];
 429                         in.read(buffer2, 8);
 430                         header.indexOffset =  be_int8(*(unsigned long int *)(&buffer2));
 431
 432                         //read index length
 433                         char buffer3 [4];
 434                         in.read(buffer3, 4);
 435                         header.indexLength =  be_int4(*(unsigned int *)(&buffer3));
 436
 437                         //read num reads
 438                         char buffer4 [4];
 439                         in.read(buffer4, 4);
 440                         header.numReads =  be_int4(*(unsigned int *)(&buffer4));
 441
 442                         //read header length
 443                         char buffer5 [2];
 444                         in.read(buffer5, 2);
 445                         header.headerLength =  be_int2(*(unsigned short *)(&buffer5));
 446
 447                         //read key length
 448                         char buffer6 [2];
 449                         in.read(buffer6, 2);
 450                         header.keyLength = be_int2(*(unsigned short *)(&buffer6));
 451
 452                         //read number of flow reads
 453                         char buffer7 [2];
 454                         in.read(buffer7, 2);
 455                         header.numFlowsPerRead =  be_int2(*(unsigned short *)(&buffer7));
 456
 457                         //read format code
 458                         char buffer8 [1];
 459                         in.read(buffer8, 1);
 460                         header.flogramFormatCode = (int)(buffer8[0]);
 461
 462                         //read flow chars
 463                         char* tempBuffer = new char[header.numFlowsPerRead];
 464                         in.read(&(*tempBuffer), header.numFlowsPerRead);
 465                         header.flowChars = tempBuffer;
 466                         if (header.flowChars.length() > header.numFlowsPerRead) { header.flowChars = header.flowChars.substr(0, header.numFlowsPerRead);  }
 467                         delete[] tempBuffer;
 468
 469                         //read key
 470                         char* tempBuffer2 = new char[header.keyLength];
 471                         in.read(&(*tempBuffer2), header.keyLength);
 472                         header.keySequence = tempBuffer2;
 473                         if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength);  }
 474                         delete[] tempBuffer2;
 475
 476                         /* Pad to 8 chars */
 477                         unsigned long int spotInFile = in.tellg();
 478                         unsigned long int spot = (spotInFile + 7)& ~7;  // ~ inverts
 479                         in.seekg(spot);
 480
 481                 }else{
 482                         m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
 483                 }
 484
 485                 return 0;
 486         }
 487         catch(exception& e) {
 488                 m->errorOut(e, "SffInfoCommand", "readCommonHeader");
 489                 exit(1);
 490         }
 491 }
 492 //**********************************************************************************************************************
 493 int SffInfoCommand::readHeader(ifstream& in, Header& header){
 494         try {
 495
 496                 if (!in.eof()) {
 497
 498                         //read header length
 499                         char buffer [2];
 500                         in.read(buffer, 2);
 501                         header.headerLength = be_int2(*(unsigned short *)(&buffer));
 502
 503                         //read name length
 504                         char buffer2 [2];
 505                         in.read(buffer2, 2);
 506                         header.nameLength = be_int2(*(unsigned short *)(&buffer2));
 507
 508                         //read num bases
 509                         char buffer3 [4];
 510                         in.read(buffer3, 4);
 511                         header.numBases =  be_int4(*(unsigned int *)(&buffer3));
 512
 513                         //read clip qual left
 514                         char buffer4 [2];
 515                         in.read(buffer4, 2);
 516                         header.clipQualLeft =  be_int2(*(unsigned short *)(&buffer4));
 517                         header.clipQualLeft = 5;
 518
 519                         //read clip qual right
 520                         char buffer5 [2];
 521                         in.read(buffer5, 2);
 522                         header.clipQualRight =  be_int2(*(unsigned short *)(&buffer5));
 523
 524                         //read clipAdapterLeft
 525                         char buffer6 [2];
 526                         in.read(buffer6, 2);
 527                         header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));
 528
 529                         //read clipAdapterRight
 530                         char buffer7 [2];
 531                         in.read(buffer7, 2);
 532                         header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));
 533
 534                         //read name
 535                         char* tempBuffer = new char[header.nameLength];
 536                         in.read(&(*tempBuffer), header.nameLength);
 537                         header.name = tempBuffer;
 538                         if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength);  }
 539                         delete[] tempBuffer;
 540
 541                         //extract info from name
 542                         decodeName(header.timestamp, header.region, header.xy, header.name);
 543
 544                         /* Pad to 8 chars */
 545                         unsigned long int spotInFile = in.tellg();
 546                         unsigned long int spot = (spotInFile + 7)& ~7;
 547                         in.seekg(spot);
 548
 549                 }else{
 550                         m->mothurOut("Error reading sff header info."); m->mothurOutEndLine();
 551                 }
 552
 553                 return 0;
 554         }
 555         catch(exception& e) {
 556                 m->errorOut(e, "SffInfoCommand", "readHeader");
 557                 exit(1);
 558         }
 559 }
 560 //**********************************************************************************************************************
 561 int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, int numBases){
 562         try {
 563
 564                 if (!in.eof()) {
 565
 566                         //read flowgram
 567                         read.flowgram.resize(numFlowReads);
 568                         for (int i = 0; i < numFlowReads; i++) {
 569                                 char buffer [2];
 570                                 in.read(buffer, 2);
 571                                 read.flowgram[i] = be_int2(*(unsigned short *)(&buffer));
 572                         }
 573
 574                         //read flowIndex
 575                         read.flowIndex.resize(numBases);
 576                         for (int i = 0; i < numBases; i++) {
 577                                 char temp[1];
 578                                 in.read(temp, 1);
 579                                 read.flowIndex[i] = be_int1(*(unsigned char *)(&temp));
 580                         }
 581
 582                         //read bases
 583                         char* tempBuffer = new char[numBases];
 584                         in.read(&(*tempBuffer), numBases);
 585                         read.bases = tempBuffer;
 586                         if (read.bases.length() > numBases) { read.bases = read.bases.substr(0, numBases);  }
 587                         delete[] tempBuffer;
 588
 589                         //read qual scores
 590                         read.qualScores.resize(numBases);
 591                         for (int i = 0; i < numBases; i++) {
 592                                 char temp[1];
 593                                 in.read(temp, 1);
 594                                 read.qualScores[i] = be_int1(*(unsigned char *)(&temp));
 595                         }
 596
 597                         /* Pad to 8 chars */
 598                         unsigned long int spotInFile = in.tellg();
 599                         unsigned long int spot = (spotInFile + 7)& ~7;
 600                         in.seekg(spot);
 601
 602                 }else{
 603                         m->mothurOut("Error reading."); m->mothurOutEndLine();
 604                 }
 605
 606                 return 0;
 607         }
 608         catch(exception& e) {
 609                 m->errorOut(e, "SffInfoCommand", "readSeqData");
 610                 exit(1);
 611         }
 612 }
 613 //**********************************************************************************************************************
 614 int SffInfoCommand::decodeName(string& timestamp, string& region, string& xy, string name) {
 615         try {
 616
 617                 string time = name.substr(0, 6);
 618                 unsigned int timeNum = m->fromBase36(time);
 619
 620                 int q1 = timeNum / 60;
 621                 int sec = timeNum - 60 * q1;
 622                 int q2 = q1 / 60;
 623                 int minute = q1 - 60 * q2;
 624                 int q3 = q2 / 24;
 625                 int hr = q2 - 24 * q3;
 626                 int q4 = q3 / 32;
 627                 int day = q3 - 32 * q4;
 628                 int q5 = q4 / 13;
 629                 int mon = q4 - 13 * q5;
 630                 int year = 2000 + q5;
 631
 632                 timestamp = toString(year) + "_" + toString(mon) + "_" + toString(day) + "_" + toString(hr) + "_" + toString(minute) + "_" + toString(sec);
 633
 634                 region = name.substr(7, 2);
 635
 636                 string xyNum = name.substr(9);
 637                 unsigned int myXy = m->fromBase36(xyNum);
 638                 int x = myXy >> 12;
 639                 int y = myXy & 4095;
 640
 641                 xy = toString(x) + "_" + toString(y);
 642
 643                 return 0;
 644         }
 645         catch(exception& e) {
 646                 m->errorOut(e, "SffInfoCommand", "decodeName");
 647                 exit(1);
 648         }
 649 }
 650 //**********************************************************************************************************************
 651 int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader& header) {
 652         try {
 653
 654                 out << "Common Header:\nMagic Number: " << header.magicNumber << endl;
 655                 out << "Version: " << header.version << endl;
 656                 out << "Index Offset: " << header.indexOffset << endl;
 657                 out << "Index Length: " << header.indexLength << endl;
 658                 out << "Number of Reads: " << header.numReads << endl;
 659                 out << "Header Length: " << header.headerLength << endl;
 660                 out << "Key Length: " << header.keyLength << endl;
 661                 out << "Number of Flows: " << header.numFlowsPerRead << endl;
 662                 out << "Format Code: " << header.flogramFormatCode << endl;
 663                 out << "Flow Chars: " << header.flowChars << endl;
 664                 out << "Key Sequence: " << header.keySequence << endl << endl;
 665
 666                 return 0;
 667         }
 668         catch(exception& e) {
 669                 m->errorOut(e, "SffInfoCommand", "printCommonHeader");
 670                 exit(1);
 671         }
 672 }
 673 //**********************************************************************************************************************
 674 int SffInfoCommand::printHeader(ofstream& out, Header& header) {
 675         try {
 676
 677                 out << ">" << header.name << endl;
 678                 out << "Run Prefix: " << header.timestamp << endl;
 679                 out << "Region #:  " << header.region << endl;
 680                 out << "XY Location: " << header.xy << endl << endl;
 681
 682                 out << "Run Name:  " << endl;
 683                 out << "Analysis Name:  " << endl;
 684                 out << "Full Path: " << endl << endl;
 685
 686                 out << "Read Header Len: " << header.headerLength << endl;
 687                 out << "Name Length: " << header.nameLength << endl;
 688                 out << "# of Bases: " << header.numBases << endl;
 689                 out << "Clip Qual Left: " << header.clipQualLeft << endl;
 690                 out << "Clip Qual Right: " << header.clipQualRight << endl;
 691                 out << "Clip Adap Left: " << header.clipAdapterLeft << endl;
 692                 out << "Clip Adap Right: " << header.clipAdapterRight << endl << endl;
 693
 694                 return 0;
 695         }
 696         catch(exception& e) {
 697                 m->errorOut(e, "SffInfoCommand", "printHeader");
 698                 exit(1);
 699         }
 700 }
 701
 702 //**********************************************************************************************************************
 703 int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& header) {
 704         try {
 705
 706                 out << "Flowgram: ";
 707                 for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }
 708
 709                 out << endl <<  "Flow Indexes: ";
 710                 int sum = 0;
 711                 for (int i = 0; i < read.flowIndex.size(); i++) {  sum +=  read.flowIndex[i];  out << sum << '\t'; }
 712
 713                 //make the bases you want to clip lowercase and the bases you want to keep upper case
 714                 if(header.clipQualRight == 0){  header.clipQualRight = read.bases.length();     }
 715                 for (int i = 0; i < (header.clipQualLeft-1); i++) { read.bases[i] = tolower(read.bases[i]); }
 716                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   read.bases[i] = toupper(read.bases[i]);  }
 717                 for (int i = (header.clipQualRight-1); i < read.bases.length(); i++) {   read.bases[i] = tolower(read.bases[i]);  }
 718
 719                 out << endl <<  "Bases: " << read.bases << endl << "Quality Scores: ";
 720                 for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
 721
 722
 723                 out << endl << endl;
 724
 725                 return 0;
 726         }
 727         catch(exception& e) {
 728                 m->errorOut(e, "SffInfoCommand", "printSffTxtSeqData");
 729                 exit(1);
 730         }
 731 }
 732 //**********************************************************************************************************************
 733 int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
 734         try {
 735
 736                 string seq = read.bases;
 737
 738                 if (trim) {
 739                         if(header.clipQualRight < header.clipQualLeft){
 740                                 seq = "NNNN";
 741                         }
 742                         else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
 743                                 seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
 744                         }
 745                         else {
 746                                 seq = seq.substr(header.clipQualLeft-1);
 747                         }
 748                 }else{
 749                         //if you wanted the sfftxt then you already converted the bases to the right case
 750                         if (!sfftxt) {
 751                                 //make the bases you want to clip lowercase and the bases you want to keep upper case
 752                                 if(header.clipQualRight == 0){  header.clipQualRight = seq.length();    }
 753                                 for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]);  }
 754                                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++)  {   seq[i] = toupper(seq[i]);  }
 755                                 for (int i = (header.clipQualRight-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
 756                         }
 757                 }
 758
 759                 out << ">" << header.name  << " xy=" << header.xy << endl;
 760                 out << seq << endl;
 761
 762                 return 0;
 763         }
 764         catch(exception& e) {
 765                 m->errorOut(e, "SffInfoCommand", "printFastaSeqData");
 766                 exit(1);
 767         }
 768 }
 769
 770 //**********************************************************************************************************************
 771 int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& header) {
 772         try {
 773
 774                 if (trim) {
 775                         if(header.clipQualRight < header.clipQualLeft){
 776                                 out << "0\t0\t0\t0";
 777                         }
 778                         else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
 779                                 out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
 780                                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   out << read.qualScores[i] << '\t'; }
 781                         }
 782                         else{
 783                                 out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
 784                                 for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';   }
 785                         }
 786                 }else{
 787                         out << ">" << header.name << " xy=" << header.xy << " length=" << read.qualScores.size() << endl;
 788                         for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
 789                 }
 790
 791                 out << endl;
 792
 793                 return 0;
 794         }
 795         catch(exception& e) {
 796                 m->errorOut(e, "SffInfoCommand", "printQualSeqData");
 797                 exit(1);
 798         }
 799 }
 800
 801 //**********************************************************************************************************************
 802 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
 803         try {
 804                 if(header.clipQualRight > header.clipQualLeft){
 805
 806                         int rightIndex = 0;
 807                         for (int i = 0; i < header.clipQualRight; i++) {  rightIndex +=  read.flowIndex[i];     }
 808
 809                         out << header.name << ' ' << rightIndex;
 810                         for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << ' ' << (read.flowgram[i]/(float)100);  }
 811                         out << endl;
 812                 }
 813
 814
 815                 return 0;
 816         }
 817         catch(exception& e) {
 818                 m->errorOut(e, "SffInfoCommand", "printFlowSeqData");
 819                 exit(1);
 820         }
 821 }
 822 //**********************************************************************************************************************
 823 int SffInfoCommand::readAccnosFile(string filename) {
 824         try {
 825                 //remove old names
 826                 seqNames.clear();
 827
 828                 ifstream in;
 829                 m->openInputFile(filename, in);
 830                 string name;
 831
 832                 while(!in.eof()){
 833                         in >> name; m->gobble(in);
 834
 835                         seqNames.insert(name);
 836
 837                         if (m->control_pressed) { seqNames.clear(); break; }
 838                 }
 839                 in.close();
 840
 841                 return 0;
 842         }
 843         catch(exception& e) {
 844                 m->errorOut(e, "SffInfoCommand", "readAccnosFile");
 845                 exit(1);
 846         }
 847 }
 848 //**********************************************************************************************************************
 849 int SffInfoCommand::parseSffTxt() {
 850         try {
 851
 852                 ifstream inSFF;
 853                 m->openInputFile(sfftxtFilename, inSFF);
 854
 855                 if (outputDir == "") {  outputDir += m->hasPath(sfftxtFilename); }
 856
 857                 //output file names
 858                 ofstream outFasta, outQual, outFlow;
 859                 string outFastaFileName, outQualFileName;
 860                 string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "flow";
 861                 if (trim) {
 862                         outFastaFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "fasta";
 863                         outQualFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "qual";
 864                 }else{
 865                         outFastaFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "raw.fasta";
 866                         outQualFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "raw.qual";
 867                 }
 868
 869                 if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
 870                 if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qual"].push_back(outQualFileName);  }
 871                 if (flow)       { m->openOutputFile(outFlowFileName, outFlow);          outputNames.push_back(outFlowFileName);  outFlow.setf(ios::fixed, ios::floatfield); outFlow.setf(ios::showpoint); outputTypes["flow"].push_back(outFlowFileName);  }
 872
 873                 //read common header
 874                 string commonHeader = m->getline(inSFF);
 875                 string magicNumber = m->getline(inSFF);
 876                 string version = m->getline(inSFF);
 877                 string indexOffset = m->getline(inSFF);
 878                 string indexLength = m->getline(inSFF);
 879                 int numReads = parseHeaderLineToInt(inSFF);
 880                 string headerLength = m->getline(inSFF);
 881                 string keyLength = m->getline(inSFF);
 882                 int numFlows = parseHeaderLineToInt(inSFF);
 883                 string flowgramCode = m->getline(inSFF);
 884                 string flowChars = m->getline(inSFF);
 885                 string keySequence = m->getline(inSFF);
 886                 m->gobble(inSFF);
 887
 888                 string seqName;
 889
 890                 if (flow)       {       outFlow << numFlows << endl;    }
 891
 892                 for(int i=0;i<numReads;i++){
 893
 894                         //sanity check
 895                         if (inSFF.eof()) { m->mothurOut("[ERROR]: Expected " + toString(numReads) + " but reached end of file at " + toString(i+1) + "."); m->mothurOutEndLine(); break; }
 896
 897                         Header header;
 898
 899                         //parse read header
 900                         inSFF >> seqName;
 901                         seqName = seqName.substr(1);
 902                         m->gobble(inSFF);
 903                         header.name = seqName;
 904
 905                         string runPrefix = parseHeaderLineToString(inSFF);              header.timestamp = runPrefix;
 906                         string regionNumber = parseHeaderLineToString(inSFF);   header.region = regionNumber;
 907                         string xyLocation = parseHeaderLineToString(inSFF);             header.xy = xyLocation;
 908                         m->gobble(inSFF);
 909
 910                         string runName = parseHeaderLineToString(inSFF);
 911                         string analysisName = parseHeaderLineToString(inSFF);
 912                         string fullPath = parseHeaderLineToString(inSFF);
 913                         m->gobble(inSFF);
 914
 915                         string readHeaderLen = parseHeaderLineToString(inSFF);  convert(readHeaderLen, header.headerLength);
 916                         string nameLength = parseHeaderLineToString(inSFF);             convert(nameLength, header.nameLength);
 917                         int numBases = parseHeaderLineToInt(inSFF);                             header.numBases = numBases;
 918                         string clipQualLeft = parseHeaderLineToString(inSFF);   convert(clipQualLeft, header.clipQualLeft);
 919                         int clipQualRight = parseHeaderLineToInt(inSFF);                header.clipQualRight = clipQualRight;
 920                         string clipAdapLeft = parseHeaderLineToString(inSFF);   convert(clipAdapLeft, header.clipAdapterLeft);
 921                         string clipAdapRight = parseHeaderLineToString(inSFF);  convert(clipAdapRight, header.clipAdapterRight);
 922                         m->gobble(inSFF);
 923
 924                         seqRead read;
 925
 926                         //parse read
 927                         vector<unsigned short> flowVector = parseHeaderLineToFloatVector(inSFF, numFlows);      read.flowgram = flowVector;
 928                         vector<unsigned int> flowIndices = parseHeaderLineToIntVector(inSFF, numBases);
 929
 930                         //adjust for print
 931                         vector<unsigned int> flowIndicesAdjusted; flowIndicesAdjusted.push_back(flowIndices[0]);
 932                         for (int j = 1; j < flowIndices.size(); j++) {   flowIndicesAdjusted.push_back(flowIndices[j] - flowIndices[j-1]);   }
 933                         read.flowIndex = flowIndicesAdjusted;
 934
 935                         string bases = parseHeaderLineToString(inSFF);                                                                          read.bases = bases;
 936                         vector<unsigned int> qualityScores = parseHeaderLineToIntVector(inSFF, numBases);       read.qualScores = qualityScores;
 937                         m->gobble(inSFF);
 938
 939                         //if you have provided an accosfile and this seq is not in it, then dont print
 940                         bool print = true;
 941                         if (seqNames.size() != 0) {   if (seqNames.count(header.name) == 0) { print = false; }  }
 942
 943                         //print
 944                         if (print) {
 945                                 if (fasta)      {       printFastaSeqData(outFasta, read, header);      }
 946                                 if (qual)       {       printQualSeqData(outQual, read, header);        }
 947                                 if (flow)       {       printFlowSeqData(outFlow, read, header);        }
 948                         }
 949
 950                         //report progress
 951                         if((i+1) % 10000 == 0){ m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 952
 953                         if (m->control_pressed) {  break;  }
 954                 }
 955
 956                 //report progress
 957                 if (!m->control_pressed) {   if((numReads) % 10000 != 0){       m->mothurOut(toString(numReads)); m->mothurOutEndLine();                }  }
 958
 959                 inSFF.close();
 960
 961                 if (fasta)      {  outFasta.close();    }
 962                 if (qual)       {  outQual.close();             }
 963                 if (flow)       {  outFlow.close();             }
 964
 965                 return 0;
 966         }
 967         catch(exception& e) {
 968                 m->errorOut(e, "SffInfoCommand", "parseSffTxt");
 969                 exit(1);
 970         }
 971 }
 972 //**********************************************************************************************************************
 973
 974 int SffInfoCommand::parseHeaderLineToInt(ifstream& file){
 975         try {
 976                 int number;
 977
 978                 while (!file.eof())     {
 979
 980                         char c = file.get();
 981                         if (c == ':'){
 982                                 file >> number;
 983                                 break;
 984                         }
 985
 986                 }
 987                 m->gobble(file);
 988                 return number;
 989         }
 990         catch(exception& e) {
 991                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToInt");
 992                 exit(1);
 993         }
 994
 995 }
 996
 997 //**********************************************************************************************************************
 998
 999 string SffInfoCommand::parseHeaderLineToString(ifstream& file){
1000         try {
1001                 string text;
1002
1003                 while (!file.eof())     {
1004                         char c = file.get();
1005
1006                         if (c == ':'){
1007                                 //m->gobble(file);
1008                                 //text = m->getline(file);
1009                                 file >> text;
1010                                 break;
1011                         }
1012                 }
1013                 m->gobble(file);
1014
1015                 return text;
1016         }
1017         catch(exception& e) {
1018                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToString");
1019                 exit(1);
1020         }
1021 }
1022
1023 //**********************************************************************************************************************
1024
1025 vector<unsigned short> SffInfoCommand::parseHeaderLineToFloatVector(ifstream& file, int length){
1026         try {
1027                 vector<unsigned short> floatVector(length);
1028
1029                 while (!file.eof())     {
1030                         char c = file.get();
1031                         if (c == ':'){
1032                                 float temp;
1033                                 for(int i=0;i<length;i++){
1034                                         file >> temp;
1035                                         floatVector[i] = temp * 100;
1036                                 }
1037                                 break;
1038                         }
1039                 }
1040                 m->gobble(file);
1041                 return floatVector;
1042         }
1043         catch(exception& e) {
1044                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToFloatVector");
1045                 exit(1);
1046         }
1047 }
1048
1049 //**********************************************************************************************************************
1050
1051 vector<unsigned int> SffInfoCommand::parseHeaderLineToIntVector(ifstream& file, int length){
1052         try {
1053                 vector<unsigned int> intVector(length);
1054
1055                 while (!file.eof())     {
1056                         char c = file.get();
1057                         if (c == ':'){
1058                                 for(int i=0;i<length;i++){
1059                                         file >> intVector[i];
1060                                 }
1061                                 break;
1062                         }
1063                 }
1064                 m->gobble(file);
1065                 return intVector;
1066         }
1067         catch(exception& e) {
1068                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToIntVector");
1069                 exit(1);
1070         }
1071 }
1072
1073 //**********************************************************************************************************************
1074
1075
1076
1077