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
  15 SffInfoCommand::SffInfoCommand(string option)  {
  16         try {
  17                 abort = false;
  18
  19                 //allow user to run help
  20                 if(option == "help") { help(); abort = true; }
  21
  22                 else {
  23                         //valid paramters for this command
  24                         string Array[] =  {"sff","outputdir","inputdir", "outputdir"};
  25                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  26
  27                         OptionParser parser(option);
  28                         map<string, string> parameters = parser.getParameters();
  29
  30                         ValidParameters validParameter;
  31                         //check to make sure all parameters are valid for command
  32                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  33                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  34                         }
  35
  36                         //if the user changes the output directory command factory will send this info to us in the output parameter
  37                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
  38
  39                         //if the user changes the input directory command factory will send this info to us in the output parameter
  40                         string inputDir = validParameter.validFile(parameters, "inputdir", false);        if (inputDir == "not found"){ inputDir = "";          }
  41
  42                         sffFilename = validParameter.validFile(parameters, "sff", false);
  43                         if (sffFilename == "not found") { m->mothurOut("sff is a required parameter for the sffinfo command."); m->mothurOutEndLine(); abort = true;  }
  44                         else {
  45                                 splitAtDash(sffFilename, filenames);
  46
  47                                 //go through files and make sure they are good, if not, then disregard them
  48                                 for (int i = 0; i < filenames.size(); i++) {
  49                                         if (inputDir != "") {
  50                                                 string path = hasPath(filenames[i]);
  51                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  52                                                 if (path == "") {       filenames[i] = inputDir + filenames[i];         }
  53                                         }
  54
  55                                         ifstream in;
  56                                         int ableToOpen = openInputFile(filenames[i], in);
  57                                         in.close();
  58
  59                                         if (ableToOpen == 1) {
  60                                                 m->mothurOut(filenames[i] + " will be disregarded."); m->mothurOutEndLine();
  61                                                 //erase from file list
  62                                                 filenames.erase(filenames.begin()+i);
  63                                                 i--;
  64                                         }
  65                                 }
  66
  67                                 //make sure there is at least one valid file left
  68                                 if (filenames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
  69                         }
  70                 }
  71         }
  72         catch(exception& e) {
  73                 m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
  74                 exit(1);
  75         }
  76 }
  77 //**********************************************************************************************************************
  78
  79 void SffInfoCommand::help(){
  80         try {
  81                 m->mothurOut("The sffinfo command reads a sff file and outputs a .sff.txt file.\n");
  82
  83                 m->mothurOut("Example sffinfo(sff=...).\n");
  84                 m->mothurOut("Note: No spaces between parameter labels (i.e. sff), '=' and parameters (i.e.yourSffFileName).\n\n");
  85         }
  86         catch(exception& e) {
  87                 m->errorOut(e, "SffInfoCommand", "help");
  88                 exit(1);
  89         }
  90 }
  91 //**********************************************************************************************************************
  92
  93 SffInfoCommand::~SffInfoCommand(){}
  94
  95 //**********************************************************************************************************************
  96 int SffInfoCommand::execute(){
  97         try {
  98
  99                 if (abort == true) { return 0; }
 100
 101                 for (int s = 0; s < filenames.size(); s++) {
 102
 103                         if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         } return 0; }
 104
 105                         m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
 106
 107                         if (outputDir == "") {  outputDir += hasPath(filenames[s]); }
 108                         string outputFileName = outputDir + getRootName(getSimpleName(filenames[s])) + "sff.txt";
 109
 110                         extractSffInfo(filenames[s], outputFileName);
 111
 112                         outputNames.push_back(outputFileName);
 113
 114                         m->mothurOut("Done."); m->mothurOutEndLine();
 115                 }
 116
 117                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         } return 0; }
 118
 119                 //report output filenames
 120                 m->mothurOutEndLine();
 121                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 122                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 123                 m->mothurOutEndLine();
 124
 125                 return 0;
 126         }
 127         catch(exception& e) {
 128                 m->errorOut(e, "SffInfoCommand", "execute");
 129                 exit(1);
 130         }
 131 }
 132 //**********************************************************************************************************************
 133 int SffInfoCommand::extractSffInfo(string input, string output){
 134         try {
 135                 ofstream out;
 136                 openOutputFile(output, out);
 137
 138                 ifstream in;
 139                 in.open(input.c_str(), ios::binary);
 140
 141                 CommonHeader* header = new CommonHeader();
 142                 readCommonHeader(in, header);
 143
 144                 cout << strlen(header->flowChars) << endl;
 145                 //cout << "magic = " << header->magicNumber << endl << "version = " << header->version << endl << "index offset = " << header->indexOffset << endl << "index length = "<< header->indexLength << endl << "numreads = " << header->numReads << endl << "header length = " << header->headerLength << endl << "key length = " << header->keyLength << endl;
 146 //cout << "numflowreads = "<< header->numFlowsPerRead << endl << "flow format code = "<< header->flogramFormatCode << endl << "flow chars = " << header->flowChars << endl << "key sequence = " << header->keySequence << endl << endl;
 147                 cout << in.tellg() << endl;
 148                 //read through the sff file
 149                 while (!in.eof()) {
 150                         //print common header
 151                         printCommonHeader(out, header, true);
 152
 153                         //read header
 154                         Header* readheader = new Header();
 155                         readHeader(in, readheader);
 156
 157                         cout << in.tellg() << endl;
 158
 159                         //print header
 160                         printHeader(out, readheader, true);
 161
 162                         //read data
 163                         seqRead* read = new seqRead();
 164                         readSeqData(in, read, header->numFlowsPerRead, readheader->numBases);
 165
 166                         cout << in.tellg() << endl;
 167
 168                         //print data
 169                         printSeqData(out, read, true);
 170
 171                 }
 172
 173
 174                 in.close();
 175                 out.close();
 176
 177                 return 0;
 178         }
 179         catch(exception& e) {
 180                 m->errorOut(e, "SffInfoCommand", "extractSffInfo");
 181                 exit(1);
 182         }
 183 }
 184 //**********************************************************************************************************************
 185 int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader*& header){
 186         try {
 187
 188                 if (!in.eof()) {
 189
 190                         //read magic number
 191                         char* buffer = new char(sizeof(header->magicNumber));
 192                         in.read(buffer, sizeof(header->magicNumber));
 193                         header->magicNumber = be_int4(*(unsigned int *)(buffer));
 194                         delete[] buffer;
 195         //cout << "here " << header->magicNumber << '\t' << in.tellg() << endl;
 196                         //read version
 197                         header->version = new char(4);
 198                         in.read(header->version, 4);
 199                         string tempBuf0 = header->version;
 200                         if (tempBuf0.length() > 4) { tempBuf0 = tempBuf0.substr(0, 4);  strcpy(header->version, tempBuf0.c_str());  }
 201                         //memcpy(header->version, buffer+4, 4);
 202         //cout << "here " << header->version  << '\t' << in.tellg() << endl;
 203                         //read offset
 204                         buffer = new char(sizeof(header->indexOffset));
 205                         in.read(buffer, sizeof(header->indexOffset));
 206                         header->indexOffset =  be_int8(*(unsigned long int *)(buffer));
 207                         delete[] buffer;
 208         //cout << "here " << header->indexOffset  << '\t' << in.tellg() << endl;
 209                         //read index length
 210                         buffer = new char(sizeof(header->indexLength));
 211                         in.read(buffer, sizeof(header->indexLength));
 212                         header->indexLength =  be_int4(*(unsigned int *)(buffer));
 213                         delete[] buffer;
 214         //cout << "here " << header->indexLength << '\t' << in.tellg() << endl;
 215                         //read num reads
 216                         buffer = new char(sizeof(header->numReads));
 217                         in.read(buffer, sizeof(header->numReads));
 218                         header->numReads =  be_int4(*(unsigned int *)(buffer));
 219                         delete[] buffer;
 220         //cout << "here " << header->numReads << '\t' << in.tellg() << endl;
 221                         //read header length
 222                         buffer = new char(sizeof(header->headerLength));
 223                         in.read(buffer, sizeof(header->headerLength));
 224                         header->headerLength =  be_int2(*(unsigned short *)(buffer));
 225                         delete[] buffer;
 226         //cout << "here " << header->headerLength << '\t' << in.tellg() << endl;
 227                         //read key length
 228                         buffer = new char(sizeof(header->keyLength));
 229                         in.read(buffer, sizeof(header->keyLength));
 230                         header->keyLength = be_int2(*(unsigned short *)(buffer));
 231                         delete[] buffer;
 232
 233 //cout << "here " << header->keyLength << '\t' << in.tellg() << endl;
 234                         //read number of flow reads
 235                         buffer = new char(sizeof(header->numFlowsPerRead));
 236                         in.read(buffer, sizeof(header->numFlowsPerRead));
 237                         header->numFlowsPerRead =  be_int2(*(unsigned short *)(buffer));
 238                         delete[] buffer;
 239                 //cout << "here " << header->numFlowsPerRead << '\t' << in.tellg() << endl;
 240                         //read format code
 241                         buffer = new char(sizeof(header->flogramFormatCode));
 242                         in.read(buffer, sizeof(header->flogramFormatCode));
 243                         header->flogramFormatCode = be_int1(*(char *)(buffer));
 244                         delete[] buffer;
 245         //cout << "here " << header->flogramFormatCode << '\t' << in.tellg() << endl;
 246
 247                         //read flow chars
 248                         //header->numFlowsPerRead = 800;
 249                         header->flowChars = new char(header->numFlowsPerRead);
 250                         buffer = new char(header->numFlowsPerRead);
 251         //cout << "here" << endl;
 252                         //in.read(header->flowChars, header->numFlowsPerRead);
 253                         in.read(buffer, header->numFlowsPerRead);
 254                         memcpy(header->flowChars, buffer, header->numFlowsPerRead);
 255                         delete[] buffer;
 256         //cout << "here" << endl;
 257                         //string tempBuf1 = header->flowChars;
 258         //cout << "here " << in.tellg() << endl;
 259                         //if (tempBuf1.length() > header->numFlowsPerRead) { tempBuf1 = tempBuf1.substr(0, header->numFlowsPerRead);  strcpy(header->flowChars, tempBuf1.c_str()); }
 260
 261         //      cout << "here " << header->flowChars << '\t' << in.tellg() << endl;
 262                         //read key
 263                         //header->keyLength = 4;
 264         //char* myAlloc2 = new char(4); cout << "alloced" << endl;
 265                         header->keySequence = new char(header->keyLength);
 266                         //char* myAlloc = new char(4);
 267         //      cout << "here " << endl;
 268                         in.read(header->keySequence, header->keyLength);
 269                         string tempBuf2 = header->keySequence;
 270                         if (tempBuf2.length() > header->keyLength) { tempBuf2 = tempBuf2.substr(0, header->keyLength);  strcpy(header->keySequence, tempBuf2.c_str()); }
 271         //cout << "here " << header->keySequence << '\t' << in.tellg() << endl;
 272
 273                         /* Pad to 8 chars */
 274                         int spotInFile = in.tellg();
 275         //cout << spotInFile << endl;
 276                         int spot = floor((spotInFile + 7) /(float) 8) * 8;
 277         //cout << spot << endl;
 278                         in.seekg(spot);
 279
 280         //exit(1);
 281
 282                 }else{
 283                         m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
 284                 }
 285
 286                 return 0;
 287         }
 288         catch(exception& e) {
 289                 m->errorOut(e, "SffInfoCommand", "readCommonHeader");
 290                 exit(1);
 291         }
 292 }
 293 //**********************************************************************************************************************
 294 int SffInfoCommand::readHeader(ifstream& in, Header*& header){
 295         try {
 296
 297                 if (!in.eof()) {
 298                         string tempBuf = "";
 299
 300                         //read header length
 301                         char* buffer = new char(sizeof(header->headerLength));
 302                         in.read(buffer, sizeof(header->headerLength));
 303                         header->headerLength = be_int2(*(unsigned short *)(buffer));
 304                         delete[] buffer;
 305
 306                         //read name length
 307                         buffer = new char(sizeof(header->nameLength));
 308                         in.read(buffer, sizeof(header->nameLength));
 309                         header->nameLength = be_int2(*(unsigned short *)(buffer));
 310                         delete[] buffer;
 311
 312                         //read num bases
 313                         buffer = new char(sizeof(header->numBases));
 314                         in.read(buffer, sizeof(header->numBases));
 315                         header->numBases =  be_int4(*(unsigned int *)(buffer));
 316                         delete[] buffer;
 317
 318                         //read clip qual left
 319                         buffer = new char(sizeof(header->clipQualLeft));
 320                         in.read(buffer, sizeof(header->clipQualLeft));
 321                         header->clipQualLeft =  be_int2(*(unsigned short *)(buffer));
 322                         delete[] buffer;
 323
 324                         //read clip qual right
 325                         buffer = new char(sizeof(header->clipQualRight));
 326                         in.read(buffer, sizeof(header->clipQualRight));
 327                         header->clipQualRight =  be_int2(*(unsigned short *)(buffer));
 328                         delete[] buffer;
 329
 330                         //read clipAdapterLeft
 331                         buffer = new char(sizeof(header->clipAdapterLeft));
 332                         in.read(buffer, sizeof(header->clipAdapterLeft));
 333                         header->clipAdapterLeft = be_int2(*(unsigned short *)(buffer));
 334                         delete[] buffer;
 335
 336                         //read clipAdapterRight
 337                         buffer = new char(sizeof(header->clipAdapterRight));
 338                         in.read(buffer, sizeof(header->clipAdapterRight));
 339                         header->clipAdapterRight =  be_int2(*(unsigned short *)(buffer));
 340                         delete[] buffer;
 341
 342                         //read name
 343                         header->name = new char(header->nameLength);
 344                         //buffer = new char(header->nameLength);
 345                         in.read(header->name, header->nameLength);
 346                         //memcpy(header->name, buffer, header->nameLength);
 347                         //delete[] buffer;
 348
 349                 }else{
 350                         m->mothurOut("Error reading sff header info."); m->mothurOutEndLine();
 351                 }
 352
 353                 return 0;
 354         }
 355         catch(exception& e) {
 356                 m->errorOut(e, "SffInfoCommand", "readHeader");
 357                 exit(1);
 358         }
 359 }
 360 //**********************************************************************************************************************
 361 int SffInfoCommand::readSeqData(ifstream& in, seqRead*& read, int numFlowReads, int numBases){
 362         try {
 363
 364                 if (!in.eof()) {
 365
 366                         string tempBuf = "";
 367                         char* buffer;
 368
 369                         //read flowgram
 370                         read->flowgram.resize(numFlowReads);
 371                         for (int i = 0; i < numFlowReads; i++) {
 372                                 buffer = new char((sizeof(unsigned short)));
 373                                 in.read(buffer, (sizeof(unsigned short)));
 374                                 read->flowgram[i] = be_int2(*(unsigned short *)(buffer));
 375                                 delete[] buffer;
 376                         }
 377
 378                         //read flowgram
 379                         read->flowIndex.resize(numBases);
 380                         for (int i = 0; i < numBases; i++) {
 381                                 buffer = new char(1);
 382                                 in.read(buffer, 1);
 383                                 read->flowgram[i] = be_int1(*(unsigned int *)(buffer));
 384                                 delete[] buffer;
 385                         }
 386
 387                         //read bases
 388                         read->bases = new char(numBases);
 389                         in.read(read->bases, numBases);
 390                         tempBuf = buffer;
 391                         if (tempBuf.length() > numBases) { tempBuf = tempBuf.substr(0, numBases); strcpy(read->bases, tempBuf.c_str());  }
 392
 393
 394                         //read flowgram
 395                         read->qualScores.resize(numBases);
 396                         for (int i = 0; i < numBases; i++) {
 397                                 buffer = new char(1);
 398                                 in.read(buffer, 1);
 399                                 read->qualScores[i] = be_int1(*(unsigned int *)(buffer));
 400                                 delete[] buffer;
 401                         }
 402
 403                         /* Pad to 8 chars */
 404                         int spotInFile = in.tellg();
 405         cout << spotInFile << endl;
 406                         int spot = floor((spotInFile + 7) /(float) 8) * 8;
 407         cout << spot << endl;
 408                         in.seekg(spot);
 409
 410                 }else{
 411                         m->mothurOut("Error reading."); m->mothurOutEndLine();
 412                 }
 413
 414                 return 0;
 415         }
 416         catch(exception& e) {
 417                 m->errorOut(e, "SffInfoCommand", "readSeqData");
 418                 exit(1);
 419         }
 420 }
 421 //**********************************************************************************************************************
 422 int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader* header, bool debug) {
 423         try {
 424
 425                 string output = "Common Header:\nMagic Number: ";
 426                 output += toString(header->magicNumber) + '\n';
 427                 output += "Version: " + toString(header->version) + '\n';
 428                 output += "Index Offset: " + toString(header->indexOffset) + '\n';
 429                 output += "Index Length: " + toString(header->indexLength) + '\n';
 430                 output += "Number of Reads: " + toString(header->numReads) + '\n';
 431                 output += "Header Length: " + toString(header->headerLength) + '\n';
 432                 output += "Key Length: " + toString(header->keyLength) + '\n';
 433                 output += "Number of Flows: " + toString(header->numFlowsPerRead) + '\n';
 434                 output += "Format Code: " + toString(header->flogramFormatCode) + '\n';
 435                 output += "Flow Chars: " + toString(header->flowChars) + '\n';
 436                 output += "Key Sequence: " + toString(header->keySequence) + '\n';
 437
 438                 out << output << endl;
 439
 440                 if (debug) { cout << output << endl; }
 441
 442                 return 0;
 443         }
 444         catch(exception& e) {
 445                 m->errorOut(e, "SffInfoCommand", "printCommonHeader");
 446                 exit(1);
 447         }
 448 }
 449 //**********************************************************************************************************************
 450 int SffInfoCommand::printHeader(ofstream& out, Header* header, bool debug) {
 451         try {
 452                 string name = header->name;
 453                 string output = ">" + name + "\nRead Header Length: " + toString(header->headerLength) + '\n';
 454                 output += "Name Length: " + toString(header->nameLength) + '\n';
 455                 output += "Number of Bases: " + toString(header->numBases) + '\n';
 456                 output += "Clip Qual Left: " + toString(header->clipQualLeft) + '\n';
 457                 output += "Clip Qual Right: " + toString(header->clipQualLeft) + '\n';
 458                 output += "Clip Adap Left: " + toString(header->clipQualLeft) + '\n';
 459                 output += "Clip Adap Right: " + toString(header->clipQualLeft) + '\n';
 460
 461                 out << output << endl;
 462
 463                 if (debug) { cout << output << endl; }
 464
 465                 return 0;
 466         }
 467         catch(exception& e) {
 468                 m->errorOut(e, "SffInfoCommand", "printHeader");
 469                 exit(1);
 470         }
 471 }
 472
 473 //**********************************************************************************************************************
 474 int SffInfoCommand::printSeqData(ofstream& out, seqRead* read, bool debug) {
 475         try {
 476
 477                 string output = "FlowGram: ";
 478                 for (int i = 0; i < read->flowgram.size(); i++) {  output += toString(read->flowgram[i]) +'\t';  }
 479                 output += "\nFlow Indexes: ";
 480                 for (int i = 0; i < read->flowIndex.size(); i++) {  output += toString(read->flowIndex[i]) +'\t';  }
 481                 string bases = read->bases;
 482                 output += "\nBases: " + bases + '\n';
 483                 for (int i = 0; i < read->qualScores.size(); i++) {  output += toString(read->qualScores[i]) +'\t';  }
 484                 output += '\n';
 485
 486                 out << output << endl;
 487
 488                 if (debug) { cout << output << endl; }
 489
 490                 return 0;
 491         }
 492         catch(exception& e) {
 493                 m->errorOut(e, "SffInfoCommand", "printSeqData");
 494                 exit(1);
 495         }
 496 }
 497 //**********************************************************************************************************************/