readblast.cpp

   1 /*
   2  *  readblast.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 12/10/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "readblast.h"
  11 #include "progress.hpp"
  12
  13 //********************************************************************************************************************
  14 //sorts lowest to highest
  15 inline bool compareOverlap(seqDist left, seqDist right){
  16         return (left.dist < right.dist);
  17 }
  18 /*********************************************************************************************/
  19 ReadBlast::ReadBlast(string file, float c, float p, int l, bool ms, bool h) : blastfile(file), cutoff(c), penalty(p), length(l), minWanted(ms), hclusterWanted(h) {
  20         try {
  21                 m = MothurOut::getInstance();
  22                 matrix = NULL;
  23         }
  24         catch(exception& e) {
  25                 m->errorOut(e, "ReadBlast", "ReadBlast");
  26                 exit(1);
  27         }
  28 }
  29 /*********************************************************************************************/
  30 //assumptions about the blast file:
  31 //1. if duplicate lines occur the first line is always best and is chosen
  32 //2. blast scores are grouped together, ie. a a .... score, a b .... score, a c ....score...
  33 int ReadBlast::read(NameAssignment* nameMap) {
  34         try {
  35
  36                 //if the user has not given a names file read names from blastfile
  37                 if (nameMap->size() == 0) { readNames(nameMap);  }
  38                 int nseqs = nameMap->size();
  39
  40                 if (m->control_pressed) { return 0; }
  41
  42                 ifstream fileHandle;
  43                 m->openInputFile(blastfile, fileHandle);
  44
  45                 string firstName, secondName, eScore, currentRow;
  46                 string repeatName = "";
  47                 int count = 1;
  48                 float distance, thisoverlap, refScore;
  49                 float percentId;
  50                 float numBases, mismatch, gap, startQuery, endQuery, startRef, endRef, score, lengthThisSeq;
  51
  52                 ofstream outDist;
  53                 ofstream outOverlap;
  54
  55                 //create objects needed for read
  56                 if (!hclusterWanted) {
  57                         matrix = new SparseMatrix();
  58                 }else{
  59                         overlapFile = m->getRootName(blastfile) + "overlap.dist";
  60                         distFile = m->getRootName(blastfile) + "hclusterDists.dist";
  61
  62                         m->openOutputFile(overlapFile, outOverlap);
  63                         m->openOutputFile(distFile, outDist);
  64                 }
  65
  66                 if (m->control_pressed) {
  67                         fileHandle.close();
  68                         if (!hclusterWanted) {  delete matrix; }
  69                         else { outOverlap.close(); remove(overlapFile.c_str()); outDist.close(); remove(distFile.c_str());  }
  70                         return 0;
  71                 }
  72
  73                 Progress* reading = new Progress("Reading blast:     ", nseqs * nseqs);
  74
  75                 //this is used to quickly find if we already have a distance for this combo
  76                 vector< map<int,float> > dists;  dists.resize(nseqs);  //dists[0][1] = distance from seq0 to seq1
  77                 map<int, float> thisRowsBlastScores;
  78
  79                 if (!fileHandle.eof()) {
  80                         //read in line from file
  81                         fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
  82                         m->gobble(fileHandle);
  83
  84                         currentRow = firstName;
  85                         lengthThisSeq = numBases;
  86                         repeatName = firstName + secondName;
  87
  88                         if (firstName == secondName) {   refScore = score;  }
  89                         else{
  90                                 //convert name to number
  91                                 map<string,int>::iterator itA = nameMap->find(firstName);
  92                                 map<string,int>::iterator itB = nameMap->find(secondName);
  93                                 if(itA == nameMap->end()){   cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n";  exit(1);  }
  94                                 if(itB == nameMap->end()){   cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);  }
  95
  96                                 thisRowsBlastScores[itB->second] = score;
  97
  98                                 //calc overlap score
  99                                 thisoverlap = 1.0 - (percentId * (lengthThisSeq - startQuery) / endRef / 100.0 - penalty);
 100
 101                                 //if there is a valid overlap, add it
 102                                 if ((startRef <= length) && ((endQuery+length) >= lengthThisSeq) && (thisoverlap < cutoff)) {
 103                                         if (!hclusterWanted) {
 104                                                 seqDist overlapValue(itA->second, itB->second, thisoverlap);
 105                                                 overlap.push_back(overlapValue);
 106                                         }else {
 107                                                 outOverlap << itA->first << '\t' << itB->first << '\t' << thisoverlap << endl;
 108                                         }
 109                                 }
 110                         }
 111                 }else { m->mothurOut("Error in your blast file, cannot read."); m->mothurOutEndLine(); exit(1); }
 112
 113
 114                 //read file
 115                 while(!fileHandle.eof()){
 116
 117                         if (m->control_pressed) {
 118                                 fileHandle.close();
 119                                 if (!hclusterWanted) {  delete matrix; }
 120                                 else { outOverlap.close(); remove(overlapFile.c_str()); outDist.close(); remove(distFile.c_str());  }
 121                                 delete reading;
 122                                 return 0;
 123                         }
 124
 125                         //read in line from file
 126                         fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
 127                         //cout << firstName << '\t' << secondName << '\t' << percentId << '\t' << numBases << '\t' << mismatch << '\t' << gap << '\t' << startQuery << '\t' << endQuery << '\t' << startRef << '\t' << endRef << '\t' << eScore << '\t' << score << endl;
 128                         m->gobble(fileHandle);
 129
 130                         string temp = firstName + secondName; //to check if this file has repeat lines, ie. is this a blast instead of a blscreen file
 131
 132                         //if this is a new pairing
 133                         if (temp != repeatName) {
 134                                 repeatName = temp;
 135
 136                                 if (currentRow == firstName) {
 137                                         //cout << "first = " << firstName << " second = " << secondName << endl;
 138                                         if (firstName == secondName) {
 139                                                 refScore = score;
 140                                                 reading->update((count + nseqs));
 141                                                 count++;
 142                                         }else{
 143                                                 //convert name to number
 144                                                 map<string,int>::iterator itA = nameMap->find(firstName);
 145                                                 map<string,int>::iterator itB = nameMap->find(secondName);
 146                                                 if(itA == nameMap->end()){   cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n";  exit(1);  }
 147                                                 if(itB == nameMap->end()){   cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);  }
 148
 149                                                 //save score
 150                                                 thisRowsBlastScores[itB->second] = score;
 151
 152                                                 //calc overlap score
 153                                                 thisoverlap = 1.0 - (percentId * (lengthThisSeq - startQuery) / endRef / 100.0 - penalty);
 154
 155                                                 //if there is a valid overlap, add it
 156                                                 if ((startRef <= length) && ((endQuery+length) >= lengthThisSeq) && (thisoverlap < cutoff)) {
 157                                                         if (!hclusterWanted) {
 158                                                                 seqDist overlapValue(itA->second, itB->second, thisoverlap);
 159                                                                 //cout << "overlap = " << itA->second << '\t' << itB->second << '\t' << thisoverlap << endl;
 160                                                                 overlap.push_back(overlapValue);
 161                                                         }else {
 162                                                                 outOverlap << itA->first << '\t' << itB->first << '\t' << thisoverlap << endl;
 163                                                         }
 164                                                 }
 165                                         } //end else
 166                                 }else { //end row
 167                                         //convert blast scores to distance and add cell to sparse matrix if we can
 168                                         map<int, float>::iterator it;
 169                                         map<int, float>::iterator itDist;
 170                                         for(it=thisRowsBlastScores.begin(); it!=thisRowsBlastScores.end(); it++) {
 171                                                 distance = 1.0 - (it->second / refScore);
 172
 173
 174                                                 //do we already have the distance calculated for b->a
 175                                                 map<string,int>::iterator itA = nameMap->find(currentRow);
 176                                                 itDist = dists[it->first].find(itA->second);
 177
 178                                                 //if we have it then compare
 179                                                 if (itDist != dists[it->first].end()) {
 180
 181                                                         //if you want the minimum blast score ratio, then pick max distance
 182                                                         if(minWanted) {  distance = max(itDist->second, distance);  }
 183                                                         else{   distance = min(itDist->second, distance);  }
 184
 185                                                         //is this distance below cutoff
 186                                                         if (distance < cutoff) {
 187                                                                 if (!hclusterWanted) {
 188                                                                         PCell value(itA->second, it->first, distance);
 189                                                                         matrix->addCell(value);
 190                                                                 }else{
 191                                                                         outDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
 192                                                                 }
 193                                                         }
 194                                                         //not going to need this again
 195                                                         dists[it->first].erase(itDist);
 196                                                 }else { //save this value until we get the other ratio
 197                                                         dists[itA->second][it->first] = distance;
 198                                                 }
 199                                         }
 200                                         //clear out last rows info
 201                                         thisRowsBlastScores.clear();
 202
 203                                         currentRow = firstName;
 204                                         lengthThisSeq = numBases;
 205
 206                                         //add this row to thisRowsBlastScores
 207                                         if (firstName == secondName) {   refScore = score;  }
 208                                         else{ //add this row to thisRowsBlastScores
 209
 210                                                 //convert name to number
 211                                                 map<string,int>::iterator itA = nameMap->find(firstName);
 212                                                 map<string,int>::iterator itB = nameMap->find(secondName);
 213                                                 if(itA == nameMap->end()){   cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n";  exit(1);  }
 214                                                 if(itB == nameMap->end()){   cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);  }
 215
 216                                                 thisRowsBlastScores[itB->second] = score;
 217
 218                                                 //calc overlap score
 219                                                 thisoverlap = 1.0 - (percentId * (lengthThisSeq - startQuery) / endRef / 100.0 - penalty);
 220
 221                                                 //if there is a valid overlap, add it
 222                                                 if ((startRef <= length) && ((endQuery+length) >= lengthThisSeq) && (thisoverlap < cutoff)) {
 223                                                         if (!hclusterWanted) {
 224                                                                 seqDist overlapValue(itA->second, itB->second, thisoverlap);
 225                                                                 overlap.push_back(overlapValue);
 226                                                         }else {
 227                                                                 outOverlap << itA->first << '\t' << itB->first << '\t' << thisoverlap << endl;
 228                                                         }
 229                                                 }
 230                                         }
 231                                 }//end if current row
 232                         }//end if repeat
 233                 }//end while
 234
 235                 //get last rows info stored
 236                 //convert blast scores to distance and add cell to sparse matrix if we can
 237                 map<int, float>::iterator it;
 238                 map<int, float>::iterator itDist;
 239                 for(it=thisRowsBlastScores.begin(); it!=thisRowsBlastScores.end(); it++) {
 240                         distance = 1.0 - (it->second / refScore);
 241
 242                         //do we already have the distance calculated for b->a
 243                         map<string,int>::iterator itA = nameMap->find(currentRow);
 244                         itDist = dists[it->first].find(itA->second);
 245
 246                         //if we have it then compare
 247                         if (itDist != dists[it->first].end()) {
 248                                 //if you want the minimum blast score ratio, then pick max distance
 249                                 if(minWanted) {  distance = max(itDist->second, distance);  }
 250                                 else{   distance = min(itDist->second, distance);  }
 251
 252                                 //is this distance below cutoff
 253                                 if (distance < cutoff) {
 254                                         if (!hclusterWanted) {
 255                                                 PCell value(itA->second, it->first, distance);
 256                                                 matrix->addCell(value);
 257                                         }else{
 258                                                 outDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
 259                                         }
 260                                 }
 261                                 //not going to need this again
 262                                 dists[it->first].erase(itDist);
 263                         }else { //save this value until we get the other ratio
 264                                 dists[itA->second][it->first] = distance;
 265                         }
 266                 }
 267                 //clear out info
 268                 thisRowsBlastScores.clear();
 269                 dists.clear();
 270
 271                 if (m->control_pressed) {
 272                                 fileHandle.close();
 273                                 if (!hclusterWanted) {  delete matrix; }
 274                                 else { outOverlap.close(); remove(overlapFile.c_str()); outDist.close(); remove(distFile.c_str());  }
 275                                 delete reading;
 276                                 return 0;
 277                 }
 278
 279                 if (!hclusterWanted) {
 280                         sort(overlap.begin(), overlap.end(), compareOverlap);
 281                 }else {
 282                         outDist.close();
 283                         outOverlap.close();
 284                 }
 285
 286                 if (m->control_pressed) {
 287                                 fileHandle.close();
 288                                 if (!hclusterWanted) {  delete matrix; }
 289                                 else {  remove(overlapFile.c_str());  remove(distFile.c_str());  }
 290                                 delete reading;
 291                                 return 0;
 292                 }
 293
 294                 reading->finish();
 295                 delete reading;
 296                 fileHandle.close();
 297
 298                 return 0;
 299         }
 300         catch(exception& e) {
 301                 m->errorOut(e, "ReadBlast", "read");
 302                 exit(1);
 303         }
 304 }
 305 /*********************************************************************************************/
 306 int ReadBlast::readNames(NameAssignment* nameMap) {
 307         try {
 308                 m->mothurOut("Reading names... "); cout.flush();
 309
 310                 string name, hold, prevName;
 311                 int num = 1;
 312
 313                 ifstream in;
 314                 m->openInputFile(blastfile, in);
 315
 316                 //ofstream outName;
 317                 //m->openOutputFile((blastfile + ".tempOutNames"), outName);
 318
 319                 //read first line
 320                 in >> prevName;
 321
 322                 for (int i = 0; i < 11; i++) {  in >> hold;  }
 323                 m->gobble(in);
 324
 325                 //save name in nameMap
 326                 nameMap->push_back(prevName);
 327
 328                 while (!in.eof()) {
 329                         if (m->control_pressed) { in.close(); return 0; }
 330
 331                         //read line
 332                         in >> name;
 333
 334                         for (int i = 0; i < 11; i++) {  in >> hold;  }
 335                         m->gobble(in);
 336
 337                         //is this a new name?
 338                         if (name != prevName) {
 339                                 prevName = name;
 340                                 nameMap->push_back(name);
 341                                 num++;
 342                         }
 343                 }
 344
 345                 in.close();
 346
 347                 //write out names file
 348                 //string outNames = m->getRootName(blastfile) + "names";
 349                 //ofstream out;
 350                 //m->openOutputFile(outNames, out);
 351                 //nameMap->print(out);
 352                 //out.close();
 353
 354                 if (m->control_pressed) { return 0; }
 355
 356                 m->mothurOut(toString(num) + " names read."); m->mothurOutEndLine();
 357
 358                 return 0;
 359
 360         }
 361         catch(exception& e) {
 362                 m->errorOut(e, "ReadBlast", "readNames");
 363                 exit(1);
 364         }
 365 }
 366 /*********************************************************************************************/
 367
 368
 369