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