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
  44         string getHelpString();
  45     string getOutputPattern(string);
  46         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"; }
  47         string getDescription()         { return "calculates pairwise distances from an unaligned fasta file"; }
  48
  49         int execute();
  50         void help() { m->mothurOut(getHelpString()); }
  51
  52 private:
  53         struct distlinePair {
  54                 int start;
  55                 int end;
  56         };
  57
  58         vector<int> processIDS;   //end line, processid
  59         vector<distlinePair> lines;
  60
  61         SequenceDB alignDB;
  62
  63         void createProcesses(string);
  64         int driver(int, int, string, float);
  65         int driver(int, int, string, string);
  66
  67         #ifdef USE_MPI
  68         int driverMPI(int, int, MPI_File&, float);
  69         int driverMPI(int, int, string, unsigned long long&);
  70         int driverMPI(int, int, string, unsigned long long&, string);
  71         #endif
  72
  73         string fastaFileName, align, calc, outputDir, output;
  74         float match, misMatch, gapOpen, gapExtend, cutoff;
  75         int processors, longestBase;
  76         vector<string> fastaFileNames, Estimators;
  77         vector<string> outputNames;
  78
  79         bool abort, countends, compress;
  80 };
  81
  82 /**************************************************************************************************/
  83 //custom data structure for threads to use.
  84 // This is passed by void pointer so it can be any data type
  85 // that can be passed using a single void pointer (LPVOID).
  86 struct pairwiseData {
  87     string outputFileName;
  88         string align, square, distcalcType, output;
  89         unsigned long long start;
  90         unsigned long long end;
  91         MothurOut* m;
  92         float match, misMatch, gapOpen, gapExtend, cutoff;
  93         int count, threadID, longestBase;
  94     bool countends;
  95     SequenceDB alignDB;
  96
  97         pairwiseData(){}
  98         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) {
  99                 outputFileName = ofn;
 100                 m = mout;
 101                 start = st;
 102                 end = en;
 103                 match = ma;
 104                 misMatch = misMa;
 105                 gapOpen = gapO;
 106                 gapExtend = gapE;
 107                 longestBase = thr;
 108                 align = al;
 109         square = sq;
 110         distcalcType = di;
 111         countends = co;
 112         alignDB = DB;
 113                 count = 0;
 114         output = op;
 115                 threadID = tid;
 116         }
 117 };
 118
 119 /**************************************************************************************************/
 120 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 121 #else
 122 static DWORD WINAPI MyPairwiseSquareThreadFunction(LPVOID lpParam){
 123         pairwiseData* pDataArray;
 124         pDataArray = (pairwiseData*)lpParam;
 125
 126         try {
 127                 ofstream outFile((pDataArray->outputFileName).c_str(), ios::trunc);
 128                 outFile.setf(ios::fixed, ios::showpoint);
 129                 outFile << setprecision(4);
 130
 131                 pDataArray->count = 0;
 132
 133         int startTime = time(NULL);
 134
 135         Alignment* alignment;
 136         if(pDataArray->align == "gotoh")                        {       alignment = new GotohOverlap(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase);                     }
 137                 else if(pDataArray->align == "needleman")       {       alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase);                                }
 138                 else if(pDataArray->align == "blast")           {       alignment = new BlastAlignment(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch);            }
 139                 else if(pDataArray->align == "noalign")         {       alignment = new NoAlign();                                                                                                      }
 140                 else {
 141                         pDataArray->m->mothurOut(pDataArray->align + " is not a valid alignment option. I will run the command using needleman.");
 142                         pDataArray->m->mothurOutEndLine();
 143                         alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase);
 144                 }
 145
 146         ValidCalculators validCalculator;
 147         Dist* distCalculator;
 148         if (pDataArray->countends) {
 149             if (validCalculator.isValidCalculator("distance", pDataArray->distcalcType) == true) {
 150                 if (pDataArray->distcalcType == "nogaps")                       {       distCalculator = new ignoreGaps();      }
 151                 else if (pDataArray->distcalcType == "eachgap") {       distCalculator = new eachGapDist();     }
 152                 else if (pDataArray->distcalcType == "onegap")          {       distCalculator = new oneGapDist();      }
 153             }
 154         }else {
 155             if (validCalculator.isValidCalculator("distance", pDataArray->distcalcType) == true) {
 156                 if (pDataArray->distcalcType == "nogaps")               {       distCalculator = new ignoreGaps();                                      }
 157                 else if (pDataArray->distcalcType == "eachgap"){        distCalculator = new eachGapIgnoreTermGapDist();        }
 158                 else if (pDataArray->distcalcType == "onegap")  {       distCalculator = new oneGapIgnoreTermGapDist();         }
 159             }
 160         }
 161
 162         if(pDataArray->start == 0){     outFile << pDataArray->alignDB.getNumSeqs() << endl;    }
 163
 164                 for(int i=pDataArray->start;i<pDataArray->end;i++){
 165             pDataArray->count++;
 166
 167                         string name = pDataArray->alignDB.get(i).getName();
 168                         //pad with spaces to make compatible
 169                         if (name.length() < 10) { while (name.length() < 10) {  name += " ";  } }
 170
 171                         outFile << name << '\t';
 172
 173                         for(int j=0;j<pDataArray->alignDB.getNumSeqs();j++){
 174
 175                                 if (pDataArray->m->control_pressed) { outFile.close(); delete alignment; delete distCalculator; return 0;  }
 176
 177                                 if (pDataArray->alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 178                                         alignment->resize(pDataArray->alignDB.get(i).getUnaligned().length()+1);
 179                                 }
 180
 181                                 if (pDataArray->alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 182                                         alignment->resize(pDataArray->alignDB.get(j).getUnaligned().length()+1);
 183                                 }
 184
 185                                 Sequence seqI(pDataArray->alignDB.get(i).getName(), pDataArray->alignDB.get(i).getAligned());
 186                                 Sequence seqJ(pDataArray->alignDB.get(j).getName(), pDataArray->alignDB.get(j).getAligned());
 187
 188                                 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
 189                                 seqI.setAligned(alignment->getSeqAAln());
 190                                 seqJ.setAligned(alignment->getSeqBAln());
 191
 192                                 distCalculator->calcDist(seqI, seqJ);
 193                                 double dist = distCalculator->getDist();
 194
 195                                 outFile << dist << '\t';
 196                         }
 197
 198                         outFile << endl;
 199
 200                         if(i % 100 == 0){
 201                                 pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
 202                         }
 203
 204                 }
 205                 pDataArray->m->mothurOut(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
 206
 207                 outFile.close();
 208         delete alignment;
 209         delete distCalculator;
 210
 211
 212     }
 213         catch(exception& e) {
 214                 pDataArray->m->errorOut(e, "PairwiseSeqsCommand", "MyPairwiseSquareThreadFunction");
 215                 exit(1);
 216         }
 217 }
 218
 219 /**************************************************************************************************/
 220 static DWORD WINAPI MyPairwiseThreadFunction(LPVOID lpParam){
 221         pairwiseData* pDataArray;
 222         pDataArray = (pairwiseData*)lpParam;
 223
 224         try {
 225                 ofstream outFile((pDataArray->outputFileName).c_str(), ios::trunc);
 226                 outFile.setf(ios::fixed, ios::showpoint);
 227                 outFile << setprecision(4);
 228
 229         pDataArray->count = pDataArray->end;
 230
 231         int startTime = time(NULL);
 232
 233         Alignment* alignment;
 234         if(pDataArray->align == "gotoh")                        {       alignment = new GotohOverlap(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase);                     }
 235                 else if(pDataArray->align == "needleman")       {       alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase);                                }
 236                 else if(pDataArray->align == "blast")           {       alignment = new BlastAlignment(pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch);            }
 237                 else if(pDataArray->align == "noalign")         {       alignment = new NoAlign();                                                                                                      }
 238                 else {
 239                         pDataArray->m->mothurOut(pDataArray->align + " is not a valid alignment option. I will run the command using needleman.");
 240                         pDataArray->m->mothurOutEndLine();
 241                         alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, pDataArray->longestBase);
 242                 }
 243
 244         ValidCalculators validCalculator;
 245         Dist* distCalculator;
 246         if (pDataArray->countends) {
 247             if (validCalculator.isValidCalculator("distance", pDataArray->distcalcType) == true) {
 248                 if (pDataArray->distcalcType == "nogaps")                       {       distCalculator = new ignoreGaps();      }
 249                 else if (pDataArray->distcalcType == "eachgap") {       distCalculator = new eachGapDist();     }
 250                 else if (pDataArray->distcalcType == "onegap")          {       distCalculator = new oneGapDist();      }
 251             }
 252         }else {
 253             if (validCalculator.isValidCalculator("distance", pDataArray->distcalcType) == true) {
 254                 if (pDataArray->distcalcType == "nogaps")               {       distCalculator = new ignoreGaps();                                      }
 255                 else if (pDataArray->distcalcType == "eachgap"){        distCalculator = new eachGapIgnoreTermGapDist();        }
 256                 else if (pDataArray->distcalcType == "onegap")  {       distCalculator = new oneGapIgnoreTermGapDist();         }
 257             }
 258         }
 259
 260         if((pDataArray->output == "lt") && pDataArray->start == 0){     outFile << pDataArray->alignDB.getNumSeqs() << endl;    }
 261
 262                 for(int i=pDataArray->start;i<pDataArray->end;i++){
 263
 264                         if(pDataArray->output == "lt")  {
 265                                 string name = pDataArray->alignDB.get(i).getName();
 266                                 if (name.length() < 10) { //pad with spaces to make compatible
 267                                         while (name.length() < 10) {  name += " ";  }
 268                                 }
 269                                 outFile << name << '\t';
 270                         }
 271
 272
 273                         for(int j=0;j<i;j++){
 274
 275                                 if (pDataArray->m->control_pressed) { outFile.close(); delete alignment; delete distCalculator; return 0;  }
 276
 277                                 if (pDataArray->alignDB.get(i).getUnaligned().length() > alignment->getnRows()) {
 278                                         alignment->resize(pDataArray->alignDB.get(i).getUnaligned().length()+1);
 279                                 }
 280
 281                                 if (pDataArray->alignDB.get(j).getUnaligned().length() > alignment->getnRows()) {
 282                                         alignment->resize(pDataArray->alignDB.get(j).getUnaligned().length()+1);
 283                                 }
 284
 285                                 Sequence seqI(pDataArray->alignDB.get(i).getName(), pDataArray->alignDB.get(i).getAligned());
 286                                 Sequence seqJ(pDataArray->alignDB.get(j).getName(), pDataArray->alignDB.get(j).getAligned());
 287
 288                                 alignment->align(seqI.getUnaligned(), seqJ.getUnaligned());
 289                                 seqI.setAligned(alignment->getSeqAAln());
 290                                 seqJ.setAligned(alignment->getSeqBAln());
 291
 292                                 distCalculator->calcDist(seqI, seqJ);
 293                                 double dist = distCalculator->getDist();
 294
 295                                 if(dist <= pDataArray->cutoff){
 296                                         if (pDataArray->output == "column") { outFile << pDataArray->alignDB.get(i).getName() << ' ' << pDataArray->alignDB.get(j).getName() << ' ' << dist << endl; }
 297                                 }
 298                                 if (pDataArray->output == "lt") {  outFile << dist << '\t'; }
 299                         }
 300
 301                         if (pDataArray->output == "lt") { outFile << endl; }
 302
 303                         if(i % 100 == 0){
 304                                 pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
 305                         }
 306
 307                 }
 308                 pDataArray->m->mothurOut(toString(pDataArray->end-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
 309
 310                 outFile.close();
 311         delete alignment;
 312         delete distCalculator;
 313
 314
 315     }
 316         catch(exception& e) {
 317                 pDataArray->m->errorOut(e, "PairwiseSeqsCommand", "MyPairwiseThreadFunction");
 318                 exit(1);
 319         }
 320 }
 321
 322 #endif
 323
 324
 325 #endif
 326