/**************************************************************************************************/
-BlastDB::BlastDB(float gO, float gE, float m, float mM) : Database(),
-gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
-
- count = 0;
-
- int randNumber = rand();
- dbFileName = toString(randNumber) + ".template.unaligned.fasta";
- queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
- blastFileName = toString(randNumber) + ".blast";
+BlastDB::BlastDB(string tag, float gO, float gE, float mm, float mM) : Database(),
+gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
+ try {
+ count = 0;
+ int randNumber = rand();
+ //int randNumber = 12345;
+ dbFileName = tag + toString(getpid()) + toString(randNumber) + ".template.unaligned.fasta";
+ queryFileName = tag + toString(getpid()) + toString(randNumber) + ".candidate.unaligned.fasta";
+ blastFileName = tag + toString(getpid()) + toString(randNumber) + ".blast";
+
+ //make sure blast exists in the write place
+ path = m->argv;
+ string tempPath = path;
+ for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+ path = path.substr(0, (tempPath.find_last_of('m')));
+
+ string formatdbCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ formatdbCommand = path + "blast/bin/formatdb"; // format the database, -o option gives us the ability
+#else
+ formatdbCommand = path + "blast\\bin\\formatdb.exe";
+ //wrap entire string in ""
+ //formatdbCommand = "\"" + formatdbCommand + "\"";
+#endif
+
+ //test to make sure formatdb exists
+ ifstream in;
+ formatdbCommand = m->getFullPathName(formatdbCommand);
+ int ableToOpen = m->openInputFile(formatdbCommand, in, "no error"); in.close();
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe to be in the ./blast/bin folder relative to the mothur.exe location."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ string blastCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ blastCommand = path + "blast/bin/blastall"; // format the database, -o option gives us the ability
+#else
+ blastCommand = path + "blast\\bin\\blastall.exe";
+ //wrap entire string in ""
+ //blastCommand = "\"" + blastCommand + "\"";
+#endif
+
+ //test to make sure formatdb exists
+ ifstream in2;
+ blastCommand = m->getFullPathName(blastCommand);
+ ableToOpen = m->openInputFile(blastCommand, in2, "no error"); in2.close();
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + blastCommand + " file does not exist. mothur requires blastall.exe to be in the ./blast/bin folder relative to the mothur.exe location."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+
+ string megablastCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ megablastCommand = path + "blast/bin/megablast"; // format the database, -o option gives us the ability
+#else
+ megablastCommand = path + "blast\\bin\\megablast.exe";
+ //wrap entire string in ""
+ //megablastCommand = "\"" + megablastCommand + "\"";
+#endif
+
+ //test to make sure formatdb exists
+ ifstream in3;
+ megablastCommand = m->getFullPathName(megablastCommand);
+ ableToOpen = m->openInputFile(megablastCommand, in3, "no error"); in3.close();
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + megablastCommand + " file does not exist. mothur requires megablast.exe to be in the ./blast/bin folder relative to the mothur.exe location."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "BlastDB");
+ exit(1);
+ }
}
/**************************************************************************************************/
count = 0;
int randNumber = rand();
- dbFileName = toString(randNumber) + ".template.unaligned.fasta";
- queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
- blastFileName = toString(randNumber) + ".blast";
+ //int randNumber = 12345;
+ dbFileName = toString(randNumber) + toString(getpid()) + ".template.unaligned.fasta";
+ queryFileName = toString(randNumber) + toString(getpid()) + ".candidate.unaligned.fasta";
+ blastFileName = toString(randNumber) + toString(getpid()) + ".blast";
+
+ //make sure blast exists in the write place
+ path = m->argv;
+ string tempPath = path;
+ for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+ path = path.substr(0, (tempPath.find_last_of('m')));
+
+ string formatdbCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ formatdbCommand = path + "blast/bin/formatdb"; // format the database, -o option gives us the ability
+#else
+ formatdbCommand = path + "blast\\bin\\formatdb.exe";
+ //wrap entire string in ""
+ //formatdbCommand = "\"" + formatdbCommand + "\"";
+#endif
+
+ //test to make sure formatdb exists
+ ifstream in;
+ formatdbCommand = m->getFullPathName(formatdbCommand);
+ int ableToOpen = m->openInputFile(formatdbCommand, in, "no error"); in.close();
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe to be in the ./blast/bin folder relative to the mothur.exe location."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ string blastCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ blastCommand = path + "blast/bin/blastall"; // format the database, -o option gives us the ability
+#else
+ blastCommand = path + "blast\\bin\\blastall.exe";
+ //wrap entire string in ""
+ //blastCommand = "\"" + blastCommand + "\"";
+#endif
+
+ //test to make sure formatdb exists
+ ifstream in2;
+ blastCommand = m->getFullPathName(blastCommand);
+ ableToOpen = m->openInputFile(blastCommand, in2, "no error"); in2.close();
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + blastCommand + " file does not exist. mothur requires blastall.exe to be in the ./blast/bin folder relative to the mothur.exe location."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+
+ string megablastCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ megablastCommand = path + "blast/bin/megablast"; // format the database, -o option gives us the ability
+#else
+ megablastCommand = path + "blast\\bin\\megablast.exe";
+ //wrap entire string in ""
+ //megablastCommand = "\"" + megablastCommand + "\"";
+#endif
+
+ //test to make sure formatdb exists
+ ifstream in3;
+ megablastCommand = m->getFullPathName(megablastCommand);
+ ableToOpen = m->openInputFile(megablastCommand, in3, "no error"); in3.close();
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + megablastCommand + " file does not exist. mothur requires megablast.exe to be in the ./blast/bin folder relative to the mothur.exe location."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+
}
catch(exception& e) {
m->errorOut(e, "BlastDB", "BlastDB");
vector<int> topMatches;
ofstream queryFile;
- m->openOutputFile((queryFileName+seq->getName()), queryFile);
+ int randNumber = rand();
+ m->openOutputFile((queryFileName+toString(getpid())+toString(randNumber)), queryFile);
queryFile << '>' << seq->getName() << endl;
queryFile << seq->getUnaligned() << endl;
queryFile.close();
// wordsize used in megablast. I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
// long. With this setting, it seems comparable in speed to the suffix tree approach.
- string blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);;
- blastCommand += (" -i " + (queryFileName+seq->getName()) + " -o " + blastFileName+seq->getName());
+ string blastCommand;
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+
+ blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
+ blastCommand += (" -i " + (queryFileName+toString(getpid())+toString(randNumber)) + " -o " + blastFileName+toString(getpid())+toString(randNumber));
+ #else
+ blastCommand = "\"" + path + "blast\\bin\\blastall\" -p blastn -d " + "\"" + dbFileName + "\"" + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
+ blastCommand += (" -i " + (queryFileName+toString(getpid())+toString(randNumber)) + " -o " + blastFileName+toString(getpid())+toString(randNumber));
+ //wrap entire string in ""
+ blastCommand = "\"" + blastCommand + "\"";
+ #endif
+
system(blastCommand.c_str());
ifstream m8FileHandle;
- m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
+ m->openInputFile(blastFileName+toString(getpid())+toString(randNumber), m8FileHandle, "no error");
string dummy;
int templateAccession;
topMatches.push_back(templateAccession);
}
m8FileHandle.close();
- remove((queryFileName+seq->getName()).c_str());
- remove((blastFileName+seq->getName()).c_str());
+ remove((queryFileName+toString(getpid())+toString(randNumber)).c_str());
+ remove((blastFileName+toString(getpid())+toString(randNumber)).c_str());
return topMatches;
}
}
/**************************************************************************************************/
//assumes you have added all the template sequences using the addSequence function and run generateDB.
-vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
+vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
try{
vector<int> topMatches;
+ float numBases, mismatch, gap, startQuery, endQuery, startRef, endRef, score;
+ Scores.clear();
ofstream queryFile;
- m->openOutputFile((queryFileName+seq->getName()), queryFile);
+ int randNumber = rand();
+ //int randNumber = 12345;
+ m->openOutputFile((queryFileName+toString(getpid())+toString(randNumber)), queryFile);
queryFile << '>' << seq->getName() << endl;
queryFile << seq->getUnaligned() << endl;
queryFile.close();
-
+// cout << seq->getUnaligned() << endl;
// the goal here is to quickly survey the database to find the closest match. To do this we are using the default
// wordsize used in megablast. I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
// long. With this setting, it seems comparable in speed to the suffix tree approach.
-
- string blastCommand = path + "blast/bin/megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
- blastCommand += (" -i " + (queryFileName+seq->getName()) + " -o " + blastFileName+seq->getName());
+//7000004128189528left 0 100 66 0 0 1 66 61 126 1e-31 131
+ string blastCommand;
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ blastCommand = path + "blast/bin/megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
+ blastCommand += (" -i " + (queryFileName+toString(getpid())+toString(randNumber)) + " -o " + blastFileName+toString(getpid())+toString(randNumber));
+ #else
+ //blastCommand = path + "blast\\bin\\megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
+ //blastCommand += (" -i " + (queryFileName+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
+
+ blastCommand = "\"" + path + "blast\\bin\\megablast\" -e 1e-10 -d " + "\"" + dbFileName + "\"" + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
+ blastCommand += (" -i " + (queryFileName+toString(getpid())+toString(randNumber)) + " -o " + blastFileName+toString(getpid())+toString(randNumber));
+ //wrap entire string in ""
+ blastCommand = "\"" + blastCommand + "\"";
+
+ #endif
system(blastCommand.c_str());
ifstream m8FileHandle;
- m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
+ m->openInputFile(blastFileName+toString(getpid())+toString(randNumber), m8FileHandle, "no error");
- string dummy;
+ string dummy, eScore;
int templateAccession;
m->gobble(m8FileHandle);
while(!m8FileHandle.eof()){
- m8FileHandle >> dummy >> templateAccession >> searchScore;
- //cout << templateAccession << '\t' << searchScore << endl;
+ m8FileHandle >> dummy >> templateAccession >> searchScore >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
+// 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;
//get rest of junk in line
- while (!m8FileHandle.eof()) { char c = m8FileHandle.get(); if (c == 10 || c == 13){ break; } }
-
+ //while (!m8FileHandle.eof()) { char c = m8FileHandle.get(); if (c == 10 || c == 13){ break; }else{ cout << c; } } //
+ //cout << endl;
m->gobble(m8FileHandle);
- topMatches.push_back(templateAccession);
+ if (searchScore >= minPerID) {
+ topMatches.push_back(templateAccession);
+ Scores.push_back(searchScore);
+ }
//cout << templateAccession << endl;
}
m8FileHandle.close();
- remove((queryFileName+seq->getName()).c_str());
- remove((blastFileName+seq->getName()).c_str());
-//cout << "\n\n" ;
+ remove((queryFileName+toString(getpid())+toString(randNumber)).c_str());
+ remove((blastFileName+toString(getpid())+toString(randNumber)).c_str());
+//cout << "\n" ;
return topMatches;
}
catch(exception& e) {
- m->errorOut(e, "BlastDB", "findClosest");
+ m->errorOut(e, "BlastDB", "findClosestMegaBlast");
exit(1);
}
}
//m->mothurOut("Generating the temporary BLAST database...\t"); cout.flush();
path = m->argv;
- path = path.substr(0, (path.find_last_of('m')));
+ string tempPath = path;
+ for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+ path = path.substr(0, (tempPath.find_last_of('m')));
- string formatdbCommand = path + "blast/bin/formatdb -p F -o T -i " + dbFileName; // format the database, -o option gives us the ability
+ string formatdbCommand;
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ formatdbCommand = path + "blast/bin/formatdb -p F -o T -i " + dbFileName; // format the database, -o option gives us the ability
+ #else
+ //formatdbCommand = path + "blast\\bin\\formatdb -p F -o T -i " + dbFileName; // format the database, -o option gives us the ability
+
+ formatdbCommand = "\"" + path + "blast\\bin\\formatdb\" -p F -o T -i " + "\"" + dbFileName + "\"";
+ //wrap entire string in ""
+ formatdbCommand = "\"" + formatdbCommand + "\"";
+ #endif
+ //cout << formatdbCommand << endl;
system(formatdbCommand.c_str()); // to get the right sequence names, i think. -p F
// option tells formatdb that seqs are DNA, not prot
//m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine(); cout.flush();
projects / mothur.git / blobdiff