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 void 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                 ifstream fileHandle;
  41                 openInputFile(blastfile, fileHandle);
  42
  43                 string firstName, secondName, eScore, currentRow;
  44                 string repeatName = "";
  45                 int count = 1;
  46                 float distance, thisoverlap, refScore;
  47                 float percentId;
  48                 float numBases, mismatch, gap, startQuery, endQuery, startRef, endRef, score, lengthThisSeq;
  49
  50                 ofstream outDist;
  51                 ofstream outOverlap;
  52
  53                 //create objects needed for read
  54                 if (!hclusterWanted) {
  55                         matrix = new SparseMatrix();
  56                 }else{
  57                         overlapFile = getRootName(blastfile) + "overlap.dist";
  58                         distFile = getRootName(blastfile) + "hclusterDists.dist";
  59
  60                         openOutputFile(overlapFile, outOverlap);
  61                         openOutputFile(distFile, outDist);
  62                 }
  63
  64                 Progress* reading = new Progress("Reading blast:     ", nseqs * nseqs);
  65
  66                 //this is used to quickly find if we already have a distance for this combo
  67                 vector< map<int,float> > dists;  dists.resize(nseqs);  //dists[0][1] = distance from seq0 to seq1
  68                 map<int, float> thisRowsBlastScores;
  69
  70                 if (!fileHandle.eof()) {
  71                         //read in line from file
  72                         fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
  73                         gobble(fileHandle);
  74
  75                         currentRow = firstName;
  76                         lengthThisSeq = numBases;
  77                         repeatName = firstName + secondName;
  78
  79                         if (firstName == secondName) {   refScore = score;  }
  80                         else{
  81                                 //convert name to number
  82                                 map<string,int>::iterator itA = nameMap->find(firstName);
  83                                 map<string,int>::iterator itB = nameMap->find(secondName);
  84                                 if(itA == nameMap->end()){   cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n";  exit(1);  }
  85                                 if(itB == nameMap->end()){   cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);  }
  86
  87                                 thisRowsBlastScores[itB->second] = score;
  88
  89                                 //calc overlap score
  90                                 thisoverlap = 1.0 - (percentId * (lengthThisSeq - startQuery) / endRef / 100.0 - penalty);
  91
  92                                 //if there is a valid overlap, add it
  93                                 if ((startRef <= length) && ((endQuery+length) >= lengthThisSeq) && (thisoverlap < cutoff)) {
  94                                         if (!hclusterWanted) {
  95                                                 seqDist overlapValue(itA->second, itB->second, thisoverlap);
  96                                                 overlap.push_back(overlapValue);
  97                                         }else {
  98                                                 outOverlap << itA->first << '\t' << itB->first << '\t' << thisoverlap << endl;
  99                                         }
 100                                 }
 101                         }
 102                 }else { m->mothurOut("Error in your blast file, cannot read."); m->mothurOutEndLine(); exit(1); }
 103
 104
 105                 //read file
 106                 while(!fileHandle.eof()){
 107
 108                         //read in line from file
 109                         fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
 110                         //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;
 111                         gobble(fileHandle);
 112
 113                         string temp = firstName + secondName; //to check if this file has repeat lines, ie. is this a blast instead of a blscreen file
 114
 115                         //if this is a new pairing
 116                         if (temp != repeatName) {
 117                                 repeatName = temp;
 118
 119                                 if (currentRow == firstName) {
 120                                         //cout << "first = " << firstName << " second = " << secondName << endl;
 121                                         if (firstName == secondName) {
 122                                                 refScore = score;
 123                                                 reading->update((count + nseqs));
 124                                                 count++;
 125                                         }else{
 126                                                 //convert name to number
 127                                                 map<string,int>::iterator itA = nameMap->find(firstName);
 128                                                 map<string,int>::iterator itB = nameMap->find(secondName);
 129                                                 if(itA == nameMap->end()){   cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n";  exit(1);  }
 130                                                 if(itB == nameMap->end()){   cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);  }
 131
 132                                                 //save score
 133                                                 thisRowsBlastScores[itB->second] = score;
 134
 135                                                 //calc overlap score
 136                                                 thisoverlap = 1.0 - (percentId * (lengthThisSeq - startQuery) / endRef / 100.0 - penalty);
 137
 138                                                 //if there is a valid overlap, add it
 139                                                 if ((startRef <= length) && ((endQuery+length) >= lengthThisSeq) && (thisoverlap < cutoff)) {
 140                                                         if (!hclusterWanted) {
 141                                                                 seqDist overlapValue(itA->second, itB->second, thisoverlap);
 142                                                                 //cout << "overlap = " << itA->second << '\t' << itB->second << '\t' << thisoverlap << endl;
 143                                                                 overlap.push_back(overlapValue);
 144                                                         }else {
 145                                                                 outOverlap << itA->first << '\t' << itB->first << '\t' << thisoverlap << endl;
 146                                                         }
 147                                                 }
 148                                         } //end else
 149                                 }else { //end row
 150                                         //convert blast scores to distance and add cell to sparse matrix if we can
 151                                         map<int, float>::iterator it;
 152                                         map<int, float>::iterator itDist;
 153                                         for(it=thisRowsBlastScores.begin(); it!=thisRowsBlastScores.end(); it++) {
 154                                                 distance = 1.0 - (it->second / refScore);
 155
 156                                                 //do we already have the distance calculated for b->a
 157                                                 map<string,int>::iterator itA = nameMap->find(currentRow);
 158                                                 itDist = dists[it->first].find(itA->second);
 159
 160                                                 //if we have it then compare
 161                                                 if (itDist != dists[it->first].end()) {
 162                                                         //if you want the minimum blast score ratio, then pick max distance
 163                                                         if(minWanted) {  distance = max(itDist->second, distance);  }
 164                                                         else{   distance = min(itDist->second, distance);  }
 165
 166                                                         //is this distance below cutoff
 167                                                         if (distance < cutoff) {
 168                                                                 if (!hclusterWanted) {
 169                                                                         PCell value(itA->second, it->first, distance);
 170                                                                         matrix->addCell(value);
 171                                                                 }else{
 172                                                                         outDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
 173                                                                 }
 174                                                         }
 175                                                         //not going to need this again
 176                                                         dists[it->first].erase(itDist);
 177                                                 }else { //save this value until we get the other ratio
 178                                                         dists[itA->second][it->first] = distance;
 179                                                 }
 180                                         }
 181                                         //clear out last rows info
 182                                         thisRowsBlastScores.clear();
 183
 184                                         currentRow = firstName;
 185                                         lengthThisSeq = numBases;
 186
 187                                         //add this row to thisRowsBlastScores
 188                                         if (firstName == secondName) {   refScore = score;  }
 189                                         else{ //add this row to thisRowsBlastScores
 190
 191                                                 //convert name to number
 192                                                 map<string,int>::iterator itA = nameMap->find(firstName);
 193                                                 map<string,int>::iterator itB = nameMap->find(secondName);
 194                                                 if(itA == nameMap->end()){   cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n";  exit(1);  }
 195                                                 if(itB == nameMap->end()){   cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);  }
 196
 197                                                 thisRowsBlastScores[itB->second] = score;
 198
 199                                                 //calc overlap score
 200                                                 thisoverlap = 1.0 - (percentId * (lengthThisSeq - startQuery) / endRef / 100.0 - penalty);
 201
 202                                                 //if there is a valid overlap, add it
 203                                                 if ((startRef <= length) && ((endQuery+length) >= lengthThisSeq) && (thisoverlap < cutoff)) {
 204                                                         if (!hclusterWanted) {
 205                                                                 seqDist overlapValue(itA->second, itB->second, thisoverlap);
 206                                                                 overlap.push_back(overlapValue);
 207                                                         }else {
 208                                                                 outOverlap << itA->first << '\t' << itB->first << '\t' << thisoverlap << endl;
 209                                                         }
 210                                                 }
 211                                         }
 212                                 }//end if current row
 213                         }//end if repeat
 214                 }//end while
 215
 216                 //get last rows info stored
 217                 //convert blast scores to distance and add cell to sparse matrix if we can
 218                 map<int, float>::iterator it;
 219                 map<int, float>::iterator itDist;
 220                 for(it=thisRowsBlastScores.begin(); it!=thisRowsBlastScores.end(); it++) {
 221                         distance = 1.0 - (it->second / refScore);
 222
 223                         //do we already have the distance calculated for b->a
 224                         map<string,int>::iterator itA = nameMap->find(currentRow);
 225                         itDist = dists[it->first].find(itA->second);
 226
 227                         //if we have it then compare
 228                         if (itDist != dists[it->first].end()) {
 229                                 //if you want the minimum blast score ratio, then pick max distance
 230                                 if(minWanted) {  distance = max(itDist->second, distance);  }
 231                                 else{   distance = min(itDist->second, distance);  }
 232
 233                                 //is this distance below cutoff
 234                                 if (distance < cutoff) {
 235                                         if (!hclusterWanted) {
 236                                                 PCell value(itA->second, it->first, distance);
 237                                                 matrix->addCell(value);
 238                                         }else{
 239                                                 outDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
 240                                         }
 241                                 }
 242                                 //not going to need this again
 243                                 dists[it->first].erase(itDist);
 244                         }else { //save this value until we get the other ratio
 245                                 dists[itA->second][it->first] = distance;
 246                         }
 247                 }
 248                 //clear out info
 249                 thisRowsBlastScores.clear();
 250                 dists.clear();
 251
 252                 if (!hclusterWanted) {
 253                         sort(overlap.begin(), overlap.end(), compareOverlap);
 254                 }else {
 255                         outDist.close();
 256                         outOverlap.close();
 257                 }
 258
 259                 reading->finish();
 260                 delete reading;
 261                 fileHandle.close();
 262         }
 263         catch(exception& e) {
 264                 m->errorOut(e, "ReadBlast", "read");
 265                 exit(1);
 266         }
 267 }
 268 /*********************************************************************************************/
 269 void ReadBlast::readNames(NameAssignment* nameMap) {
 270         try {
 271                 m->mothurOut("Reading names... "); cout.flush();
 272
 273                 string name, hold, prevName;
 274                 int num = 1;
 275
 276                 ifstream in;
 277                 openInputFile(blastfile, in);
 278
 279                 //read first line
 280                 in >> prevName;
 281                 for (int i = 0; i < 11; i++) {  in >> hold;  }
 282                 gobble(in);
 283
 284                 //save name in nameMap
 285                 nameMap->push_back(prevName);
 286
 287                 while (!in.eof()) {
 288
 289                         //read line
 290                         in >> name;
 291                         for (int i = 0; i < 11; i++) {  in >> hold;  }
 292                         gobble(in);
 293
 294                         //is this a new name?
 295                         if (name != prevName) {
 296                                 prevName = name;
 297                                 nameMap->push_back(name);
 298                                 num++;
 299                         }
 300                 }
 301
 302                 in.close();
 303
 304                 //write out names file
 305                 //string outNames = getRootName(blastfile) + "names";
 306                 //ofstream out;
 307                 //openOutputFile(outNames, out);
 308                 //nameMap->print(out);
 309                 //out.close();
 310
 311                 m->mothurOut(toString(num) + " names read."); m->mothurOutEndLine();
 312
 313         }
 314         catch(exception& e) {
 315                 m->errorOut(e, "ReadBlast", "readNames");
 316                 exit(1);
 317         }
 318 }
 319 /*********************************************************************************************/
 320
 321
 322