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