clusterfragmentscommand.cpp

   1 /*
   2  *  ryanscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 9/23/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "clusterfragmentscommand.h"
  11 #include "needlemanoverlap.hpp"
  12
  13 //**********************************************************************************************************************
  14 //sort by unaligned
  15 inline bool comparePriority(seqRNode first, seqRNode second) {
  16         bool better = false;
  17
  18         if (first.length > second.length) {
  19                 better = true;
  20         }else if (first.length == second.length) {
  21                 if (first.numIdentical > second.numIdentical) {
  22                         better = true;
  23                 }
  24         }
  25
  26         return better;
  27 }
  28 //**********************************************************************************************************************
  29 vector<string> ClusterFragmentsCommand::setParameters(){
  30         try {
  31                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  32                 CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
  33         CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
  34                 CommandParameter pdiffs("diffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pdiffs);
  35                 CommandParameter ppercent("percent", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppercent);
  36                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  37                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  38
  39                 vector<string> myArray;
  40                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  41                 return myArray;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "ClusterFragmentsCommand", "setParameters");
  45                 exit(1);
  46         }
  47 }
  48 //**********************************************************************************************************************
  49 string ClusterFragmentsCommand::getHelpString(){
  50         try {
  51                 string helpString = "";
  52                 helpString += "The cluster.fragments command groups sequences that are part of a larger sequence.\n";
  53                 helpString += "The cluster.fragments command outputs a new fasta and name or count file.\n";
  54                 helpString += "The cluster.fragments command parameters are fasta, name, count, diffs and percent. The fasta parameter is required, unless you have a valid current file. \n";
  55                 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";
  56                 helpString += "The diffs parameter allows you to set the number of differences allowed, default=0. \n";
  57                 helpString += "The percent parameter allows you to set percentage of differences allowed, default=0. percent=2 means if the number of difference is less than or equal to two percent of the length of the fragment, then cluster.\n";
  58                 helpString += "You may use diffs and percent at the same time to say something like: If the number or differences is greater than 1 or more than 2% of the fragment length, don't merge. \n";
  59                 helpString += "The cluster.fragments command should be in the following format: \n";
  60                 helpString += "cluster.fragments(fasta=yourFastaFile, names=yourNamesFile) \n";
  61                 helpString += "Example cluster.fragments(fasta=amazon.fasta).\n";
  62                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  63                 return helpString;
  64         }
  65         catch(exception& e) {
  66                 m->errorOut(e, "ClusterFragmentsCommand", "getHelpString");
  67                 exit(1);
  68         }
  69 }
  70 //**********************************************************************************************************************
  71 string ClusterFragmentsCommand::getOutputFileNameTag(string type, string inputName=""){
  72         try {
  73         string outputFileName = "";
  74                 map<string, vector<string> >::iterator it;
  75
  76         //is this a type this command creates
  77         it = outputTypes.find(type);
  78         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  79         else {
  80             if (type == "fasta") {  outputFileName =  "fragclust.fasta"; }
  81             else if (type == "name") {  outputFileName =  "fragclust.names"; }
  82             else if (type == "count") {  outputFileName =  "fragclust.count_table"; }
  83             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  84         }
  85         return outputFileName;
  86         }
  87         catch(exception& e) {
  88                 m->errorOut(e, "ClusterFragmentsCommand", "getOutputFileNameTag");
  89                 exit(1);
  90         }
  91 }
  92
  93 //**********************************************************************************************************************
  94 ClusterFragmentsCommand::ClusterFragmentsCommand(){
  95         try {
  96                 abort = true; calledHelp = true;
  97                 setParameters();
  98                 vector<string> tempOutNames;
  99                 outputTypes["fasta"] = tempOutNames;
 100                 outputTypes["name"] = tempOutNames;
 101         outputTypes["count"] = tempOutNames;
 102         }
 103         catch(exception& e) {
 104                 m->errorOut(e, "ClusterFragmentsCommand", "ClusterFragmentsCommand");
 105                 exit(1);
 106         }
 107 }
 108 //**********************************************************************************************************************
 109 ClusterFragmentsCommand::ClusterFragmentsCommand(string option) {
 110         try {
 111                 abort = false; calledHelp = false;
 112
 113                 //allow user to run help
 114                 if(option == "help") { help(); abort = true; calledHelp = true; }
 115                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 116
 117                 else {
 118                         vector<string> myArray = setParameters();
 119
 120                         OptionParser parser(option);
 121                         map<string, string> parameters = parser.getParameters();
 122
 123                         ValidParameters validParameter;
 124                         map<string, string>::iterator it;
 125
 126                         //check to make sure all parameters are valid for command
 127                         for (map<string, string>::iterator it2 = parameters.begin(); it2 != parameters.end(); it2++) {
 128                                 if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) {  abort = true;  }
 129                         }
 130
 131                         //initialize outputTypes
 132                         vector<string> tempOutNames;
 133                         outputTypes["fasta"] = tempOutNames;
 134                         outputTypes["name"] = tempOutNames;
 135             outputTypes["count"] = tempOutNames;
 136
 137                         //if the user changes the input directory command factory will send this info to us in the output parameter
 138                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 139                         if (inputDir == "not found"){   inputDir = "";          }
 140                         else {
 141                                 string path;
 142                                 it = parameters.find("fasta");
 143                                 //user has given a template file
 144                                 if(it != parameters.end()){
 145                                         path = m->hasPath(it->second);
 146                                         //if the user has not given a path then, add inputdir. else leave path alone.
 147                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 148                                 }
 149
 150                                 it = parameters.find("name");
 151                                 //user has given a template file
 152                                 if(it != parameters.end()){
 153                                         path = m->hasPath(it->second);
 154                                         //if the user has not given a path then, add inputdir. else leave path alone.
 155                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 156                                 }
 157
 158                 it = parameters.find("count");
 159                                 //user has given a template file
 160                                 if(it != parameters.end()){
 161                                         path = m->hasPath(it->second);
 162                                         //if the user has not given a path then, add inputdir. else leave path alone.
 163                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 164                                 }
 165                         }
 166
 167                         //check for required parameters
 168                         fastafile = validParameter.validFile(parameters, "fasta", true);
 169                         if (fastafile == "not found") {
 170                                 fastafile = m->getFastaFile();
 171                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 172                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 173                         }
 174                         else if (fastafile == "not open") { fastafile = ""; abort = true; }
 175                         else { m->setFastaFile(fastafile); }
 176
 177                         //if the user changes the output directory command factory will send this info to us in the output parameter
 178                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);      }
 179
 180                         //check for optional parameter and set defaults
 181                         // ...at some point should added some additional type checking...
 182                         namefile = validParameter.validFile(parameters, "name", true);
 183                         if (namefile == "not found") { namefile =  "";  }
 184                         else if (namefile == "not open") { namefile = ""; abort = true; }
 185                         else {  readNameFile(); m->setNameFile(namefile); }
 186
 187             countfile = validParameter.validFile(parameters, "count", true);
 188                         if (countfile == "not open") { abort = true; countfile = ""; }
 189                         else if (countfile == "not found") { countfile = ""; }
 190                         else { ct.readTable(countfile); m->setCountTableFile(countfile); }
 191
 192             if ((countfile != "") && (namefile != "")) { m->mothurOut("When executing a cluster.fragments command you must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
 193
 194                         string temp;
 195                         temp = validParameter.validFile(parameters, "diffs", false);            if (temp == "not found"){       temp = "0";                             }
 196                         m->mothurConvert(temp, diffs);
 197
 198                         temp = validParameter.validFile(parameters, "percent", false);          if (temp == "not found"){       temp = "0";                             }
 199                         m->mothurConvert(temp, percent);
 200
 201                         if (countfile == "") {
 202                 if (namefile == "") {
 203                     vector<string> files; files.push_back(fastafile);
 204                     parser.getNameFile(files);
 205                 }
 206             }
 207
 208                 }
 209
 210         }
 211         catch(exception& e) {
 212                 m->errorOut(e, "ClusterFragmentsCommand", "ClusterFragmentsCommand");
 213                 exit(1);
 214         }
 215 }
 216 //**********************************************************************************************************************
 217 int ClusterFragmentsCommand::execute(){
 218         try {
 219
 220                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 221
 222                 int start = time(NULL);
 223
 224                 //reads fasta file and return number of seqs
 225                 int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
 226
 227                 if (m->control_pressed) { return 0; }
 228
 229                 if (numSeqs == 0) { m->mothurOut("Error reading fasta file...please correct."); m->mothurOutEndLine(); return 0;  }
 230
 231                 //sort seqs by length of unaligned sequence
 232                 sort(alignSeqs.begin(), alignSeqs.end(), comparePriority);
 233
 234                 int count = 0;
 235
 236                 //think about running through twice...
 237                 for (int i = 0; i < numSeqs; i++) {
 238
 239                         if (alignSeqs[i].active) {  //this sequence has not been merged yet
 240
 241                                 string iBases = alignSeqs[i].seq.getUnaligned();
 242
 243                                 //try to merge it with all smaller seqs
 244                                 for (int j = i+1; j < numSeqs; j++) {
 245
 246                                         if (m->control_pressed) { return 0; }
 247
 248                                         if (alignSeqs[j].active) {  //this sequence has not been merged yet
 249
 250                                                 string jBases = alignSeqs[j].seq.getUnaligned();
 251
 252                                                 if (isFragment(iBases, jBases)) {
 253                             if (countfile != "") {
 254                                 ct.mergeCounts(alignSeqs[i].names, alignSeqs[j].names);
 255                             }else {
 256                                 //merge
 257                                 alignSeqs[i].names += ',' + alignSeqs[j].names;
 258                                 alignSeqs[i].numIdentical += alignSeqs[j].numIdentical;
 259                             }
 260                                                         alignSeqs[j].active = 0;
 261                                                         alignSeqs[j].numIdentical = 0;
 262                                                         count++;
 263                                                 }
 264                                         }//end if j active
 265                                 }//end if i != j
 266
 267                                 //remove from active list
 268                                 alignSeqs[i].active = 0;
 269
 270                         }//end if active i
 271                         if(i % 100 == 0)        { m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine(); }
 272                 }
 273
 274                 if(numSeqs % 100 != 0)  { m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); m->mothurOutEndLine();   }
 275
 276
 277                 string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
 278
 279                 string newFastaFile = fileroot + getOutputFileNameTag("fasta");
 280                 string newNamesFile = fileroot + getOutputFileNameTag("name");
 281         if (countfile != "") { newNamesFile = fileroot + getOutputFileNameTag("count"); }
 282
 283                 if (m->control_pressed) { return 0; }
 284
 285                 m->mothurOutEndLine();
 286                 m->mothurOut("Total number of sequences before cluster.fragments was " + toString(alignSeqs.size()) + "."); m->mothurOutEndLine();
 287                 m->mothurOut("cluster.fragments removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
 288
 289                 printData(newFastaFile, newNamesFile);
 290
 291                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 292
 293                 if (m->control_pressed) { m->mothurRemove(newFastaFile); m->mothurRemove(newNamesFile); return 0; }
 294
 295                 m->mothurOutEndLine();
 296                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 297                 m->mothurOut(newFastaFile); m->mothurOutEndLine();
 298                 m->mothurOut(newNamesFile); m->mothurOutEndLine();
 299                 outputNames.push_back(newFastaFile);  outputNames.push_back(newNamesFile); outputTypes["fasta"].push_back(newFastaFile); outputTypes["name"].push_back(newNamesFile);
 300                 m->mothurOutEndLine();
 301
 302                 //set fasta file as new current fastafile
 303                 string current = "";
 304                 itTypes = outputTypes.find("fasta");
 305                 if (itTypes != outputTypes.end()) {
 306                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 307                 }
 308
 309                 itTypes = outputTypes.find("name");
 310                 if (itTypes != outputTypes.end()) {
 311                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 312                 }
 313
 314         itTypes = outputTypes.find("count");
 315                 if (itTypes != outputTypes.end()) {
 316                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 317                 }
 318
 319                 return 0;
 320
 321         }
 322         catch(exception& e) {
 323                 m->errorOut(e, "ClusterFragmentsCommand", "execute");
 324                 exit(1);
 325         }
 326 }
 327 //***************************************************************************************************************
 328 bool ClusterFragmentsCommand::isFragment(string seq1, string seq2){
 329         try {
 330                 bool fragment = false;
 331
 332                 //exact match
 333                 int pos = seq1.find(seq2);
 334                 if (pos != string::npos) { return true; }
 335                 //no match, no diffs wanted
 336                 else if ((diffs == 0) && (percent == 0)) { return false; }
 337                 else { //try aligning and see if you can find it
 338
 339                         //find number of acceptable differences for this sequence fragment
 340                         int totalDiffs;
 341                         if (diffs == 0) { //you didnt set diffs you want a percentage
 342                                 totalDiffs = floor((seq2.length() * (percent / 100.0)));
 343                         }else if (percent == 0) { //you didn't set percent you want diffs
 344                                 totalDiffs = diffs;
 345                         }else if ((percent != 0) && (diffs != 0)) { //you want both, set total diffs to smaller of 2
 346                                 totalDiffs = diffs;
 347                                 int percentDiff = floor((seq2.length() * (percent / 100.0)));
 348                                 if (percentDiff < totalDiffs) { totalDiffs = percentDiff; }
 349                         }
 350
 351                         Alignment* alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (seq1.length()+totalDiffs+1));
 352
 353                         //use needleman to align
 354                         alignment->align(seq2, seq1);
 355                         string tempSeq2 = alignment->getSeqAAln();
 356                         string temp = alignment->getSeqBAln();
 357
 358                         delete alignment;
 359
 360                         //chop gap ends
 361                         int startPos = 0;
 362                         int endPos = tempSeq2.length()-1;
 363                         for (int i = 0; i < tempSeq2.length(); i++) {  if (isalpha(tempSeq2[i])) { startPos = i; break; } }
 364                         for (int i = tempSeq2.length()-1; i >= 0; i--) {  if (isalpha(tempSeq2[i])) { endPos = i; break; } }
 365
 366                         //count number of diffs
 367                         int numDiffs = 0;
 368                         for (int i = startPos; i <= endPos; i++) {
 369                                 if (tempSeq2[i] != temp[i]) { numDiffs++; }
 370                         }
 371
 372                         if (numDiffs <= totalDiffs) { fragment = true; }
 373
 374                 }
 375
 376                 return fragment;
 377
 378         }
 379         catch(exception& e) {
 380                 m->errorOut(e, "ClusterFragmentsCommand", "isFragment");
 381                 exit(1);
 382         }
 383 }
 384 /**************************************************************************************************/
 385 int ClusterFragmentsCommand::readFASTA(){
 386         try {
 387
 388                 ifstream inFasta;
 389                 m->openInputFile(fastafile, inFasta);
 390
 391                 while (!inFasta.eof()) {
 392
 393                         if (m->control_pressed) { inFasta.close(); return 0; }
 394
 395                         Sequence seq(inFasta);  m->gobble(inFasta);
 396
 397                         if (seq.getName() != "") {  //can get "" if commented line is at end of fasta file
 398                                 if (namefile != "") {
 399                                         itSize = sizes.find(seq.getName());
 400
 401                                         if (itSize == sizes.end()) { m->mothurOut(seq.getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); exit(1); }
 402                                         else{
 403                                                 seqRNode tempNode(itSize->second, seq, names[seq.getName()], seq.getUnaligned().length());
 404                                                 alignSeqs.push_back(tempNode);
 405                                         }
 406                 }else if(countfile != "") {
 407                     seqRNode tempNode(ct.getNumSeqs(seq.getName()), seq, seq.getName(), seq.getUnaligned().length());
 408                     alignSeqs.push_back(tempNode);
 409                                 }else { //no names file, you are identical to yourself
 410                                         seqRNode tempNode(1, seq, seq.getName(), seq.getUnaligned().length());
 411                                         alignSeqs.push_back(tempNode);
 412                                 }
 413                         }
 414                 }
 415
 416                 inFasta.close();
 417                 return alignSeqs.size();
 418         }
 419
 420         catch(exception& e) {
 421                 m->errorOut(e, "ClusterFragmentsCommand", "readFASTA");
 422                 exit(1);
 423         }
 424 }
 425 /**************************************************************************************************/
 426 void ClusterFragmentsCommand::printData(string newfasta, string newname){
 427         try {
 428                 ofstream outFasta;
 429                 ofstream outNames;
 430
 431                 m->openOutputFile(newfasta, outFasta);
 432                 if (countfile == "") {  m->openOutputFile(newname, outNames); }
 433
 434                 for (int i = 0; i < alignSeqs.size(); i++) {
 435                         if (alignSeqs[i].numIdentical != 0) {
 436                                 alignSeqs[i].seq.printSequence(outFasta);
 437                                 if (countfile == "") {  outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl;  }
 438                         }
 439                 }
 440
 441                 outFasta.close();
 442                 if (countfile == "") {  outNames.close(); }
 443         else { ct.printTable(newname); }
 444         }
 445         catch(exception& e) {
 446                 m->errorOut(e, "ClusterFragmentsCommand", "printData");
 447                 exit(1);
 448         }
 449 }
 450 /**************************************************************************************************/
 451
 452 void ClusterFragmentsCommand::readNameFile(){
 453         try {
 454                 ifstream in;
 455                 m->openInputFile(namefile, in);
 456                 string firstCol, secondCol;
 457
 458                 while (!in.eof()) {
 459                         in >> firstCol >> secondCol; m->gobble(in);
 460                         names[firstCol] = secondCol;
 461                         int size = 1;
 462
 463                         for(int i=0;i<secondCol.size();i++){
 464                                 if(secondCol[i] == ','){        size++; }
 465                         }
 466                         sizes[firstCol] = size;
 467                 }
 468                 in.close();
 469         }
 470         catch(exception& e) {
 471                 m->errorOut(e, "ClusterFragmentsCommand", "readNameFile");
 472                 exit(1);
 473         }
 474 }
 475 /**************************************************************************************************/
 476