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(float gO, float gE, float m, float mM) : Database(),
  18 gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
  19
  20         globaldata = GlobalData::getInstance();
  21         count = 0;
  22
  23         int randNumber = rand();
  24         dbFileName = toString(randNumber) + ".template.unaligned.fasta";
  25         queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
  26         blastFileName = toString(randNumber) + ".blast";
  27
  28 }
  29 /**************************************************************************************************/
  30
  31 BlastDB::BlastDB() : Database() {
  32
  33         globaldata = GlobalData::getInstance();
  34         count = 0;
  35
  36         int randNumber = rand();
  37         dbFileName = toString(randNumber) + ".template.unaligned.fasta";
  38         queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
  39         blastFileName = toString(randNumber) + ".blast";
  40
  41 }
  42
  43 /**************************************************************************************************/
  44
  45 BlastDB::~BlastDB(){
  46         remove(queryFileName.c_str());                          //      let's clean stuff up and remove the temp files
  47         remove(dbFileName.c_str());                                     //      let's clean stuff up and remove the temp files
  48         remove(blastFileName.c_str());                          //      let's clean stuff up and remove the temp files
  49 }
  50 /**************************************************************************************************/
  51 //assumes you have added all the template sequences using the addSequence function and run generateDB.
  52 vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
  53         try{
  54                 vector<int> topMatches;
  55
  56                 ofstream queryFile;
  57                 openOutputFile(queryFileName, queryFile);
  58                 queryFile << '>' << seq->getName() << endl;
  59                 queryFile << seq->getUnaligned() << endl;
  60                 queryFile.close();
  61
  62                 //      the goal here is to quickly survey the database to find the closest match.  To do this we are using the default
  63                 //      wordsize used in megablast.  I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
  64                 //      long.  With this setting, it seems comparable in speed to the suffix tree approach.
  65
  66                 string blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);;
  67                 blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
  68                 system(blastCommand.c_str());
  69
  70                 ifstream m8FileHandle;
  71                 openInputFile(blastFileName, m8FileHandle);
  72
  73                 string dummy;
  74                 int templateAccession;
  75                 gobble(m8FileHandle);
  76
  77                 while(!m8FileHandle.eof()){
  78                         m8FileHandle >> dummy >> templateAccession >> searchScore;
  79
  80                         //get rest of junk in line
  81                         while (!m8FileHandle.eof())     {       char c = m8FileHandle.get(); if (c == 10 || c == 13){   break;  }       }
  82
  83                         gobble(m8FileHandle);
  84                         topMatches.push_back(templateAccession);
  85                 }
  86                 m8FileHandle.close();
  87
  88                 return topMatches;
  89         }
  90         catch(exception& e) {
  91                 m->errorOut(e, "BlastDB", "findClosestSequences");
  92                 exit(1);
  93         }
  94
  95 }
  96 /**************************************************************************************************/
  97 //assumes you have added all the template sequences using the addSequence function and run generateDB.
  98 vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
  99         try{
 100                 vector<int> topMatches;
 101
 102                 ofstream queryFile;
 103                 openOutputFile(queryFileName, queryFile);
 104                 queryFile << '>' << seq->getName() << endl;
 105                 queryFile << seq->getUnaligned() << endl;
 106                 queryFile.close();
 107
 108                 //      the goal here is to quickly survey the database to find the closest match.  To do this we are using the default
 109                 //      wordsize used in megablast.  I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
 110                 //      long.  With this setting, it seems comparable in speed to the suffix tree approach.
 111
 112                 string blastCommand = path + "blast/bin/megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
 113                 blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
 114                 system(blastCommand.c_str());
 115
 116                 ifstream m8FileHandle;
 117                 openInputFile(blastFileName, m8FileHandle, "no error");
 118
 119                 string dummy;
 120                 int templateAccession;
 121                 gobble(m8FileHandle);
 122
 123                 while(!m8FileHandle.eof()){
 124                         m8FileHandle >> dummy >> templateAccession >> searchScore;
 125
 126                         //get rest of junk in line
 127                         while (!m8FileHandle.eof())     {       char c = m8FileHandle.get(); if (c == 10 || c == 13){   break;  }       }
 128
 129                         gobble(m8FileHandle);
 130                         topMatches.push_back(templateAccession);
 131 //cout << templateAccession << endl;
 132                 }
 133                 m8FileHandle.close();
 134 //cout << "\n\n" ;
 135                 return topMatches;
 136         }
 137         catch(exception& e) {
 138                 m->errorOut(e, "BlastDB", "findClosest");
 139                 exit(1);
 140         }
 141 }
 142 /**************************************************************************************************/
 143 void BlastDB::addSequence(Sequence seq) {
 144         try {
 145
 146                 ofstream unalignedFastaFile;
 147                 openOutputFileAppend(dbFileName, unalignedFastaFile);
 148
 149                 //      generating a fasta file with unaligned template
 150                 unalignedFastaFile << '>' << count << endl;                                     //      sequences, which will be input to formatdb
 151                 unalignedFastaFile << seq.getUnaligned() << endl;
 152                 unalignedFastaFile.close();
 153
 154                 count++;
 155         }
 156         catch(exception& e) {
 157                 m->errorOut(e, "BlastDB", "addSequence");
 158                 exit(1);
 159         }
 160 }
 161 /**************************************************************************************************/
 162 void BlastDB::generateDB() {
 163         try {
 164
 165                 //m->mothurOut("Generating the temporary BLAST database...\t"); cout.flush();
 166
 167                 path = globaldata->argv;
 168                 path = path.substr(0, (path.find_last_of('m')));
 169
 170                 string formatdbCommand = path + "blast/bin/formatdb -p F -o T -i " + dbFileName;        //      format the database, -o option gives us the ability
 171                 system(formatdbCommand.c_str());                                                                //      to get the right sequence names, i think. -p F
 172                                                                                                                                         //      option tells formatdb that seqs are DNA, not prot
 173                 //m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine(); cout.flush();
 174         }
 175         catch(exception& e) {
 176                 m->errorOut(e, "BlastDB", "generateDB");
 177                 exit(1);
 178         }
 179 }
 180 #ifdef USE_MPI
 181 /**************************************************************************************************/
 182 int BlastDB::MPISend(int receiver) {
 183         try {
 184
 185                 //send gapOpen - float
 186                 MPI_Send(&gapOpen, 1, MPI_FLOAT, receiver, 2001, MPI_COMM_WORLD);
 187
 188                 //send gapExtend - float
 189                 MPI_Send(&gapExtend, 1, MPI_FLOAT, receiver, 2001, MPI_COMM_WORLD);
 190
 191                 //send match - float
 192                 MPI_Send(&match, 1, MPI_FLOAT, receiver, 2001, MPI_COMM_WORLD);
 193
 194                 //send mismatch - float
 195                 MPI_Send(&misMatch, 1, MPI_FLOAT, receiver, 2001, MPI_COMM_WORLD);
 196
 197                 return 0;
 198         }
 199         catch(exception& e) {
 200                 m->errorOut(e, "BlastDB", "MPISend");
 201                 exit(1);
 202         }
 203 }
 204 /**************************************************************************************************/
 205 int BlastDB::MPIRecv(int sender) {
 206         try {
 207                 MPI_Status status;
 208
 209                 //receive gapOpen - float
 210                 MPI_Recv(&gapOpen, 1, MPI_FLOAT, sender, 2001, MPI_COMM_WORLD, &status);
 211
 212                 //receive gapExtend - float
 213                 MPI_Recv(&gapExtend, 1, MPI_FLOAT, sender, 2001, MPI_COMM_WORLD, &status);
 214
 215                 //receive match - float
 216                 MPI_Recv(&match, 1, MPI_FLOAT, sender, 2001, MPI_COMM_WORLD, &status);
 217
 218                 //receive mismatch - float
 219                 MPI_Recv(&misMatch, 1, MPI_FLOAT, sender, 2001, MPI_COMM_WORLD, &status);
 220
 221                 return 0;
 222         }
 223         catch(exception& e) {
 224                 m->errorOut(e, "BlastDB", "MPIRecv");
 225                 exit(1);
 226         }
 227 }
 228 #endif
 229 /**************************************************************************************************/
 230
 231 /**************************************************************************************************/
 232