pairwiseseqscommand.h

   1 #ifndef PAIRWISESEQSCOMMAND_H
   2 #define PAIRWISESEQSCOMMAND_H
   3
   4 /*
   5  *  pairwiseseqscommand.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 10/20/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "command.hpp"
  15 #include "database.hpp"
  16 #include "alignment.hpp"
  17 #include "validcalculator.h"
  18 #include "dist.h"
  19 #include "sequencedb.h"
  20 #include "sequence.hpp"
  21
  22 #include "gotohoverlap.hpp"
  23 #include "needlemanoverlap.hpp"
  24 #include "blastalign.hpp"
  25 #include "noalign.hpp"
  26
  27 #include "ignoregaps.h"
  28 #include "eachgapdist.h"
  29 #include "eachgapignore.h"
  30 #include "onegapdist.h"
  31 #include "onegapignore.h"
  32
  33 class PairwiseSeqsCommand : public Command {
  34
  35 public:
  36         PairwiseSeqsCommand(string);
  37         PairwiseSeqsCommand();
  38         ~PairwiseSeqsCommand() {}
  39
  40         vector<string> setParameters();
  41         string getCommandName()                 { return "pairwise.seqs";               }
  42         string getCommandCategory()             { return "Sequence Processing"; }
  43         string getOutputFileNameTag(string, string);
  44         string getHelpString();
  45         string getCitation() { return "Needleman SB, Wunsch CD (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-53. [ for needleman ]\nGotoh O (1982). An improved algorithm for matching biological sequences. J Mol Biol 162: 705-8. [ for gotoh ] \nhttp://www.mothur.org/wiki/Pairwise.seqs"; }
  46         string getDescription()         { return "calculates pairwise distances from an unaligned fasta file"; }
  47
  48         int execute();
  49         void help() { m->mothurOut(getHelpString()); }
  50
  51 private:
  52         struct distlinePair {
  53                 int start;
  54                 int end;
  55         };
  56
  57         vector<int> processIDS;   //end line, processid
  58         vector<distlinePair> lines;
  59
  60         SequenceDB alignDB;
  61
  62         void createProcesses(string);
  63         int driver(int, int, string, float);
  64         int driver(int, int, string, string);
  65
  66         #ifdef USE_MPI
  67         int driverMPI(int, int, MPI_File&, float);
  68         int driverMPI(int, int, string, unsigned long long&);
  69         int driverMPI(int, int, string, unsigned long long&, string);
  70         #endif
  71
  72         string fastaFileName, align, calc, outputDir, output;
  73         float match, misMatch, gapOpen, gapExtend, cutoff;
  74         int processors, longestBase;
  75         vector<string> fastaFileNames, Estimators;
  76         vector<string> outputNames;
  77
  78         bool abort, countends, compress;
  79 };
  80
  81 /**************************************************************************************************/
  82 //custom data structure for threads to use.
  83 // This is passed by void pointer so it can be any data type
  84 // that can be passed using a single void pointer (LPVOID).
  85 struct pairwiseData {
  86     string outputFileName;
  87         string align, square, distcalcType, output;
  88         unsigned long long start;
  89         unsigned long long end;
  90         MothurOut* m;
  91         float match, misMatch, gapOpen, gapExtend, cutoff;
  92         int count, threadID, longestBase;
  93     bool countends;
  94     SequenceDB alignDB;
  95
  96         pairwiseData(){}
  97         pairwiseData(string ofn, string al, string sq, string di, bool co, string op, SequenceDB DB, MothurOut* mout, unsigned long long st, unsigned long long en, float ma, float misMa, float gapO, float gapE, int thr, int tid) {
  98                 outputFileName = ofn;
  99                 m = mout;
 100                 start = st;
 101                 end = en;
 102                 match = ma;
 103                 misMatch = misMa;
 104                 gapOpen = gapO;
 105                 gapExtend = gapE;
 106                 longestBase = thr;
 107                 align = al;
 108         square = sq;
 109         distcalcType = di;
 110         countends = co;
 111         alignDB = DB;
 112                 count = 0;
 113         output = op;
 114                 threadID = tid;
 115         }
 116 };
 117
 118 /**************************************************************************************************/
 119 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 120 #else
 121 static DWORD WINAPI MyPairwiseSquareThreadFunction(LPVOID lpParam){
 122         pairwiseData* pDataArray;
 123         pDataArray = (pairwiseData*)lpParam;
 124
 125         try {
 126                 ofstream outFile((pDataArray->outputFileName).c_str(), ios::trunc);
 127                 outFile.setf(ios::fixed, ios::showpoint);
 128                 outFile << setprecision(4);
 129
 130                 pDataArray->count = pDataArray->end;
 131
 132         int startTime = time(NULL);
 133
 134         Alignment* alignment;
 135         if(pDataArray->align == "gotoh")                        {       alignment = new GotohOverlap(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase);                     }
 136                 else if(pDataArray->align == "needleman")       {       alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase);                                }
 137                 else if(pDataArray->align == "blast")           {       alignment = new BlastAlignment(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch);            }
 138                 else if(pDataArray->align == "noalign")         {       alignment = new NoAlign();                                                                                                      }
 139                 else {
 140                         pDataArray->m->mothurOut(pDataArray->align + " is not a valid alignment option. I will run the command using needleman.");
 141                         pDataArray->m->mothurOutEndLine();
 142                         alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase);
 143                 }
 144
 145         ValidCalculators validCalculator;
 146         Dist* distCalculator;
 147         if (pDataArray->countends) {
 148             if (validCalculator.isValidCalculator("distance", pDataArray->distcalcType) == true) {
 149                 if (pDataArray->distcalcType == "nogaps")                       {       distCalculator = new ignoreGaps();      }
 150                 else if (pDataArray->distcalcType == "eachgap") {       distCalculator = new eachGapDist();     }
 151                 else if (pDataArray->distcalcType == "onegap")          {       distCalculator = new oneGapDist();      }
 152             }
 153         }else {
 154             if (validCalculator.isValidCalculator("distance", pDataArray->distcalcType) == true) {
 155                 if (pDataArray->distcalcType == "nogaps")               {       distCalculator = new ignoreGaps();                                      }
 156                 else if (pDataArray->distcalcType == "eachgap"){        distCalculator = new eachGapIgnoreTermGapDist();        }
 157                 else if (pDataArray->distcalcType == "onegap")  {       distCalculator = new oneGapIgnoreTermGapDist();         }
 158             }
 159         }
 160
 161         if(pDataArray->start == 0){     outFile << pDataArray->alignDB.getNumSeqs() << endl;    }
 162
 163                 for(int i=pDataArray->start;i<pDataArray->end;i++){
 164
 165                         string name = pDataArray->alignDB.get(i).getName();
 166                         //pad with spaces to make compatible
 167                         if (name.length() < 10) { while (name.length() < 10) {  name += " ";  } }
 168
 169                         outFile << name << '\t';
 170
 171                         for(int j=0;j<pDataArray->alignDB.getNumSeqs();j++){
 172
 173                                 if (pDataArray->m->control_pressed) { outFile.close(); delete alignment; delete distCalculator; return 0;  }
 174
 175                                 if (pDataArray->alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 176                                         alignment->resize(pDataArray->alignDB.get(i).getUnaligned().length()+1);
 177                                 }
 178
 179                                 if (pDataArray->alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 180                                         alignment->resize(pDataArray->alignDB.get(j).getUnaligned().length()+1);
 181                                 }
 182
 183                                 Sequence seqI(pDataArray->alignDB.get(i).getName(), pDataArray->alignDB.get(i).getAligned());
 184                                 Sequence seqJ(pDataArray->alignDB.get(j).getName(), pDataArray->alignDB.get(j).getAligned());
 185
 186                                 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
 187                                 seqI.setAligned(alignment->getSeqAAln());
 188                                 seqJ.setAligned(alignment->getSeqBAln());
 189
 190                                 distCalculator->calcDist(seqI, seqJ);
 191                                 double dist = distCalculator->getDist();
 192
 193                                 outFile << dist << '\t';
 194                         }
 195
 196                         outFile << endl;
 197
 198                         if(i % 100 == 0){
 199                                 pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
 200                         }
 201
 202                 }
 203                 pDataArray->m->mothurOut(toString(pDataArray->end-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
 204
 205                 outFile.close();
 206         delete alignment;
 207         delete distCalculator;
 208
 209
 210     }
 211         catch(exception& e) {
 212                 pDataArray->m->errorOut(e, "PairwiseSeqsCommand", "MyPairwiseSquareThreadFunction");
 213                 exit(1);
 214         }
 215 }
 216
 217 /**************************************************************************************************/
 218 static DWORD WINAPI MyPairwiseThreadFunction(LPVOID lpParam){
 219         pairwiseData* pDataArray;
 220         pDataArray = (pairwiseData*)lpParam;
 221
 222         try {
 223                 ofstream outFile((pDataArray->outputFileName).c_str(), ios::trunc);
 224                 outFile.setf(ios::fixed, ios::showpoint);
 225                 outFile << setprecision(4);
 226
 227         pDataArray->count = pDataArray->end;
 228
 229         int startTime = time(NULL);
 230
 231         Alignment* alignment;
 232         if(pDataArray->align == "gotoh")                        {       alignment = new GotohOverlap(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase);                     }
 233                 else if(pDataArray->align == "needleman")       {       alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase);                                }
 234                 else if(pDataArray->align == "blast")           {       alignment = new BlastAlignment(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch);            }
 235                 else if(pDataArray->align == "noalign")         {       alignment = new NoAlign();                                                                                                      }
 236                 else {
 237                         pDataArray->m->mothurOut(pDataArray->align + " is not a valid alignment option. I will run the command using needleman.");
 238                         pDataArray->m->mothurOutEndLine();
 239                         alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase);
 240                 }
 241
 242         ValidCalculators validCalculator;
 243         Dist* distCalculator;
 244         if (pDataArray->countends) {
 245             if (validCalculator.isValidCalculator("distance", pDataArray->distcalcType) == true) {
 246                 if (pDataArray->distcalcType == "nogaps")                       {       distCalculator = new ignoreGaps();      }
 247                 else if (pDataArray->distcalcType == "eachgap") {       distCalculator = new eachGapDist();     }
 248                 else if (pDataArray->distcalcType == "onegap")          {       distCalculator = new oneGapDist();      }
 249             }
 250         }else {
 251             if (validCalculator.isValidCalculator("distance", pDataArray->distcalcType) == true) {
 252                 if (pDataArray->distcalcType == "nogaps")               {       distCalculator = new ignoreGaps();                                      }
 253                 else if (pDataArray->distcalcType == "eachgap"){        distCalculator = new eachGapIgnoreTermGapDist();        }
 254                 else if (pDataArray->distcalcType == "onegap")  {       distCalculator = new oneGapIgnoreTermGapDist();         }
 255             }
 256         }
 257
 258         if((pDataArray->output == "lt") && pDataArray->start == 0){     outFile << pDataArray->alignDB.getNumSeqs() << endl;    }
 259
 260                 for(int i=pDataArray->start;i<pDataArray->end;i++){
 261
 262                         if(pDataArray->output == "lt")  {
 263                                 string name = pDataArray->alignDB.get(i).getName();
 264                                 if (name.length() < 10) { //pad with spaces to make compatible
 265                                         while (name.length() < 10) {  name += " ";  }
 266                                 }
 267                                 outFile << name << '\t';
 268                         }
 269
 270
 271                         for(int j=0;j<i;j++){
 272
 273                                 if (pDataArray->m->control_pressed) { outFile.close(); delete alignment; delete distCalculator; return 0;  }
 274
 275                                 if (pDataArray->alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 276                                         alignment->resize(pDataArray->alignDB.get(i).getUnaligned().length()+1);
 277                                 }
 278
 279                                 if (pDataArray->alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 280                                         alignment->resize(pDataArray->alignDB.get(j).getUnaligned().length()+1);
 281                                 }
 282
 283                                 Sequence seqI(pDataArray->alignDB.get(i).getName(), pDataArray->alignDB.get(i).getAligned());
 284                                 Sequence seqJ(pDataArray->alignDB.get(j).getName(), pDataArray->alignDB.get(j).getAligned());
 285
 286                                 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
 287                                 seqI.setAligned(alignment->getSeqAAln());
 288                                 seqJ.setAligned(alignment->getSeqBAln());
 289
 290                                 distCalculator->calcDist(seqI, seqJ);
 291                                 double dist = distCalculator->getDist();
 292
 293                                 if(dist <= pDataArray->cutoff){
 294                                         if (pDataArray->output == "column") { outFile << pDataArray->alignDB.get(i).getName() << ' ' << pDataArray->alignDB.get(j).getName() << ' ' << dist << endl; }
 295                                 }
 296                                 if (pDataArray->output == "lt") {  outFile << dist << '\t'; }
 297                         }
 298
 299                         if (pDataArray->output == "lt") { outFile << endl; }
 300
 301                         if(i % 100 == 0){
 302                                 pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
 303                         }
 304
 305                 }
 306                 pDataArray->m->mothurOut(toString(pDataArray->end-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
 307
 308                 outFile.close();
 309         delete alignment;
 310         delete distCalculator;
 311
 312
 313     }
 314         catch(exception& e) {
 315                 pDataArray->m->errorOut(e, "PairwiseSeqsCommand", "MyPairwiseThreadFunction");
 316                 exit(1);
 317         }
 318 }
 319
 320 #endif
 321
 322
 323 #endif
 324