blastdb.cpp

   1 /*
   2  *  blastdb.cpp
   3  *
   4  *
   5  *  Created by Pat Schloss on 12/22/08.
   6  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10
  11 #include "database.hpp"
  12 #include "sequence.hpp"
  13 #include "blastdb.hpp"
  14
  15 /**************************************************************************************************/
  16
  17 BlastDB::BlastDB(string tag, float gO, float gE, float m, float mM) : Database(),
  18 gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
  19
  20         count = 0;
  21
  22         int randNumber = rand();
  23         dbFileName = tag + toString(randNumber) + ".template.unaligned.fasta";
  24         queryFileName = tag + toString(randNumber) + ".candidate.unaligned.fasta";
  25         blastFileName = tag + toString(randNumber) + ".blast";
  26
  27 }
  28 /**************************************************************************************************/
  29
  30 BlastDB::BlastDB() : Database() {
  31         try {
  32                 count = 0;
  33
  34                 int randNumber = rand();
  35                 dbFileName = toString(randNumber) + ".template.unaligned.fasta";
  36                 queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
  37                 blastFileName = toString(randNumber) + ".blast";
  38         }
  39         catch(exception& e) {
  40                 m->errorOut(e, "BlastDB", "BlastDB");
  41                 exit(1);
  42         }
  43 }
  44
  45 /**************************************************************************************************/
  46
  47 BlastDB::~BlastDB(){
  48         try{
  49                 remove(queryFileName.c_str());                          //      let's clean stuff up and remove the temp files
  50                 remove(dbFileName.c_str());                                     //      let's clean stuff up and remove the temp files
  51                 remove((dbFileName+".nsq").c_str());                                    //      let's clean stuff up and remove the temp files
  52                 remove((dbFileName+".nsi").c_str());                                    //      let's clean stuff up and remove the temp files
  53                 remove((dbFileName+".nsd").c_str());                                    //      let's clean stuff up and remove the temp files
  54                 remove((dbFileName+".nin").c_str());                                    //      let's clean stuff up and remove the temp files
  55                 remove((dbFileName+".nhr").c_str());                                    //      let's clean stuff up and remove the temp files
  56                 remove(blastFileName.c_str());                          //      let's clean stuff up and remove the temp files
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "BlastDB", "~BlastDB");
  60                 exit(1);
  61         }
  62 }
  63 /**************************************************************************************************/
  64 //assumes you have added all the template sequences using the addSequence function and run generateDB.
  65 vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
  66         try{
  67                 vector<int> topMatches;
  68
  69                 ofstream queryFile;
  70                 int randNumber = rand();
  71                 m->openOutputFile((queryFileName+toString(randNumber)), queryFile);
  72                 queryFile << '>' << seq->getName() << endl;
  73                 queryFile << seq->getUnaligned() << endl;
  74                 queryFile.close();
  75
  76
  77                 //      the goal here is to quickly survey the database to find the closest match.  To do this we are using the default
  78                 //      wordsize used in megablast.  I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
  79                 //      long.  With this setting, it seems comparable in speed to the suffix tree approach.
  80
  81                 string blastCommand;
  82                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  83
  84                         blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
  85                         blastCommand += (" -i " + (queryFileName+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
  86                 #else
  87                         blastCommand =  "\"" + path + "blast\\bin\\blastall\" -p blastn -d " + "\"" + dbFileName + "\"" + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
  88                         blastCommand += (" -i " + (queryFileName+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
  89                         //wrap entire string in ""
  90                         blastCommand = "\"" + blastCommand + "\"";
  91                 #endif
  92                 system(blastCommand.c_str());
  93
  94                 ifstream m8FileHandle;
  95                 m->openInputFile(blastFileName+toString(randNumber), m8FileHandle, "no error");
  96
  97                 string dummy;
  98                 int templateAccession;
  99                 m->gobble(m8FileHandle);
 100
 101                 while(!m8FileHandle.eof()){
 102                         m8FileHandle >> dummy >> templateAccession >> searchScore;
 103
 104                         //get rest of junk in line
 105                         while (!m8FileHandle.eof())     {       char c = m8FileHandle.get(); if (c == 10 || c == 13){   break;  }       }
 106
 107                         m->gobble(m8FileHandle);
 108                         topMatches.push_back(templateAccession);
 109                 }
 110                 m8FileHandle.close();
 111                 remove((queryFileName+toString(randNumber)).c_str());
 112                 remove((blastFileName+toString(randNumber)).c_str());
 113
 114                 return topMatches;
 115         }
 116         catch(exception& e) {
 117                 m->errorOut(e, "BlastDB", "findClosestSequences");
 118                 exit(1);
 119         }
 120
 121 }
 122 /**************************************************************************************************/
 123 //assumes you have added all the template sequences using the addSequence function and run generateDB.
 124 vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
 125         try{
 126                 vector<int> topMatches;
 127                 float numBases, mismatch, gap, startQuery, endQuery, startRef, endRef, score;
 128                 Scores.clear();
 129
 130                 ofstream queryFile;
 131                 int randNumber = rand();
 132                 m->openOutputFile((queryFileName+toString(randNumber)), queryFile);
 133                 queryFile << '>' << seq->getName() << endl;
 134                 queryFile << seq->getUnaligned() << endl;
 135                 queryFile.close();
 136 //              cout << seq->getUnaligned() << endl;
 137                 //      the goal here is to quickly survey the database to find the closest match.  To do this we are using the default
 138                 //      wordsize used in megablast.  I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
 139                 //      long.  With this setting, it seems comparable in speed to the suffix tree approach.
 140 //7000004128189528left  0       100             66      0       0       1       66      61      126     1e-31    131
 141                 string blastCommand;
 142                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 143                         blastCommand = path + "blast/bin/megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
 144                         blastCommand += (" -i " + (queryFileName+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
 145                 #else
 146                         blastCommand =  "\"" + path + "blast\\bin\\megablast\" -e 1e-10 -d " + "\"" + dbFileName + "\"" + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
 147                         blastCommand += (" -i " + (queryFileName+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
 148                         //wrap entire string in ""
 149                         blastCommand = "\"" + blastCommand + "\"";
 150
 151                 #endif
 152
 153                 system(blastCommand.c_str());
 154
 155                 ifstream m8FileHandle;
 156                 m->openInputFile(blastFileName+toString(randNumber), m8FileHandle, "no error");
 157
 158                 string dummy, eScore;
 159                 int templateAccession;
 160                 m->gobble(m8FileHandle);
 161
 162                 while(!m8FileHandle.eof()){
 163                         m8FileHandle >> dummy >> templateAccession >> searchScore >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
 164 //                      cout << dummy << '\t' << templateAccession << '\t' << searchScore << '\t' << numBases << '\t' << mismatch << '\t' << gap << '\t' << startQuery << '\t' << endQuery << '\t' << startRef << '\t' << endRef << '\t' << eScore << '\t' << score << endl;
 165
 166                         //get rest of junk in line
 167                         //while (!m8FileHandle.eof())   {       char c = m8FileHandle.get(); if (c == 10 || c == 13){   break;  }else{ cout << c; }     } //
 168                                 //cout << endl;
 169                         m->gobble(m8FileHandle);
 170                         if (searchScore >= minPerID) {
 171                                 topMatches.push_back(templateAccession);
 172                                 Scores.push_back(searchScore);
 173                         }
 174 //cout << templateAccession << endl;
 175                 }
 176                 m8FileHandle.close();
 177                 remove((queryFileName+toString(randNumber)).c_str());
 178                 remove((blastFileName+toString(randNumber)).c_str());
 179 //cout << "\n" ;
 180                 return topMatches;
 181         }
 182         catch(exception& e) {
 183                 m->errorOut(e, "BlastDB", "findClosestMegaBlast");
 184                 exit(1);
 185         }
 186 }
 187 /**************************************************************************************************/
 188 void BlastDB::addSequence(Sequence seq) {
 189         try {
 190
 191                 ofstream unalignedFastaFile;
 192                 m->openOutputFileAppend(dbFileName, unalignedFastaFile);
 193
 194                 //      generating a fasta file with unaligned template
 195                 unalignedFastaFile << '>' << count << endl;                                     //      sequences, which will be input to formatdb
 196                 unalignedFastaFile << seq.getUnaligned() << endl;
 197                 unalignedFastaFile.close();
 198
 199                 count++;
 200         }
 201         catch(exception& e) {
 202                 m->errorOut(e, "BlastDB", "addSequence");
 203                 exit(1);
 204         }
 205 }
 206 /**************************************************************************************************/
 207 void BlastDB::generateDB() {
 208         try {
 209
 210                 //m->mothurOut("Generating the temporary BLAST database...\t"); cout.flush();
 211
 212                 path = m->argv;
 213                 string tempPath = path;
 214                 for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
 215                 path = path.substr(0, (tempPath.find_last_of('m')));
 216
 217                 string formatdbCommand;
 218
 219                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 220                         formatdbCommand = path + "blast/bin/formatdb -p F -o T -i " + dbFileName;       //      format the database, -o option gives us the ability
 221                 #else
 222                         formatdbCommand = "\"" + path + "blast\\bin\\formatdb\" -p F -o T -i " + "\"" +  dbFileName + "\"";
 223                         //wrap entire string in ""
 224                         formatdbCommand = "\"" + formatdbCommand + "\"";
 225                 #endif
 226                 system(formatdbCommand.c_str());                                                                //      to get the right sequence names, i think. -p F
 227                                                                                                                                         //      option tells formatdb that seqs are DNA, not prot
 228                 //m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine(); cout.flush();
 229         }
 230         catch(exception& e) {
 231                 m->errorOut(e, "BlastDB", "generateDB");
 232                 exit(1);
 233         }
 234 }
 235 /**************************************************************************************************/
 236
 237 /**************************************************************************************************/
 238