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 SparseDistanceMatrix();
  58             matrix->resize(nseqs);
  59                 }else{
  60                         overlapFile = m->getRootName(blastfile) + "overlap.dist";
  61                         distFile = m->getRootName(blastfile) + "hclusterDists.dist";
  62
  63                         m->openOutputFile(overlapFile, outOverlap);
  64                         m->openOutputFile(distFile, outDist);
  65                 }
  66
  67                 if (m->control_pressed) {
  68                         fileHandle.close();
  69                         if (!hclusterWanted) {  delete matrix; }
  70                         else { outOverlap.close(); m->mothurRemove(overlapFile); outDist.close(); m->mothurRemove(distFile);  }
  71                         return 0;
  72                 }
  73
  74                 Progress* reading = new Progress("Reading blast:     ", nseqs * nseqs);
  75
  76                 //this is used to quickly find if we already have a distance for this combo
  77                 vector< map<int,float> > dists;  dists.resize(nseqs);  //dists[0][1] = distance from seq0 to seq1
  78                 map<int, float> thisRowsBlastScores;
  79
  80                 if (!fileHandle.eof()) {
  81                         //read in line from file
  82                         fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
  83                         m->gobble(fileHandle);
  84
  85                         currentRow = firstName;
  86                         lengthThisSeq = numBases;
  87                         repeatName = firstName + secondName;
  88
  89                         if (firstName == secondName) {   refScore = score;  }
  90                         else{
  91                                 //convert name to number
  92                                 map<string,int>::iterator itA = nameMap->find(firstName);
  93                                 map<string,int>::iterator itB = nameMap->find(secondName);
  94                                 if(itA == nameMap->end()){  m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1);  }
  95                                 if(itB == nameMap->end()){  m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1);  }
  96
  97                                 thisRowsBlastScores[itB->second] = score;
  98
  99                                 //calc overlap score
 100                                 thisoverlap = 1.0 - (percentId * (lengthThisSeq - startQuery) / endRef / 100.0 - penalty);
 101
 102                                 //if there is a valid overlap, add it
 103                                 if ((startRef <= length) && ((endQuery+length) >= lengthThisSeq) && (thisoverlap < cutoff)) {
 104                                         if (!hclusterWanted) {
 105                                                 seqDist overlapValue(itA->second, itB->second, thisoverlap);
 106                                                 overlap.push_back(overlapValue);
 107                                         }else {
 108                                                 outOverlap << itA->first << '\t' << itB->first << '\t' << thisoverlap << endl;
 109                                         }
 110                                 }
 111                         }
 112                 }else { m->mothurOut("Error in your blast file, cannot read."); m->mothurOutEndLine(); exit(1); }
 113
 114
 115                 //read file
 116                 while(!fileHandle.eof()){
 117
 118                         if (m->control_pressed) {
 119                                 fileHandle.close();
 120                                 if (!hclusterWanted) {  delete matrix; }
 121                                 else { outOverlap.close(); m->mothurRemove(overlapFile); outDist.close(); m->mothurRemove(distFile);  }
 122                                 delete reading;
 123                                 return 0;
 124                         }
 125
 126                         //read in line from file
 127                         fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
 128                         //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;
 129                         m->gobble(fileHandle);
 130
 131                         string temp = firstName + secondName; //to check if this file has repeat lines, ie. is this a blast instead of a blscreen file
 132
 133                         //if this is a new pairing
 134                         if (temp != repeatName) {
 135                                 repeatName = temp;
 136
 137                                 if (currentRow == firstName) {
 138                                         //cout << "first = " << firstName << " second = " << secondName << endl;
 139                                         if (firstName == secondName) {
 140                                                 refScore = score;
 141                                                 reading->update((count + nseqs));
 142                                                 count++;
 143                                         }else{
 144                                                 //convert name to number
 145                                                 map<string,int>::iterator itA = nameMap->find(firstName);
 146                                                 map<string,int>::iterator itB = nameMap->find(secondName);
 147                                                 if(itA == nameMap->end()){  m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1);  }
 148                                                 if(itB == nameMap->end()){  m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1);  }
 149
 150                                                 //save score
 151                                                 thisRowsBlastScores[itB->second] = score;
 152
 153                                                 //calc overlap score
 154                                                 thisoverlap = 1.0 - (percentId * (lengthThisSeq - startQuery) / endRef / 100.0 - penalty);
 155
 156                                                 //if there is a valid overlap, add it
 157                                                 if ((startRef <= length) && ((endQuery+length) >= lengthThisSeq) && (thisoverlap < cutoff)) {
 158                                                         if (!hclusterWanted) {
 159                                                                 seqDist overlapValue(itA->second, itB->second, thisoverlap);
 160                                                                 //cout << "overlap = " << itA->second << '\t' << itB->second << '\t' << thisoverlap << endl;
 161                                                                 overlap.push_back(overlapValue);
 162                                                         }else {
 163                                                                 outOverlap << itA->first << '\t' << itB->first << '\t' << thisoverlap << endl;
 164                                                         }
 165                                                 }
 166                                         } //end else
 167                                 }else { //end row
 168                                         //convert blast scores to distance and add cell to sparse matrix if we can
 169                                         map<int, float>::iterator it;
 170                                         map<int, float>::iterator itDist;
 171                                         for(it=thisRowsBlastScores.begin(); it!=thisRowsBlastScores.end(); it++) {
 172                                                 distance = 1.0 - (it->second / refScore);
 173
 174
 175                                                 //do we already have the distance calculated for b->a
 176                                                 map<string,int>::iterator itA = nameMap->find(currentRow);
 177                                                 itDist = dists[it->first].find(itA->second);
 178
 179                                                 //if we have it then compare
 180                                                 if (itDist != dists[it->first].end()) {
 181
 182                                                         //if you want the minimum blast score ratio, then pick max distance
 183                                                         if(minWanted) {  distance = max(itDist->second, distance);  }
 184                                                         else{   distance = min(itDist->second, distance);  }
 185
 186                                                         //is this distance below cutoff
 187                                                         if (distance < cutoff) {
 188                                                                 if (!hclusterWanted) {
 189                                     if (itA->second < it->first) {
 190                                         PDistCell value(it->first, distance);
 191                                         matrix->addCell(itA->second, value);
 192                                     }else {
 193                                         PDistCell value(itA->second, distance);
 194                                         matrix->addCell(it->first, value);
 195                                     }
 196                                 }else{
 197                                                                         outDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
 198                                                                 }
 199                                                         }
 200                                                         //not going to need this again
 201                                                         dists[it->first].erase(itDist);
 202                                                 }else { //save this value until we get the other ratio
 203                                                         dists[itA->second][it->first] = distance;
 204                                                 }
 205                                         }
 206                                         //clear out last rows info
 207                                         thisRowsBlastScores.clear();
 208
 209                                         currentRow = firstName;
 210                                         lengthThisSeq = numBases;
 211
 212                                         //add this row to thisRowsBlastScores
 213                                         if (firstName == secondName) {   refScore = score;  }
 214                                         else{ //add this row to thisRowsBlastScores
 215
 216                                                 //convert name to number
 217                                                 map<string,int>::iterator itA = nameMap->find(firstName);
 218                                                 map<string,int>::iterator itB = nameMap->find(secondName);
 219                                                 if(itA == nameMap->end()){  m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1);  }
 220                                                 if(itB == nameMap->end()){  m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1);  }
 221
 222                                                 thisRowsBlastScores[itB->second] = score;
 223
 224                                                 //calc overlap score
 225                                                 thisoverlap = 1.0 - (percentId * (lengthThisSeq - startQuery) / endRef / 100.0 - penalty);
 226
 227                                                 //if there is a valid overlap, add it
 228                                                 if ((startRef <= length) && ((endQuery+length) >= lengthThisSeq) && (thisoverlap < cutoff)) {
 229                                                         if (!hclusterWanted) {
 230                                                                 seqDist overlapValue(itA->second, itB->second, thisoverlap);
 231                                                                 overlap.push_back(overlapValue);
 232                                                         }else {
 233                                                                 outOverlap << itA->first << '\t' << itB->first << '\t' << thisoverlap << endl;
 234                                                         }
 235                                                 }
 236                                         }
 237                                 }//end if current row
 238                         }//end if repeat
 239                 }//end while
 240
 241                 //get last rows info stored
 242                 //convert blast scores to distance and add cell to sparse matrix if we can
 243                 map<int, float>::iterator it;
 244                 map<int, float>::iterator itDist;
 245                 for(it=thisRowsBlastScores.begin(); it!=thisRowsBlastScores.end(); it++) {
 246                         distance = 1.0 - (it->second / refScore);
 247
 248                         //do we already have the distance calculated for b->a
 249                         map<string,int>::iterator itA = nameMap->find(currentRow);
 250                         itDist = dists[it->first].find(itA->second);
 251
 252                         //if we have it then compare
 253                         if (itDist != dists[it->first].end()) {
 254                                 //if you want the minimum blast score ratio, then pick max distance
 255                                 if(minWanted) {  distance = max(itDist->second, distance);  }
 256                                 else{   distance = min(itDist->second, distance);  }
 257
 258                                 //is this distance below cutoff
 259                                 if (distance < cutoff) {
 260                                         if (!hclusterWanted) {
 261                                                 if (itA->second < it->first) {
 262                             PDistCell value(it->first, distance);
 263                             matrix->addCell(itA->second, value);
 264                         }else {
 265                             PDistCell value(itA->second, distance);
 266                             matrix->addCell(it->first, value);
 267                         }
 268                                         }else{
 269                                                 outDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
 270                                         }
 271                                 }
 272                                 //not going to need this again
 273                                 dists[it->first].erase(itDist);
 274                         }else { //save this value until we get the other ratio
 275                                 dists[itA->second][it->first] = distance;
 276                         }
 277                 }
 278                 //clear out info
 279                 thisRowsBlastScores.clear();
 280                 dists.clear();
 281
 282                 if (m->control_pressed) {
 283                                 fileHandle.close();
 284                                 if (!hclusterWanted) {  delete matrix; }
 285                                 else { outOverlap.close(); m->mothurRemove(overlapFile); outDist.close(); m->mothurRemove(distFile);  }
 286                                 delete reading;
 287                                 return 0;
 288                 }
 289
 290                 if (!hclusterWanted) {
 291                         sort(overlap.begin(), overlap.end(), compareOverlap);
 292                 }else {
 293                         outDist.close();
 294                         outOverlap.close();
 295                 }
 296
 297                 if (m->control_pressed) {
 298                                 fileHandle.close();
 299                                 if (!hclusterWanted) {  delete matrix; }
 300                                 else {  m->mothurRemove(overlapFile);  m->mothurRemove(distFile);  }
 301                                 delete reading;
 302                                 return 0;
 303                 }
 304
 305                 reading->finish();
 306                 delete reading;
 307                 fileHandle.close();
 308
 309                 return 0;
 310         }
 311         catch(exception& e) {
 312                 m->errorOut(e, "ReadBlast", "read");
 313                 exit(1);
 314         }
 315 }
 316 /*********************************************************************************************/
 317 int ReadBlast::readNames(NameAssignment* nameMap) {
 318         try {
 319                 m->mothurOut("Reading names... "); cout.flush();
 320
 321                 string name, hold, prevName;
 322                 int num = 1;
 323
 324                 ifstream in;
 325                 m->openInputFile(blastfile, in);
 326
 327                 //ofstream outName;
 328                 //m->openOutputFile((blastfile + ".tempOutNames"), outName);
 329
 330                 //read first line
 331                 in >> prevName;
 332
 333                 for (int i = 0; i < 11; i++) {  in >> hold;  }
 334                 m->gobble(in);
 335
 336                 //save name in nameMap
 337                 nameMap->push_back(prevName);
 338
 339                 while (!in.eof()) {
 340                         if (m->control_pressed) { in.close(); return 0; }
 341
 342                         //read line
 343                         in >> name;
 344
 345                         for (int i = 0; i < 11; i++) {  in >> hold;  }
 346                         m->gobble(in);
 347
 348                         //is this a new name?
 349                         if (name != prevName) {
 350                                 prevName = name;
 351
 352                 if (nameMap->get(name) != -1) { m->mothurOut("[ERROR]: trying to exact names from blast file, and I found dups.  Are you sequence names unique? quitting.\n"); m->control_pressed = true; }
 353                 else {
 354                     nameMap->push_back(name);
 355                 }
 356                 //outName << name << '\t' << name << endl;
 357                                 num++;
 358                         }
 359                 }
 360
 361                 in.close();
 362
 363                 //write out names file
 364                 //string outNames = m->getRootName(blastfile) + "names";
 365                 //ofstream out;
 366                 //m->openOutputFile(outNames, out);
 367                 //nameMap->print(out);
 368                 //out.close();
 369
 370                 if (m->control_pressed) { return 0; }
 371
 372                 m->mothurOut(toString(num) + " names read."); m->mothurOutEndLine();
 373
 374                 return 0;
 375
 376         }
 377         catch(exception& e) {
 378                 m->errorOut(e, "ReadBlast", "readNames");
 379                 exit(1);
 380         }
 381 }
 382 /*********************************************************************************************/
 383
 384
 385