preclustercommand.h

   1 #ifndef PRECLUSTERCOMMAND_H
   2 #define PRECLUSTERCOMMAND_H
   3
   4
   5 /*
   6  *  preclustercommand.h
   7  *  Mothur
   8  *
   9  *  Created by westcott on 12/21/09.
  10  *  Copyright 2009 Schloss Lab. All rights reserved.
  11  *
  12  */
  13
  14
  15 #include "command.hpp"
  16 #include "sequence.hpp"
  17 #include "sequenceparser.h"
  18 #include "sequencecountparser.h"
  19
  20 /************************************************************/
  21 struct seqPNode {
  22         int numIdentical;
  23         Sequence seq;
  24         string names;
  25         bool active;
  26         int diffs;
  27         seqPNode() {}
  28         seqPNode(int n, Sequence s, string nm) : numIdentical(n), seq(s), names(nm), active(1) { diffs = 0; }
  29         ~seqPNode() {}
  30 };
  31 /************************************************************/
  32 inline bool comparePriority(seqPNode first, seqPNode second) {
  33     if (first.numIdentical > second.numIdentical) { return true;  }
  34     else if (first.numIdentical == second.numIdentical) {
  35         if (first.seq.getName() > second.seq.getName()) { return true; }
  36     }
  37     return false;
  38 }
  39 //************************************************************/
  40
  41 class PreClusterCommand : public Command {
  42
  43 public:
  44         PreClusterCommand(string);
  45         PreClusterCommand();
  46         ~PreClusterCommand(){}
  47
  48         vector<string> setParameters();
  49         string getCommandName()                 { return "pre.cluster";                         }
  50         string getCommandCategory()             { return "Sequence Processing";         }
  51
  52         string getHelpString();
  53     string getOutputPattern(string);
  54         string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011).  Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.  PLoS ONE.  6:e27310.\nhttp://www.mothur.org/wiki/Pre.cluster"; }
  55         string getDescription()         { return "implements a pseudo-single linkage algorithm with the goal of removing sequences that are likely due to pyrosequencing errors"; }
  56
  57
  58         int execute();
  59         void help() { m->mothurOut(getHelpString()); }
  60
  61 private:
  62
  63         struct linePair {
  64                 int start;
  65                 int end;
  66                 linePair(int i, int j) : start(i), end(j) {}
  67         };
  68
  69     SequenceParser* parser;
  70     SequenceCountParser* cparser;
  71     CountTable ct;
  72
  73         int diffs, length, processors;
  74         bool abort, bygroup;
  75         string fastafile, namefile, outputDir, groupfile, countfile;
  76         vector<seqPNode> alignSeqs; //maps the number of identical seqs to a sequence
  77         map<string, string> names; //represents the names file first column maps to second column
  78         map<string, int> sizes;  //this map a seq name to the number of identical seqs in the names file
  79         map<string, int>::iterator itSize;
  80 //      map<string, bool> active; //maps sequence name to whether it has already been merged or not.
  81         vector<string> outputNames;
  82         map<string, vector<string> > outputTypes;
  83
  84         int readFASTA();
  85         void readNameFile();
  86         //int readNamesFASTA();
  87         int calcMisMatches(string, string);
  88         void printData(string, string, string); //fasta filename, names file name
  89         int process(string);
  90         int loadSeqs(map<string, string>&, vector<Sequence>&, string);
  91         int driverGroups(string, string, string, int, int, vector<string> groups);
  92         int createProcessesGroups(string, string, string, vector<string>);
  93     int mergeGroupCounts(string, string, string);
  94 };
  95
  96 /**************************************************************************************************/
  97 //custom data structure for threads to use.
  98 // This is passed by void pointer so it can be any data type
  99 // that can be passed using a single void pointer (LPVOID).
 100 struct preClusterData {
 101         string fastafile;
 102         string namefile;
 103         string groupfile, countfile;
 104         string newFName, newNName, newMName;
 105         MothurOut* m;
 106         int start;
 107         int end;
 108         int diffs, threadID;
 109         vector<string> groups;
 110         vector<string> mapFileNames;
 111
 112         preClusterData(){}
 113         preClusterData(string f, string n, string g, string c, string nff,  string nnf, string nmf, vector<string> gr, MothurOut* mout, int st, int en, int d, int tid) {
 114                 fastafile = f;
 115                 namefile = n;
 116                 groupfile = g;
 117                 newFName = nff;
 118                 newNName = nnf;
 119                 newMName = nmf;
 120                 m = mout;
 121                 start = st;
 122                 end = en;
 123                 diffs = d;
 124                 threadID = tid;
 125                 groups = gr;
 126         countfile = c;
 127         }
 128 };
 129
 130 /**************************************************************************************************/
 131 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 132 #else
 133 static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
 134         preClusterData* pDataArray;
 135         pDataArray = (preClusterData*)lpParam;
 136
 137         try {
 138
 139                 //parse fasta and name file by group
 140                 SequenceParser* parser;
 141         SequenceCountParser* cparser;
 142         if (pDataArray->countfile != "") {
 143             cparser = new SequenceCountParser(pDataArray->countfile, pDataArray->fastafile);
 144         }else {
 145             if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile);  }
 146             else                                { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile);                    }
 147         }
 148
 149                 int numSeqs = 0;
 150                 vector<seqPNode> alignSeqs;
 151                 //clear out old files
 152                 ofstream outF; pDataArray->m->openOutputFile(pDataArray->newFName, outF); outF.close();
 153                 ofstream outN; pDataArray->m->openOutputFile(pDataArray->newNName, outN);  outN.close();
 154
 155                 //precluster each group
 156                 for (int k = pDataArray->start; k < pDataArray->end; k++) {
 157
 158                         int start = time(NULL);
 159
 160                         if (pDataArray->m->control_pressed) {  delete parser; return 0; }
 161
 162                         pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOut("Processing group " + pDataArray->groups[k] + ":"); pDataArray->m->mothurOutEndLine();
 163
 164                         map<string, string> thisNameMap;
 165             vector<Sequence> thisSeqs;
 166                         if (pDataArray->groupfile != "") {
 167                 thisSeqs = parser->getSeqs(pDataArray->groups[k]);
 168             }else if (pDataArray->countfile != "") {
 169                 thisSeqs = cparser->getSeqs(pDataArray->groups[k]);
 170             }
 171                         if (pDataArray->namefile != "") {  thisNameMap = parser->getNameMap(pDataArray->groups[k]); }
 172
 173                         //fill alignSeqs with this groups info.
 174                         ////////////////////////////////////////////////////
 175                         //numSeqs = loadSeqs(thisNameMap, thisSeqs); same function below
 176
 177                         int length = 0;
 178                         alignSeqs.clear();
 179                         map<string, string>::iterator it;
 180                         bool error = false;
 181             map<string, int> thisCount;
 182             if (pDataArray->countfile != "") { thisCount = cparser->getCountTable(pDataArray->groups[k]);  }
 183
 184
 185                         for (int i = 0; i < thisSeqs.size(); i++) {
 186
 187                                 if (pDataArray->m->control_pressed) { delete parser; return 0; }
 188
 189                                 if (pDataArray->namefile != "") {
 190                                         it = thisNameMap.find(thisSeqs[i].getName());
 191
 192                                         //should never be true since parser checks for this
 193                                         if (it == thisNameMap.end()) { pDataArray->m->mothurOut(thisSeqs[i].getName() + " is not in your names file, please correct."); pDataArray->m->mothurOutEndLine(); error = true; }
 194                                         else{
 195                                                 //get number of reps
 196                                                 int numReps = 1;
 197                                                 for(int j=0;j<(it->second).length();j++){
 198                                                         if((it->second)[j] == ','){     numReps++;      }
 199                                                 }
 200
 201                                                 seqPNode tempNode(numReps, thisSeqs[i], it->second);
 202                                                 alignSeqs.push_back(tempNode);
 203                                                 if (thisSeqs[i].getAligned().length() > length) {  length = thisSeqs[i].getAligned().length();  }
 204                                         }
 205                                 }else { //no names file, you are identical to yourself
 206                                         int numRep = 1;
 207                     if (pDataArray->countfile != "") {
 208                         map<string, int>::iterator it2 = thisCount.find(thisSeqs[i].getName());
 209
 210                         //should never be true since parser checks for this
 211                         if (it2 == thisCount.end()) { pDataArray->m->mothurOut(thisSeqs[i].getName() + " is not in your count file, please correct."); pDataArray->m->mothurOutEndLine(); error = true; }
 212                         else { numRep = it2->second;  }
 213                     }
 214                     seqPNode tempNode(numRep, thisSeqs[i], thisSeqs[i].getName());
 215                     alignSeqs.push_back(tempNode);
 216                                         if (thisSeqs[i].getAligned().length() > length) {  length = thisSeqs[i].getAligned().length();  }
 217                                 }
 218                         }
 219
 220                         //sanity check
 221                         if (error) { pDataArray->m->control_pressed = true; }
 222
 223                         thisSeqs.clear();
 224                         numSeqs = alignSeqs.size();
 225
 226                         ////////////////////////////////////////////////////
 227
 228                         if (pDataArray->m->control_pressed) {   delete parser; return 0; }
 229
 230                         if (pDataArray->diffs > length) { pDataArray->m->mothurOut("Error: diffs is greater than your sequence length."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; return 0;  }
 231
 232                         ////////////////////////////////////////////////////
 233                         //int count = process(); - same function below
 234
 235                         ofstream out;
 236                         pDataArray->m->openOutputFile(pDataArray->newMName+pDataArray->groups[k]+".map", out);
 237                         pDataArray->mapFileNames.push_back(pDataArray->newMName+pDataArray->groups[k]+".map");
 238
 239                         //sort seqs by number of identical seqs
 240                         sort(alignSeqs.begin(), alignSeqs.end(), comparePriority);
 241
 242                         int count = 0;
 243
 244                         //think about running through twice...
 245                         for (int i = 0; i < numSeqs; i++) {
 246
 247                                 //are you active
 248                                 //                      itActive = active.find(alignSeqs[i].seq.getName());
 249
 250                                 if (alignSeqs[i].active) {  //this sequence has not been merged yet
 251
 252                                         string chunk = alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(0) + "\t" + alignSeqs[i].seq.getAligned() + "\n";
 253
 254                                         //try to merge it with all smaller seqs
 255                                         for (int j = i+1; j < numSeqs; j++) {
 256
 257                                                 if (pDataArray->m->control_pressed) { delete parser; return 0; }
 258
 259                                                 if (alignSeqs[j].active) {  //this sequence has not been merged yet
 260                                                         //are you within "diff" bases
 261                                                         //int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
 262                                                         int mismatch = 0;
 263
 264                                                         for (int k = 0; k < alignSeqs[i].seq.getAligned().length(); k++) {
 265                                                                 //do they match
 266                                                                 if (alignSeqs[i].seq.getAligned()[k] != alignSeqs[j].seq.getAligned()[k]) { mismatch++; }
 267                                                                 if (mismatch > pDataArray->diffs) { mismatch = length; break; } //to far to cluster
 268                                                         }
 269
 270                                                         if (mismatch <= pDataArray->diffs) {
 271                                                                 //merge
 272                                                                 alignSeqs[i].names += ',' + alignSeqs[j].names;
 273                                                                 alignSeqs[i].numIdentical += alignSeqs[j].numIdentical;
 274
 275                                                                 alignSeqs[j].active = 0;
 276                                                                 alignSeqs[j].numIdentical = 0;
 277                                                                 alignSeqs[j].diffs = mismatch;
 278                                                                 count++;
 279                                                                 chunk += alignSeqs[j].seq.getName() + "\t" + toString(alignSeqs[j].numIdentical) + "\t" + toString(mismatch) + "\t" + alignSeqs[j].seq.getAligned() + "\n";
 280                                                         }
 281                                                 }//end if j active
 282                                         }//end for loop j
 283
 284                                         //remove from active list
 285                                         alignSeqs[i].active = 0;
 286
 287                                         out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << chunk << endl;
 288
 289                                 }//end if active i
 290                                 if(i % 100 == 0)        { pDataArray->m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); pDataArray->m->mothurOutEndLine(); }
 291                         }
 292                         out.close();
 293                         if(numSeqs % 100 != 0)  { pDataArray->m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); pDataArray->m->mothurOutEndLine();   }
 294                         ////////////////////////////////////////////////////
 295
 296                         if (pDataArray->m->control_pressed) {  delete parser; return 0; }
 297
 298                         pDataArray->m->mothurOut("Total number of sequences before pre.cluster was " + toString(alignSeqs.size()) + ".");pDataArray-> m->mothurOutEndLine();
 299                         pDataArray->m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOutEndLine();
 300
 301                         ////////////////////////////////////////////////////
 302                         //printData(pDataArray->newFFile, pDataArray->newNFile); - same as below
 303                         ofstream outFasta;
 304                         ofstream outNames;
 305
 306                         pDataArray->m->openOutputFileAppend(pDataArray->newFName, outFasta);
 307                         pDataArray->m->openOutputFileAppend(pDataArray->newNName, outNames);
 308
 309                         for (int i = 0; i < alignSeqs.size(); i++) {
 310                                 if (alignSeqs[i].numIdentical != 0) {
 311                                         alignSeqs[i].seq.printSequence(outFasta);
 312                                         if (pDataArray->countfile != "") {  outNames << pDataArray->groups[k] << '\t' << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl;
 313                     }else {  outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl;  }
 314
 315                                 }
 316                         }
 317
 318                         outFasta.close();
 319                         outNames.close();
 320                         ////////////////////////////////////////////////////
 321
 322                         pDataArray->m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); pDataArray->m->mothurOutEndLine();
 323
 324                 }
 325
 326                 return numSeqs;
 327
 328
 329         }
 330         catch(exception& e) {
 331                 pDataArray->m->errorOut(e, "PreClusterCommand", "MyPreclusterThreadFunction");
 332                 exit(1);
 333         }
 334 }
 335 #endif
 336
 337 /**************************************************************************************************/
 338
 339
 340 #endif
 341
 342