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