preclustercommand.cpp

   1 /*
   2  *  preclustercommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 12/21/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "preclustercommand.h"
  11
  12 //**********************************************************************************************************************
  13 inline bool comparePriority(seqPNode first, seqPNode second) {  return (first.numIdentical > second.numIdentical); }
  14 //**********************************************************************************************************************
  15 vector<string> PreClusterCommand::getValidParameters(){
  16         try {
  17                 string Array[] =  {"fasta", "name", "diffs", "outputdir","inputdir"};
  18                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  19                 return myArray;
  20         }
  21         catch(exception& e) {
  22                 m->errorOut(e, "PreClusterCommand", "getValidParameters");
  23                 exit(1);
  24         }
  25 }
  26 //**********************************************************************************************************************
  27 PreClusterCommand::PreClusterCommand(){
  28         try {
  29                 abort = true;
  30                 //initialize outputTypes
  31                 vector<string> tempOutNames;
  32                 outputTypes["fasta"] = tempOutNames;
  33                 outputTypes["name"] = tempOutNames;
  34         }
  35         catch(exception& e) {
  36                 m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
  37                 exit(1);
  38         }
  39 }
  40 //**********************************************************************************************************************
  41 vector<string> PreClusterCommand::getRequiredParameters(){
  42         try {
  43                 string Array[] =  {"fasta"};
  44                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  45                 return myArray;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "PreClusterCommand", "getRequiredParameters");
  49                 exit(1);
  50         }
  51 }
  52 //**********************************************************************************************************************
  53 vector<string> PreClusterCommand::getRequiredFiles(){
  54         try {
  55                 vector<string> myArray;
  56                 return myArray;
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "PreClusterCommand", "getRequiredFiles");
  60                 exit(1);
  61         }
  62 }
  63 //**********************************************************************************************************************
  64
  65 PreClusterCommand::PreClusterCommand(string option) {
  66         try {
  67                 abort = false;
  68
  69                 //allow user to run help
  70                 if(option == "help") { help(); abort = true; }
  71
  72                 else {
  73                         //valid paramters for this command
  74                         string Array[] =  {"fasta", "name", "diffs", "outputdir","inputdir"};
  75                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  76
  77                         OptionParser parser(option);
  78                         map<string, string> parameters = parser.getParameters();
  79
  80                         ValidParameters validParameter;
  81                         map<string, string>::iterator it;
  82
  83                         //check to make sure all parameters are valid for command
  84                         for (map<string, string>::iterator it2 = parameters.begin(); it2 != parameters.end(); it2++) {
  85                                 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) {  abort = true;  }
  86                         }
  87
  88                         //initialize outputTypes
  89                         vector<string> tempOutNames;
  90                         outputTypes["fasta"] = tempOutNames;
  91                         outputTypes["name"] = tempOutNames;
  92
  93                         //if the user changes the input directory command factory will send this info to us in the output parameter
  94                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  95                         if (inputDir == "not found"){   inputDir = "";          }
  96                         else {
  97                                 string path;
  98                                 it = parameters.find("fasta");
  99                                 //user has given a template file
 100                                 if(it != parameters.end()){
 101                                         path = m->hasPath(it->second);
 102                                         //if the user has not given a path then, add inputdir. else leave path alone.
 103                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 104                                 }
 105
 106                                 it = parameters.find("name");
 107                                 //user has given a template file
 108                                 if(it != parameters.end()){
 109                                         path = m->hasPath(it->second);
 110                                         //if the user has not given a path then, add inputdir. else leave path alone.
 111                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 112                                 }
 113                         }
 114
 115                         //check for required parameters
 116                         fastafile = validParameter.validFile(parameters, "fasta", true);
 117                         if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the pre.cluster command."); m->mothurOutEndLine(); abort = true; }
 118                         else if (fastafile == "not open") { abort = true; }
 119
 120                         //if the user changes the output directory command factory will send this info to us in the output parameter
 121                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 122                                 outputDir = "";
 123                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 124                         }
 125
 126                         //check for optional parameter and set defaults
 127                         // ...at some point should added some additional type checking...
 128                         namefile = validParameter.validFile(parameters, "name", true);
 129                         if (namefile == "not found") { namefile =  "";  }
 130                         else if (namefile == "not open") { abort = true; }
 131                         else {  readNameFile();  }
 132
 133                         string temp     = validParameter.validFile(parameters, "diffs", false);                         if(temp == "not found"){        temp = "1"; }
 134                         convert(temp, diffs);
 135                 }
 136
 137         }
 138         catch(exception& e) {
 139                 m->errorOut(e, "PreClusterCommand", "PreClusterCommand");
 140                 exit(1);
 141         }
 142 }
 143
 144 //**********************************************************************************************************************
 145 PreClusterCommand::~PreClusterCommand(){}
 146 //**********************************************************************************************************************
 147
 148 void PreClusterCommand::help(){
 149         try {
 150                 m->mothurOut("The pre.cluster command groups sequences that are within a given number of base mismatches.\n");
 151                 m->mothurOut("The pre.cluster command outputs a new fasta and name file.\n");
 152                 m->mothurOut("The pre.cluster command parameters are fasta, names and diffs. The fasta parameter is required. \n");
 153                 m->mothurOut("The names parameter allows you to give a list of seqs that are identical. This file is 2 columns, first column is name or representative sequence, second column is a list of its identical sequences separated by commas.\n");
 154                 m->mothurOut("The diffs parameter allows you to specify maximum number of mismatched bases allowed between sequences in a grouping. The default is 1.\n");
 155                 m->mothurOut("The pre.cluster command should be in the following format: \n");
 156                 m->mothurOut("pre.cluster(fasta=yourFastaFile, names=yourNamesFile, diffs=yourMaxDiffs) \n");
 157                 m->mothurOut("Example pre.cluster(fasta=amazon.fasta, diffs=2).\n");
 158                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
 159         }
 160         catch(exception& e) {
 161                 m->errorOut(e, "PreClusterCommand", "help");
 162                 exit(1);
 163         }
 164 }
 165 //**********************************************************************************************************************
 166
 167 int PreClusterCommand::execute(){
 168         try {
 169
 170                 if (abort == true) { return 0; }
 171
 172                 int start = time(NULL);
 173
 174                 //reads fasta file and return number of seqs
 175                 int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
 176
 177                 if (m->control_pressed) { return 0; }
 178
 179                 if (numSeqs == 0) { m->mothurOut("Error reading fasta file...please correct."); m->mothurOutEndLine(); return 0;  }
 180                 if (diffs > length) { m->mothurOut("Error: diffs is greater than your sequence length."); m->mothurOutEndLine(); return 0;  }
 181
 182                 //clear sizes since you only needed this info to build the alignSeqs seqPNode structs
 183 //              sizes.clear();
 184
 185                 //sort seqs by number of identical seqs
 186                 sort(alignSeqs.begin(), alignSeqs.end(), comparePriority);
 187
 188                 int count = 0;
 189
 190                 //think about running through twice...
 191                 for (int i = 0; i < numSeqs; i++) {
 192
 193                         //are you active
 194                         //                      itActive = active.find(alignSeqs[i].seq.getName());
 195
 196                         if (alignSeqs[i].active) {  //this sequence has not been merged yet
 197
 198                                 //try to merge it with all smaller seqs
 199                                 for (int j = i+1; j < numSeqs; j++) {
 200
 201                                         if (m->control_pressed) { return 0; }
 202
 203                                         if (alignSeqs[j].active) {  //this sequence has not been merged yet
 204                                                 //are you within "diff" bases
 205                                                 int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
 206
 207                                                 if (mismatch <= diffs) {
 208                                                         //merge
 209                                                         alignSeqs[i].names += ',' + alignSeqs[j].names;
 210                                                         alignSeqs[i].numIdentical += alignSeqs[j].numIdentical;
 211
 212                                                         alignSeqs[j].active = 0;
 213                                                         alignSeqs[j].numIdentical = 0;
 214                                                         count++;
 215                                                 }
 216                                         }//end if j active
 217                                 }//end if i != j
 218
 219                         //remove from active list
 220                                 alignSeqs[i].active = 0;
 221
 222                         }//end if active i
 223                         if(i % 100 == 0)        { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
 224                 }
 225
 226                 if(numSeqs % 100 != 0)  { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine();   }
 227
 228
 229                 string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
 230
 231                 string newFastaFile = fileroot + "precluster" + m->getExtension(fastafile);
 232                 string newNamesFile = fileroot + "precluster.names";
 233
 234                 if (m->control_pressed) { return 0; }
 235
 236                 m->mothurOut("Total number of sequences before precluster was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
 237                 m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 238                 printData(newFastaFile, newNamesFile);
 239
 240                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 241
 242                 if (m->control_pressed) { remove(newFastaFile.c_str()); remove(newNamesFile.c_str()); return 0; }
 243
 244                 m->mothurOutEndLine();
 245                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 246                 m->mothurOut(newFastaFile); m->mothurOutEndLine();      outputNames.push_back(newFastaFile); outputTypes["fasta"].push_back(newFastaFile);
 247                 m->mothurOut(newNamesFile); m->mothurOutEndLine();      outputNames.push_back(newNamesFile); outputTypes["name"].push_back(newNamesFile);
 248                 m->mothurOutEndLine();
 249
 250                 return 0;
 251
 252         }
 253         catch(exception& e) {
 254                 m->errorOut(e, "PreClusterCommand", "execute");
 255                 exit(1);
 256         }
 257 }
 258
 259 /**************************************************************************************************/
 260
 261 //this requires the names and fasta file to be in the same order
 262
 263 int PreClusterCommand::readFASTA(){
 264         try {
 265                 //ifstream inNames;
 266                 ifstream inFasta;
 267
 268                 //m->openInputFile(namefile, inNames);
 269                 m->openInputFile(fastafile, inFasta);
 270
 271                 //string firstCol, secondCol, nameString;
 272                 length = 0;
 273
 274                 while (!inFasta.eof()) {
 275
 276                         if (m->control_pressed) { inFasta.close(); return 0; }
 277
 278                         //inNames >> firstCol >> secondCol;
 279                         //nameString = secondCol;
 280
 281                         //m->gobble(inNames);
 282                         //int size = 1;
 283                         //while (secondCol.find_first_of(',') != -1) {
 284                         //      size++;
 285                         //      secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
 286                         //}
 287
 288                         Sequence seq(inFasta);  m->gobble(inFasta);
 289
 290                         if (seq.getName() != "") {  //can get "" if commented line is at end of fasta file
 291                                 if (namefile != "") {
 292                                         itSize = sizes.find(seq.getName());
 293
 294                                         if (itSize == sizes.end()) { m->mothurOut(seq.getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); exit(1); }
 295                                         else{
 296                                                 seqPNode tempNode(itSize->second, seq, names[seq.getName()]);
 297                                                 alignSeqs.push_back(tempNode);
 298                                                 if (seq.getAligned().length() > length) {  length = seq.getAligned().length();  }
 299                                         }
 300                                 }else { //no names file, you are identical to yourself
 301                                         seqPNode tempNode(1, seq, seq.getName());
 302                                         alignSeqs.push_back(tempNode);
 303                                         if (seq.getAligned().length() > length) {  length = seq.getAligned().length();  }
 304                                 }
 305                         }
 306                 }
 307                 inFasta.close();
 308                 //inNames.close();
 309                 return alignSeqs.size();
 310         }
 311
 312         catch(exception& e) {
 313                 m->errorOut(e, "PreClusterCommand", "readFASTA");
 314                 exit(1);
 315         }
 316 }
 317
 318 /**************************************************************************************************/
 319
 320 int PreClusterCommand::calcMisMatches(string seq1, string seq2){
 321         try {
 322                 int numBad = 0;
 323
 324                 for (int i = 0; i < seq1.length(); i++) {
 325                         //do they match
 326                         if (seq1[i] != seq2[i]) { numBad++; }
 327                         if (numBad > diffs) { return length;  } //to far to cluster
 328                 }
 329
 330                 return numBad;
 331         }
 332         catch(exception& e) {
 333                 m->errorOut(e, "PreClusterCommand", "calcMisMatches");
 334                 exit(1);
 335         }
 336 }
 337
 338 /**************************************************************************************************/
 339
 340 void PreClusterCommand::printData(string newfasta, string newname){
 341         try {
 342                 ofstream outFasta;
 343                 ofstream outNames;
 344
 345                 m->openOutputFile(newfasta, outFasta);
 346                 m->openOutputFile(newname, outNames);
 347
 348
 349                 for (int i = 0; i < alignSeqs.size(); i++) {
 350                         if (alignSeqs[i].numIdentical != 0) {
 351                                 alignSeqs[i].seq.printSequence(outFasta);
 352                                 outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl;
 353                         }
 354                 }
 355
 356                 outFasta.close();
 357                 outNames.close();
 358
 359         }
 360         catch(exception& e) {
 361                 m->errorOut(e, "PreClusterCommand", "printData");
 362                 exit(1);
 363         }
 364 }
 365 /**************************************************************************************************/
 366
 367 void PreClusterCommand::readNameFile(){
 368         try {
 369                 ifstream in;
 370                 m->openInputFile(namefile, in);
 371                 string firstCol, secondCol;
 372
 373                 while (!in.eof()) {
 374                         in >> firstCol >> secondCol; m->gobble(in);
 375                         names[firstCol] = secondCol;
 376                         int size = 1;
 377
 378                         for(int i=0;i<secondCol.size();i++){
 379                                 if(secondCol[i] == ','){        size++; }
 380                         }
 381                         sizes[firstCol] = size;
 382                 }
 383                 in.close();
 384         }
 385         catch(exception& e) {
 386                 m->errorOut(e, "PreClusterCommand", "readNameFile");
 387                 exit(1);
 388         }
 389 }
 390
 391 /**************************************************************************************************/
 392
 393