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
  32 BlastDB::~BlastDB(){
  33         remove(queryFileName.c_str());                          //      let's clean stuff up and remove the temp files
  34         remove(dbFileName.c_str());                                     //      let's clean stuff up and remove the temp files
  35         remove(blastFileName.c_str());                          //      let's clean stuff up and remove the temp files
  36 }
  37 /**************************************************************************************************/
  38 //assumes you have added all the template sequences using the addSequence function and run generateDB.
  39 vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
  40         try{
  41                 vector<int> topMatches;
  42
  43                 ofstream queryFile;
  44                 openOutputFile(queryFileName, queryFile);
  45                 queryFile << '>' << seq->getName() << endl;
  46                 queryFile << seq->getUnaligned() << endl;
  47                 queryFile.close();
  48
  49                 //      the goal here is to quickly survey the database to find the closest match.  To do this we are using the default
  50                 //      wordsize used in megablast.  I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
  51                 //      long.  With this setting, it seems comparable in speed to the suffix tree approach.
  52
  53                 string blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -b 1 -m 8 -W 28 -v " + toString(n);
  54                 blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
  55                 system(blastCommand.c_str());
  56
  57                 ifstream m8FileHandle;
  58                 openInputFile(blastFileName, m8FileHandle);
  59
  60                 string dummy;
  61                 int templateAccession;
  62                 gobble(m8FileHandle);
  63
  64                 while(!m8FileHandle.eof()){
  65                         m8FileHandle >> dummy >> templateAccession >> searchScore;
  66
  67                         //get rest of junk in line
  68                         while (!m8FileHandle.eof())     {       char c = m8FileHandle.get(); if (c == 10 || c == 13){   break;  }       }
  69
  70                         gobble(m8FileHandle);
  71                         topMatches.push_back(templateAccession);
  72                 }
  73                 m8FileHandle.close();
  74
  75                 return topMatches;
  76         }
  77         catch(exception& e) {
  78                 errorOut(e, "BlastDB", "findClosestSequences");
  79                 exit(1);
  80         }
  81
  82 }
  83 /**************************************************************************************************/
  84 //assumes you have added all the template sequences using the addSequence function and run generateDB.
  85 map<int, float> BlastDB::findClosest(Sequence* seq, int n) {
  86         try{
  87                 map<int, float> topMatches;
  88
  89                 ofstream queryFile;
  90                 openOutputFile(queryFileName, queryFile);
  91                 queryFile << '>' << seq->getName() << endl;
  92                 queryFile << seq->getUnaligned() << endl;
  93                 queryFile.close();
  94
  95                 //      the goal here is to quickly survey the database to find the closest match.  To do this we are using the default
  96                 //      wordsize used in megablast.  I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
  97                 //      long.  With this setting, it seems comparable in speed to the suffix tree approach.
  98
  99                 string blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -b " + toString(n) + " -v " + toString(n);
 100                 blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
 101                 system(blastCommand.c_str());
 102
 103                 ifstream m8FileHandle;
 104                 openInputFile(blastFileName, m8FileHandle);
 105
 106                 string dummy;
 107                 int templateAccession;
 108                 gobble(m8FileHandle);
 109 //string name = seq->getName();
 110 //ofstream out;
 111 //openOutputFileAppend(name, out);
 112                 while(!m8FileHandle.eof()){
 113                         m8FileHandle >> dummy >> templateAccession >> searchScore;
 114 //out << dummy << '\t' <<  templateAccession    << '\t' << searchScore << endl;
 115                         //get rest of junk in line
 116                         while (!m8FileHandle.eof())     {       char c = m8FileHandle.get();
 117                         //out << c;
 118                         if (c == 10 || c == 13){        break;  }       }
 119
 120                         gobble(m8FileHandle);
 121                         topMatches[templateAccession] = searchScore;
 122                 }
 123                 m8FileHandle.close();
 124 //out.close();
 125                 return topMatches;
 126         }
 127         catch(exception& e) {
 128                 errorOut(e, "BlastDB", "findClosest");
 129                 exit(1);
 130         }
 131 }
 132 /**************************************************************************************************/
 133 void BlastDB::addSequence(Sequence seq) {
 134         try {
 135
 136                 ofstream unalignedFastaFile;
 137                 openOutputFileAppend(dbFileName, unalignedFastaFile);
 138
 139                 //      generating a fasta file with unaligned template
 140                 unalignedFastaFile << '>' << count << endl;                                     //      sequences, which will be input to formatdb
 141                 unalignedFastaFile << seq.getUnaligned() << endl;
 142                 unalignedFastaFile.close();
 143
 144                 count++;
 145         }
 146         catch(exception& e) {
 147                 errorOut(e, "BlastDB", "addSequence");
 148                 exit(1);
 149         }
 150 }
 151 /**************************************************************************************************/
 152 void BlastDB::generateDB() {
 153         try {
 154
 155                 //mothurOut("Generating the temporary BLAST database...\t");    cout.flush();
 156
 157                 path = globaldata->argv;
 158                 path = path.substr(0, (path.find_last_of('m')));
 159
 160                 string formatdbCommand = path + "blast/bin/formatdb -p F -o T -i " + dbFileName;        //      format the database, -o option gives us the ability
 161                 system(formatdbCommand.c_str());                                                                //      to get the right sequence names, i think. -p F
 162                                                                                                                                         //      option tells formatdb that seqs are DNA, not prot
 163                 //mothurOut("DONE."); mothurOutEndLine();       mothurOutEndLine(); cout.flush();
 164         }
 165         catch(exception& e) {
 166                 errorOut(e, "BlastDB", "generateDB");
 167                 exit(1);
 168         }
 169 }
 170
 171 /**************************************************************************************************/
 172