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 = readCommonHeader(in);
 142
 143                 //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;
 144 //cout << "numflowreads = "<< header->numFlowsPerRead << endl << "flow format code = "<< header->flogramFormatCode << endl << "flow chars = " << header->flowChars << endl << "key sequence = " << header->keySequence << endl << endl;
 145                 cout << in.tellg() << endl;
 146                 //read through the sff file
 147                 while (!in.eof()) {
 148
 149                         //read header
 150                         Header* readheader = readHeader(in);
 151
 152                         //read data
 153                         seqRead* read = readSeqData(in, header->numFlowsPerRead, readheader->numBases);
 154
 155                         cout << in.tellg() << endl;
 156
 157                         //print common header
 158                         printCommonHeader(out, header, true);
 159
 160                         //print header
 161                         printHeader(out, readheader, true);
 162
 163                         //print data
 164                         printSeqData(out, read, true);
 165
 166                 }
 167
 168
 169                 in.close();
 170                 out.close();
 171
 172                 return 0;
 173         }
 174         catch(exception& e) {
 175                 m->errorOut(e, "SffInfoCommand", "extractSffInfo");
 176                 exit(1);
 177         }
 178 }
 179 //**********************************************************************************************************************
 180 CommonHeader* SffInfoCommand::readCommonHeader(ifstream& in){
 181         try {
 182                 CommonHeader* header = new CommonHeader();
 183
 184                 if (!in.eof()) {
 185                         string tempBuf = "";
 186
 187                         //read magic number
 188                         char* buffer = new char(sizeof(header->magicNumber));
 189                         in.read(buffer, sizeof(header->magicNumber));
 190                         header->magicNumber = be_int4(*(uint32_t *)(buffer));
 191                         delete[] buffer;
 192
 193                         //read version
 194                         header->version = new char(4);
 195                         in.read(header->version, 4);
 196                         tempBuf = buffer;
 197                         if (tempBuf.length() > 4) { tempBuf = tempBuf.substr(0, 4); strcpy(header->version, tempBuf.c_str());  }
 198
 199                         //read offset
 200                         buffer = new char(sizeof(header->indexOffset));
 201                         in.read(buffer, sizeof(header->indexOffset));
 202                         header->indexOffset =  be_int8(*(uint64_t *)(buffer));
 203                         delete[] buffer;
 204
 205                         //read index length
 206                         buffer = new char(sizeof(header->indexLength));
 207                         in.read(buffer, sizeof(header->indexLength));
 208                         header->indexLength =  be_int4(*(uint32_t *)(buffer));
 209                         delete[] buffer;
 210
 211                         //read num reads
 212                         buffer = new char(sizeof(header->numReads));
 213                         in.read(buffer, sizeof(header->numReads));
 214                         header->numReads =  be_int4(*(uint32_t *)(buffer));
 215                         delete[] buffer;
 216
 217                         //read header length
 218                         buffer = new char(sizeof(header->headerLength));
 219                         in.read(buffer, sizeof(header->headerLength));
 220                         header->headerLength =  be_int2(*(uint16_t *)(buffer));
 221                         delete[] buffer;
 222
 223                         //read key length
 224                         buffer = new char(sizeof(header->keyLength));
 225                         in.read(buffer, sizeof(header->keyLength));
 226                         header->keyLength = be_int2(*(uint16_t *)(buffer));
 227                         delete[] buffer;
 228
 229                         //read number of flow reads
 230                         buffer = new char(sizeof(header->numFlowsPerRead));
 231                         in.read(buffer, sizeof(header->numFlowsPerRead));
 232                         header->numFlowsPerRead =  be_int2(*(uint16_t *)(buffer));
 233                         delete[] buffer;
 234
 235                         //read format code
 236                         buffer = new char(sizeof(header->flogramFormatCode));
 237                         in.read(buffer, sizeof(header->flogramFormatCode));
 238                         header->flogramFormatCode = be_int1(*(uint8_t *)(buffer));
 239                         delete[] buffer;
 240
 241                         //read flow chars
 242                         header->flowChars = new char(header->numFlowsPerRead);
 243                         in.read(header->flowChars, header->numFlowsPerRead);
 244                         tempBuf = buffer;
 245                         if (tempBuf.length() > header->numFlowsPerRead) { tempBuf = tempBuf.substr(0, header->numFlowsPerRead); strcpy(header->flowChars, tempBuf.c_str());  }
 246
 247                         //read key
 248                         header->keySequence = new char(header->keyLength);
 249                         in.read(header->keySequence, header->keyLength);
 250                         tempBuf = header->keySequence;
 251                         if (tempBuf.length() > header->keyLength) { tempBuf = tempBuf.substr(0, header->keyLength); strcpy(header->keySequence, tempBuf.c_str());  }
 252
 253                 }else{
 254                         m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
 255                 }
 256
 257                 return header;
 258         }
 259         catch(exception& e) {
 260                 m->errorOut(e, "SffInfoCommand", "readCommonHeader");
 261                 exit(1);
 262         }
 263 }
 264 //**********************************************************************************************************************
 265 Header* SffInfoCommand::readHeader(ifstream& in){
 266         try {
 267                 Header* header = new Header();
 268
 269                 if (!in.eof()) {
 270                         string tempBuf = "";
 271
 272                         //read header length
 273                         char* buffer = new char(sizeof(header->headerLength));
 274                         in.read(buffer, sizeof(header->headerLength));
 275                         header->headerLength = be_int2(*(unsigned short *)(buffer));
 276                         delete[] buffer;
 277
 278                         //read name length
 279                         buffer = new char(sizeof(header->nameLength));
 280                         in.read(buffer, sizeof(header->nameLength));
 281                         header->nameLength = be_int2(*(unsigned short *)(buffer));
 282                         delete[] buffer;
 283
 284                         //read num bases
 285                         buffer = new char(sizeof(header->numBases));
 286                         in.read(buffer, sizeof(header->numBases));
 287                         header->numBases =  be_int4(*(unsigned int *)(buffer));
 288                         delete[] buffer;
 289
 290                         //read clip qual left
 291                         buffer = new char(sizeof(header->clipQualLeft));
 292                         in.read(buffer, sizeof(header->clipQualLeft));
 293                         header->clipQualLeft =  be_int2(*(unsigned short *)(buffer));
 294                         delete[] buffer;
 295
 296                         //read clip qual right
 297                         buffer = new char(sizeof(header->clipQualRight));
 298                         in.read(buffer, sizeof(header->clipQualRight));
 299                         header->clipQualRight =  be_int2(*(unsigned short *)(buffer));
 300                         delete[] buffer;
 301
 302                         //read clipAdapterLeft
 303                         buffer = new char(sizeof(header->clipAdapterLeft));
 304                         in.read(buffer, sizeof(header->clipAdapterLeft));
 305                         header->clipAdapterLeft = be_int2(*(unsigned short *)(buffer));
 306                         delete[] buffer;
 307
 308                         //read clipAdapterRight
 309                         buffer = new char(sizeof(header->clipAdapterRight));
 310                         in.read(buffer, sizeof(header->clipAdapterRight));
 311                         header->clipAdapterRight =  be_int2(*(unsigned short *)(buffer));
 312                         delete[] buffer;
 313
 314                         //read name
 315                         header->name = new char(header->nameLength);
 316                         in.read(header->name, header->nameLength);
 317                         tempBuf = header->name;
 318                         if (tempBuf.length() > header->nameLength) { tempBuf = tempBuf.substr(0, header->nameLength); strcpy(header->name, tempBuf.c_str());  }
 319
 320                 }else{
 321                         m->mothurOut("Error reading sff header info."); m->mothurOutEndLine();
 322                 }
 323
 324                 return header;
 325         }
 326         catch(exception& e) {
 327                 m->errorOut(e, "SffInfoCommand", "readHeader");
 328                 exit(1);
 329         }
 330 }
 331 //**********************************************************************************************************************
 332 seqRead* SffInfoCommand::readSeqData(ifstream& in, int numFlowReads, int numBases){
 333         try {
 334                 seqRead* read = new seqRead();
 335
 336                 if (!in.eof()) {
 337
 338                         string tempBuf = "";
 339                         char* buffer;
 340
 341                         //read flowgram
 342                         read->flowgram.resize(numFlowReads);
 343                         for (int i = 0; i < numFlowReads; i++) {
 344                                 buffer = new char((sizeof(unsigned short)));
 345                                 in.read(buffer, (sizeof(unsigned short)));
 346                                 read->flowgram[i] = be_int2(*(unsigned short *)(buffer));
 347                                 delete[] buffer;
 348                         }
 349
 350                         //read flowgram
 351                         read->flowIndex.resize(numBases);
 352                         for (int i = 0; i < numBases; i++) {
 353                                 buffer = new char(1);
 354                                 in.read(buffer, 1);
 355                                 read->flowgram[i] = be_int1(*(unsigned int *)(buffer));
 356                                 delete[] buffer;
 357                         }
 358
 359                         //read bases
 360                         read->bases = new char(numBases);
 361                         in.read(read->bases, numBases);
 362                         tempBuf = buffer;
 363                         if (tempBuf.length() > numBases) { tempBuf = tempBuf.substr(0, numBases); strcpy(read->bases, tempBuf.c_str());  }
 364
 365
 366                         //read flowgram
 367                         read->qualScores.resize(numBases);
 368                         for (int i = 0; i < numBases; i++) {
 369                                 buffer = new char(1);
 370                                 in.read(buffer, 1);
 371                                 read->qualScores[i] = be_int1(*(unsigned int *)(buffer));
 372                                 delete[] buffer;
 373                         }
 374
 375                         /* Pad to 8 chars */
 376                         int spotInFile = in.tellg();
 377         cout << spotInFile << endl;
 378                         int spot = floor((spotInFile + 7) /(float) 8) * 8;
 379         cout << spot << endl;
 380                         in.seekg(spot);
 381
 382                 }else{
 383                         m->mothurOut("Error reading."); m->mothurOutEndLine();
 384                 }
 385
 386                 return read;
 387         }
 388         catch(exception& e) {
 389                 m->errorOut(e, "SffInfoCommand", "readSeqData");
 390                 exit(1);
 391         }
 392 }
 393 //**********************************************************************************************************************
 394 int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader* header, bool debug) {
 395         try {
 396
 397                 string output = "Common Header:\nMagic Number: ";
 398                 output += toString(header->magicNumber) + '\n';
 399                 output += "Version: " + toString(header->version) + '\n';
 400                 output += "Index Offset: " + toString(header->indexOffset) + '\n';
 401                 output += "Index Length: " + toString(header->indexLength) + '\n';
 402                 output += "Number of Reads: " + toString(header->numReads) + '\n';
 403                 output += "Header Length: " + toString(header->headerLength) + '\n';
 404                 output += "Key Length: " + toString(header->keyLength) + '\n';
 405                 output += "Number of Flows: " + toString(header->numFlowsPerRead) + '\n';
 406                 output += "Format Code: " + toString(header->flogramFormatCode) + '\n';
 407                 output += "Flow Chars: " + toString(header->flowChars) + '\n';
 408                 output += "Key Sequence: " + toString(header->keySequence) + '\n';
 409
 410                 out << output << endl;
 411
 412                 if (debug) { cout << output << endl; }
 413
 414                 return 0;
 415         }
 416         catch(exception& e) {
 417                 m->errorOut(e, "SffInfoCommand", "printCommonHeader");
 418                 exit(1);
 419         }
 420 }
 421 //**********************************************************************************************************************
 422 int SffInfoCommand::printHeader(ofstream& out, Header* header, bool debug) {
 423         try {
 424                 string name = header->name;
 425                 string output = ">" + name + "\nRead Header Length: " + toString(header->headerLength) + '\n';
 426                 output += "Name Length: " + toString(header->nameLength) + '\n';
 427                 output += "Number of Bases: " + toString(header->numBases) + '\n';
 428                 output += "Clip Qual Left: " + toString(header->clipQualLeft) + '\n';
 429                 output += "Clip Qual Right: " + toString(header->clipQualLeft) + '\n';
 430                 output += "Clip Adap Left: " + toString(header->clipQualLeft) + '\n';
 431                 output += "Clip Adap Right: " + toString(header->clipQualLeft) + '\n';
 432
 433                 out << output << endl;
 434
 435                 if (debug) { cout << output << endl; }
 436
 437                 return 0;
 438         }
 439         catch(exception& e) {
 440                 m->errorOut(e, "SffInfoCommand", "printHeader");
 441                 exit(1);
 442         }
 443 }
 444
 445 //**********************************************************************************************************************
 446 int SffInfoCommand::printSeqData(ofstream& out, seqRead* read, bool debug) {
 447         try {
 448
 449                 string output = "FlowGram: ";
 450                 for (int i = 0; i < read->flowgram.size(); i++) {  output += toString(read->flowgram[i]) +'\t';  }
 451                 output += "\nFlow Indexes: ";
 452                 for (int i = 0; i < read->flowIndex.size(); i++) {  output += toString(read->flowIndex[i]) +'\t';  }
 453                 string bases = read->bases;
 454                 output += "\nBases: " + bases + '\n';
 455                 for (int i = 0; i < read->qualScores.size(); i++) {  output += toString(read->qualScores[i]) +'\t';  }
 456                 output += '\n';
 457
 458                 out << output << endl;
 459
 460                 if (debug) { cout << output << endl; }
 461
 462                 return 0;
 463         }
 464         catch(exception& e) {
 465                 m->errorOut(e, "SffInfoCommand", "printSeqData");
 466                 exit(1);
 467         }
 468 }
 469 //**********************************************************************************************************************/