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