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                 hasAccnos = false;
  19
  20                 //allow user to run help
  21                 if(option == "help") { help(); abort = true; }
  22
  23                 else {
  24                         //valid paramters for this command
  25                         string Array[] =  {"sff","qfile","fasta","flow","trim","accnos","sfftxt","outputdir","inputdir", "outputdir"};
  26                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  27
  28                         OptionParser parser(option);
  29                         map<string, string> parameters = parser.getParameters();
  30
  31                         ValidParameters validParameter;
  32                         //check to make sure all parameters are valid for command
  33                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  34                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  35                         }
  36
  37                         //if the user changes the output directory command factory will send this info to us in the output parameter
  38                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
  39
  40                         //if the user changes the input directory command factory will send this info to us in the output parameter
  41                         string inputDir = validParameter.validFile(parameters, "inputdir", false);        if (inputDir == "not found"){ inputDir = "";          }
  42
  43                         sffFilename = validParameter.validFile(parameters, "sff", false);
  44                         if (sffFilename == "not found") { m->mothurOut("sff is a required parameter for the sffinfo command."); m->mothurOutEndLine(); abort = true;  }
  45                         else {
  46                                 splitAtDash(sffFilename, filenames);
  47
  48                                 //go through files and make sure they are good, if not, then disregard them
  49                                 for (int i = 0; i < filenames.size(); i++) {
  50                                         if (inputDir != "") {
  51                                                 string path = hasPath(filenames[i]);
  52                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  53                                                 if (path == "") {       filenames[i] = inputDir + filenames[i];         }
  54                                         }
  55
  56                                         ifstream in;
  57                                         int ableToOpen = openInputFile(filenames[i], in, "noerror");
  58
  59                                         //if you can't open it, try default location
  60                                         if (ableToOpen == 1) {
  61                                                 if (m->getDefaultPath() != "") { //default path is set
  62                                                         string tryPath = m->getDefaultPath() + getSimpleName(filenames[i]);
  63                                                         m->mothurOut("Unable to open " + filenames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
  64                                                         ableToOpen = openInputFile(tryPath, in, "noerror");
  65                                                         filenames[i] = tryPath;
  66                                                 }
  67                                         }
  68                                         in.close();
  69
  70                                         if (ableToOpen == 1) {
  71                                                 m->mothurOut("Unable to open " + filenames[i] + ". It will be disregarded."); m->mothurOutEndLine();
  72                                                 //erase from file list
  73                                                 filenames.erase(filenames.begin()+i);
  74                                                 i--;
  75                                         }
  76                                 }
  77
  78                                 //make sure there is at least one valid file left
  79                                 if (filenames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
  80                         }
  81
  82                         accnosName = validParameter.validFile(parameters, "accnos", false);
  83                         if (accnosName == "not found") { accnosName = "";  }
  84                         else {
  85                                 hasAccnos = true;
  86                                 splitAtDash(accnosName, accnosFileNames);
  87
  88                                 //go through files and make sure they are good, if not, then disregard them
  89                                 for (int i = 0; i < accnosFileNames.size(); i++) {
  90                                         if (inputDir != "") {
  91                                                 string path = hasPath(accnosFileNames[i]);
  92                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  93                                                 if (path == "") {       accnosFileNames[i] = inputDir + accnosFileNames[i];             }
  94                                         }
  95
  96                                         ifstream in;
  97                                         int ableToOpen = openInputFile(accnosFileNames[i], in, "noerror");
  98
  99                                         //if you can't open it, try default location
 100                                         if (ableToOpen == 1) {
 101                                                 if (m->getDefaultPath() != "") { //default path is set
 102                                                         string tryPath = m->getDefaultPath() + getSimpleName(accnosFileNames[i]);
 103                                                         m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 104                                                         ableToOpen = openInputFile(tryPath, in, "noerror");
 105                                                         accnosFileNames[i] = tryPath;
 106                                                 }
 107                                         }
 108                                         in.close();
 109
 110                                         if (ableToOpen == 1) {
 111                                                 m->mothurOut("Unable to open " + accnosFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 112                                                 //erase from file list
 113                                                 accnosFileNames.erase(accnosFileNames.begin()+i);
 114                                                 i--;
 115                                         }
 116                                 }
 117
 118                                 //make sure there is at least one valid file left
 119                                 if (accnosFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 120                         }
 121
 122                         if (hasAccnos) {
 123                                 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(); }
 124                         }
 125
 126                         string temp = validParameter.validFile(parameters, "qfile", false);                     if (temp == "not found"){       temp = "T";                             }
 127                         qual = isTrue(temp);
 128
 129                         temp = validParameter.validFile(parameters, "fasta", false);                            if (temp == "not found"){       temp = "T";                             }
 130                         fasta = isTrue(temp);
 131
 132                         temp = validParameter.validFile(parameters, "flow", false);                                     if (temp == "not found"){       temp = "F";                             }
 133                         flow = isTrue(temp);
 134
 135                         temp = validParameter.validFile(parameters, "trim", false);                                     if (temp == "not found"){       temp = "T";                             }
 136                         trim = isTrue(temp);
 137
 138                         temp = validParameter.validFile(parameters, "sfftxt", false);                           if (temp == "not found"){       temp = "F";                             }
 139                         sfftxt = isTrue(temp);
 140                 }
 141         }
 142         catch(exception& e) {
 143                 m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
 144                 exit(1);
 145         }
 146 }
 147 //**********************************************************************************************************************
 148
 149 void SffInfoCommand::help(){
 150         try {
 151                 m->mothurOut("The sffinfo command reads a sff file and outputs a .sff.txt file.\n");
 152
 153                 m->mothurOut("Example sffinfo(sff=...).\n");
 154                 m->mothurOut("Note: No spaces between parameter labels (i.e. sff), '=' and parameters (i.e.yourSffFileName).\n\n");
 155         }
 156         catch(exception& e) {
 157                 m->errorOut(e, "SffInfoCommand", "help");
 158                 exit(1);
 159         }
 160 }
 161 //**********************************************************************************************************************
 162
 163 SffInfoCommand::~SffInfoCommand(){}
 164
 165 //**********************************************************************************************************************
 166 int SffInfoCommand::execute(){
 167         try {
 168
 169                 if (abort == true) { return 0; }
 170
 171                 for (int s = 0; s < filenames.size(); s++) {
 172
 173                         if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         } return 0; }
 174
 175                         int start = time(NULL);
 176
 177                         m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
 178
 179                         string accnos = "";
 180                         if (hasAccnos) { accnos = accnosFileNames[s]; }
 181
 182                         int numReads = extractSffInfo(filenames[s], accnos);
 183
 184                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to extract " + toString(numReads) + ".");
 185                 }
 186
 187                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         } return 0; }
 188
 189                 //report output filenames
 190                 m->mothurOutEndLine();
 191                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 192                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 193                 m->mothurOutEndLine();
 194
 195                 return 0;
 196         }
 197         catch(exception& e) {
 198                 m->errorOut(e, "SffInfoCommand", "execute");
 199                 exit(1);
 200         }
 201 }
 202 //**********************************************************************************************************************
 203 int SffInfoCommand::extractSffInfo(string input, string accnos){
 204         try {
 205
 206                 if (outputDir == "") {  outputDir += hasPath(input); }
 207
 208                 if (accnos != "")       {  readAccnosFile(accnos);  }
 209                 else                            {       seqNames.clear();               }
 210
 211                 ofstream outSfftxt, outFasta, outQual, outFlow;
 212                 string outFastaFileName, outQualFileName;
 213                 string sfftxtFileName = outputDir + getRootName(getSimpleName(input)) + "sff.txt";
 214                 string outFlowFileName = outputDir + getRootName(getSimpleName(input)) + "flow";
 215                 if (trim) {
 216                         outFastaFileName = outputDir + getRootName(getSimpleName(input)) + "fasta";
 217                         outQualFileName = outputDir + getRootName(getSimpleName(input)) + "qual";
 218                 }else{
 219                         outFastaFileName = outputDir + getRootName(getSimpleName(input)) + "raw.fasta";
 220                         outQualFileName = outputDir + getRootName(getSimpleName(input)) + "raw.qual";
 221                 }
 222
 223                 if (sfftxt) { openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint);  outputNames.push_back(sfftxtFileName); }
 224                 if (fasta)      { openOutputFile(outFastaFileName, outFasta);   outputNames.push_back(outFastaFileName); }
 225                 if (qual)       { openOutputFile(outQualFileName, outQual);             outputNames.push_back(outQualFileName);  }
 226                 if (flow)       { openOutputFile(outFlowFileName, outFlow);             outputNames.push_back(outFlowFileName);  }
 227
 228                 ifstream in;
 229                 in.open(input.c_str(), ios::binary);
 230
 231                 CommonHeader header;
 232                 readCommonHeader(in, header);
 233
 234                 int count = 0;
 235
 236                 //check magic number and version
 237                 if (header.magicNumber != 779314790) { m->mothurOut("Magic Number is not correct, not a valid .sff file"); m->mothurOutEndLine(); return count; }
 238                 if (header.version != "0001") { m->mothurOut("Version is not supported, only support version 0001."); m->mothurOutEndLine(); return count; }
 239
 240                 //print common header
 241                 if (sfftxt) { printCommonHeader(outSfftxt, header); }
 242
 243                 //read through the sff file
 244                 while (!in.eof()) {
 245
 246                         bool print = true;
 247
 248                         //read header
 249                         Header readheader;
 250                         readHeader(in, readheader);
 251
 252                         //read data
 253                         seqRead read;
 254                         readSeqData(in, read, header.numFlowsPerRead, readheader.numBases);
 255
 256                         //if you have provided an accosfile and this seq is not in it, then dont print
 257                         if (seqNames.size() != 0) {   if (seqNames.count(readheader.name) == 0) { print = false; }  }
 258
 259                         //print
 260                         if (print) {
 261                                 if (sfftxt) { printHeader(outSfftxt, readheader); printSffTxtSeqData(outSfftxt, read); }
 262                                 if (fasta)      {       printFastaSeqData(outFasta, read, readheader);  }
 263                                 if (qual)       {       printQualSeqData(outQual, read, readheader);    }
 264                                 if (flow)       {       printFlowSeqData(outFlow, read, readheader);    }
 265                         }
 266
 267                         count++;
 268
 269                         //report progress
 270                         if((count+1) % 500 == 0){       m->mothurOut(toString(count+1)); m->mothurOutEndLine();         }
 271
 272                         if (m->control_pressed) { count = 0; break;   }
 273
 274                         if (count >= header.numReads) { break; }
 275                 }
 276
 277                 //report progress
 278                 if (!m->control_pressed) {   if((count) % 500 != 0){    m->mothurOut(toString(count)); m->mothurOutEndLine();           }  }
 279
 280                 in.close();
 281
 282                 if (sfftxt) {  outSfftxt.close();       }
 283                 if (fasta)      {  outFasta.close();    }
 284                 if (qual)       {  outQual.close();             }
 285                 if (flow)       {  outFlow.close();             }
 286
 287                 return count;
 288         }
 289         catch(exception& e) {
 290                 m->errorOut(e, "SffInfoCommand", "extractSffInfo");
 291                 exit(1);
 292         }
 293 }
 294 //**********************************************************************************************************************
 295 int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
 296         try {
 297
 298                 if (!in.eof()) {
 299
 300                         //read magic number
 301                         char buffer[sizeof(header.magicNumber)];
 302                         in.read(buffer, sizeof(header.magicNumber));
 303                         header.magicNumber = be_int4(*(unsigned int *)(&buffer));
 304
 305                         //read version
 306                         char buffer9[4];
 307                         in.read(buffer9, 4);
 308                         header.version = "";
 309                         for (int i = 0; i < 4; i++) {  header.version += toString((int)(buffer9[i])); }
 310
 311                         //read offset
 312                         char buffer2 [sizeof(header.indexOffset)];
 313                         in.read(buffer2, sizeof(header.indexOffset));
 314                         header.indexOffset =  be_int8(*(unsigned long int *)(&buffer2));
 315
 316                         //read index length
 317                         char buffer3 [sizeof(header.indexLength)];
 318                         in.read(buffer3, sizeof(header.indexLength));
 319                         header.indexLength =  be_int4(*(unsigned int *)(&buffer3));
 320
 321                         //read num reads
 322                         char buffer4 [sizeof(header.numReads)];
 323                         in.read(buffer4, sizeof(header.numReads));
 324                         header.numReads =  be_int4(*(unsigned int *)(&buffer4));
 325
 326                         //read header length
 327                         char buffer5 [sizeof(header.headerLength)];
 328                         in.read(buffer5, sizeof(header.headerLength));
 329                         header.headerLength =  be_int2(*(unsigned short *)(&buffer5));
 330
 331                         //read key length
 332                         char buffer6 [sizeof(header.keyLength)];
 333                         in.read(buffer6, sizeof(header.keyLength));
 334                         header.keyLength = be_int2(*(unsigned short *)(&buffer6));
 335
 336                         //read number of flow reads
 337                         char buffer7 [sizeof(header.numFlowsPerRead)];
 338                         in.read(buffer7, sizeof(header.numFlowsPerRead));
 339                         header.numFlowsPerRead =  be_int2(*(unsigned short *)(&buffer7));
 340
 341                         //read format code
 342                         char buffer8 [1];
 343                         in.read(buffer8, 1);
 344                         header.flogramFormatCode = (int)(buffer8[0]);
 345
 346                         //read flow chars
 347                         char tempBuffer [header.numFlowsPerRead];
 348                         in.read(tempBuffer, header.numFlowsPerRead);
 349                         header.flowChars = tempBuffer;
 350                         if (header.flowChars.length() > header.numFlowsPerRead) { header.flowChars = header.flowChars.substr(0, header.numFlowsPerRead);  }
 351
 352                         //read key
 353                         char tempBuffer2 [header.keyLength];
 354                         in.read(tempBuffer2, header.keyLength);
 355                         header.keySequence = tempBuffer2;
 356                         if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength);  }
 357
 358                         /* Pad to 8 chars */
 359                         int spotInFile = in.tellg();
 360                         int spot = (spotInFile + 7)& ~7;  // ~ inverts
 361                         in.seekg(spot);
 362
 363                 }else{
 364                         m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
 365                 }
 366
 367                 return 0;
 368         }
 369         catch(exception& e) {
 370                 m->errorOut(e, "SffInfoCommand", "readCommonHeader");
 371                 exit(1);
 372         }
 373 }
 374 //**********************************************************************************************************************
 375 int SffInfoCommand::readHeader(ifstream& in, Header& header){
 376         try {
 377
 378                 if (!in.eof()) {
 379
 380                         //read header length
 381                         char buffer [sizeof(header.headerLength)];
 382                         in.read(buffer, sizeof(header.headerLength));
 383                         header.headerLength = be_int2(*(unsigned short *)(&buffer));
 384
 385                         //read name length
 386                         char buffer2 [sizeof(header.nameLength)];
 387                         in.read(buffer2, sizeof(header.nameLength));
 388                         header.nameLength = be_int2(*(unsigned short *)(&buffer2));
 389
 390                         //read num bases
 391                         char buffer3 [sizeof(header.numBases)];
 392                         in.read(buffer3, sizeof(header.numBases));
 393                         header.numBases =  be_int4(*(unsigned int *)(&buffer3));
 394
 395                         //read clip qual left
 396                         char buffer4 [sizeof(header.clipQualLeft)];
 397                         in.read(buffer4, sizeof(header.clipQualLeft));
 398                         header.clipQualLeft =  be_int2(*(unsigned short *)(&buffer4));
 399
 400                         //read clip qual right
 401                         char buffer5 [sizeof(header.clipQualRight)];
 402                         in.read(buffer5, sizeof(header.clipQualRight));
 403                         header.clipQualRight =  be_int2(*(unsigned short *)(&buffer5));
 404
 405                         //read clipAdapterLeft
 406                         char buffer6 [sizeof(header.clipAdapterLeft)];
 407                         in.read(buffer6, sizeof(header.clipAdapterLeft));
 408                         header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));
 409
 410                         //read clipAdapterRight
 411                         char buffer7 [sizeof(header.clipAdapterRight)];
 412                         in.read(buffer7, sizeof(header.clipAdapterRight));
 413                         header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));
 414
 415                         //read name
 416                         char tempBuffer [header.nameLength];
 417                         in.read(tempBuffer, header.nameLength);
 418                         header.name = tempBuffer;
 419                         if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength);  }
 420
 421                         /* Pad to 8 chars */
 422                         int spotInFile = in.tellg();
 423                         int spot = (spotInFile + 7)& ~7;
 424                         in.seekg(spot);
 425
 426                 }else{
 427                         m->mothurOut("Error reading sff header info."); m->mothurOutEndLine();
 428                 }
 429
 430                 return 0;
 431         }
 432         catch(exception& e) {
 433                 m->errorOut(e, "SffInfoCommand", "readHeader");
 434                 exit(1);
 435         }
 436 }
 437 //**********************************************************************************************************************
 438 int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, int numBases){
 439         try {
 440
 441                 if (!in.eof()) {
 442
 443                         //read flowgram
 444                         read.flowgram.resize(numFlowReads);
 445                         for (int i = 0; i < numFlowReads; i++) {
 446                                 char buffer [sizeof(unsigned short)];
 447                                 in.read(buffer, (sizeof(unsigned short)));
 448                                 read.flowgram[i] = be_int2(*(unsigned short *)(&buffer));
 449                         }
 450
 451                         //read flowIndex
 452                         read.flowIndex.resize(numBases);
 453                         for (int i = 0; i < numBases; i++) {
 454                                 char temp[1];
 455                                 in.read(temp, 1);
 456                                 read.flowIndex[i] = be_int1(*(unsigned char *)(&temp));
 457                         }
 458
 459                         //read bases
 460                         char tempBuffer[numBases];
 461                         in.read(tempBuffer, numBases);
 462                         read.bases = tempBuffer;
 463                         if (read.bases.length() > numBases) { read.bases = read.bases.substr(0, numBases);  }
 464
 465                         //read flowgram
 466                         read.qualScores.resize(numBases);
 467                         for (int i = 0; i < numBases; i++) {
 468                                 char temp[1];
 469                                 in.read(temp, 1);
 470                                 read.qualScores[i] = be_int1(*(unsigned char *)(&temp));
 471                         }
 472
 473                         /* Pad to 8 chars */
 474                         int spotInFile = in.tellg();
 475                         int spot = (spotInFile + 7)& ~7;
 476                         in.seekg(spot);
 477
 478                 }else{
 479                         m->mothurOut("Error reading."); m->mothurOutEndLine();
 480                 }
 481
 482                 return 0;
 483         }
 484         catch(exception& e) {
 485                 m->errorOut(e, "SffInfoCommand", "readSeqData");
 486                 exit(1);
 487         }
 488 }
 489 //**********************************************************************************************************************
 490 int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader& header) {
 491         try {
 492
 493                 out << "Common Header:\nMagic Number: " << header.magicNumber << endl;
 494                 out << "Version: " << header.version << endl;
 495                 out << "Index Offset: " << header.indexOffset << endl;
 496                 out << "Index Length: " << header.indexLength << endl;
 497                 out << "Number of Reads: " << header.numReads << endl;
 498                 out << "Header Length: " << header.headerLength << endl;
 499                 out << "Key Length: " << header.keyLength << endl;
 500                 out << "Number of Flows: " << header.numFlowsPerRead << endl;
 501                 out << "Format Code: " << header.flogramFormatCode << endl;
 502                 out << "Flow Chars: " << header.flowChars << endl;
 503                 out << "Key Sequence: " << header.keySequence << endl << endl;
 504
 505                 return 0;
 506         }
 507         catch(exception& e) {
 508                 m->errorOut(e, "SffInfoCommand", "printCommonHeader");
 509                 exit(1);
 510         }
 511 }
 512 //**********************************************************************************************************************
 513 int SffInfoCommand::printHeader(ofstream& out, Header& header) {
 514         try {
 515
 516                 out << ">" << header.name << endl;
 517                 out << "Run Prefix: " << endl;
 518                 out << "Region #:  " << endl;
 519                 out << "XY Location: " << endl << endl;
 520
 521                 out << "Run Name:  " << endl;
 522                 out << "Analysis Name:  " << endl;
 523                 out << "Full Path: " << endl << endl;
 524
 525                 out << "Read Header Len: " << header.headerLength << endl;
 526                 out << "Name Length: " << header.nameLength << endl;
 527                 out << "# of Bases: " << header.numBases << endl;
 528                 out << "Clip Qual Left: " << header.clipQualLeft << endl;
 529                 out << "Clip Qual Right: " << header.clipQualRight << endl;
 530                 out << "Clip Adap Left: " << header.clipAdapterLeft << endl;
 531                 out << "Clip Adap Right: " << header.clipAdapterRight << endl << endl;
 532
 533                 return 0;
 534         }
 535         catch(exception& e) {
 536                 m->errorOut(e, "SffInfoCommand", "printHeader");
 537                 exit(1);
 538         }
 539 }
 540
 541 //**********************************************************************************************************************
 542 int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read) {
 543         try {
 544
 545                 out << "FlowGram: ";
 546                 for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }
 547
 548                 out << endl <<  "Flow Indexes: ";
 549                 int sum = 0;
 550                 for (int i = 0; i < read.flowIndex.size(); i++) {  sum +=  read.flowIndex[i];  out << sum << '\t'; }
 551
 552                 out << endl <<  "Bases: " << read.bases << endl << "Quality Scores: ";
 553                 for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
 554                 out << endl << endl;
 555
 556                 return 0;
 557         }
 558         catch(exception& e) {
 559                 m->errorOut(e, "SffInfoCommand", "printSffTxtSeqData");
 560                 exit(1);
 561         }
 562 }
 563 //**********************************************************************************************************************
 564 int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
 565         try {
 566
 567                 string seq = read.bases;
 568
 569
 570                 if (trim) {
 571                         seq = seq.substr(header.clipQualLeft, (header.clipQualRight-header.clipQualLeft));
 572                 }
 573
 574                 out << ">" << header.name << endl;
 575                 out << seq << endl;
 576
 577                 return 0;
 578         }
 579         catch(exception& e) {
 580                 m->errorOut(e, "SffInfoCommand", "printFastaSeqData");
 581                 exit(1);
 582         }
 583 }
 584
 585 //**********************************************************************************************************************
 586 int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& header) {
 587         try {
 588
 589                 if (trim) {
 590                         out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
 591                         for (int i = header.clipQualLeft; i < (header.clipQualRight-header.clipQualLeft); i++) {   out << read.qualScores[i] << '\t';  }
 592                 }else{
 593                         out << ">" << header.name << " length=" << read.qualScores.size() << endl;
 594                         for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
 595                 }
 596
 597                 out << endl;
 598
 599                 return 0;
 600         }
 601         catch(exception& e) {
 602                 m->errorOut(e, "SffInfoCommand", "printQualSeqData");
 603                 exit(1);
 604         }
 605 }
 606
 607 //**********************************************************************************************************************
 608 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
 609         try {
 610
 611                 out << ">" << header.name << endl;
 612                 for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }
 613                 out << endl;
 614
 615                 return 0;
 616         }
 617         catch(exception& e) {
 618                 m->errorOut(e, "SffInfoCommand", "printFlowSeqData");
 619                 exit(1);
 620         }
 621 }
 622 //**********************************************************************************************************************
 623 int SffInfoCommand::readAccnosFile(string filename) {
 624         try {
 625                 //remove old names
 626                 seqNames.clear();
 627
 628                 ifstream in;
 629                 openInputFile(filename, in);
 630                 string name;
 631
 632                 while(!in.eof()){
 633                         in >> name; gobble(in);
 634
 635                         seqNames.insert(name);
 636
 637                         if (m->control_pressed) { seqNames.clear(); break; }
 638                 }
 639                 in.close();
 640
 641                 return 0;
 642         }
 643         catch(exception& e) {
 644                 m->errorOut(e, "SffInfoCommand", "readAccnosFile");
 645                 exit(1);
 646         }
 647 }
 648 //**********************************************************************************************************************/