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