/**************************************************************************************************/
-BlastDB::BlastDB(string tag, float gO, float gE, float m, float mM) : Database(),
-gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
-
- count = 0;
-
- int randNumber = rand();
- dbFileName = tag + toString(randNumber) + ".template.unaligned.fasta";
- queryFileName = tag + toString(randNumber) + ".candidate.unaligned.fasta";
- blastFileName = tag + toString(randNumber) + ".blast";
+BlastDB::BlastDB(string tag, float gO, float gE, float mm, float mM, string b, int tid) : Database(),
+gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
+ try {
+ count = 0;
+ path = b;
+ threadID = tid;
+ int randNumber = rand();
+ //int randNumber = 12345;
+ string pid = "";
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ pid += getpid();
+#else
+ pid += toString(threadID);
+#endif
+
+
+ dbFileName = tag + pid + toString(randNumber) + ".template.unaligned.fasta";
+ queryFileName = tag + pid + toString(randNumber) + ".candidate.unaligned.fasta";
+ blastFileName = tag + pid + toString(randNumber) + ".blast";
+
+ //make sure blast exists in the write place
+ if (path == "") {
+ 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')));
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ path += "blast/bin/";
+#else
+ path += "blast\\bin\\";
+#endif
+ }
+
+
+ string formatdbCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ formatdbCommand = path + "formatdb"; // format the database, -o option gives us the ability
+#else
+ formatdbCommand = path + "formatdb.exe";
+#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."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ string blastCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ blastCommand = path + "blastall"; // format the database, -o option gives us the ability
+#else
+ blastCommand = path + "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."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+
+ string megablastCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ megablastCommand = path + "megablast"; // format the database, -o option gives us the ability
+#else
+ megablastCommand = path + "megablast.exe";
+#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."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "BlastDB");
+ exit(1);
+ }
}
/**************************************************************************************************/
-BlastDB::BlastDB() : Database() {
+BlastDB::BlastDB(string b, int tid) : Database() {
try {
count = 0;
-
+
+ path = b;
+ threadID = tid;
+
+ //make sure blast exists in the write place
+ if (path == "") {
+ 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')));
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ path += "blast/bin/";
+#else
+ path += "blast\\bin\\";
+#endif
+ }
+
int randNumber = rand();
- dbFileName = toString(randNumber) + ".template.unaligned.fasta";
- queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
- blastFileName = toString(randNumber) + ".blast";
+ string pid = "";
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ pid += getpid();
+#else
+ pid += toString(threadID);
+#endif
+
+ dbFileName = pid + toString(randNumber) + ".template.unaligned.fasta";
+ queryFileName = pid + toString(randNumber) + ".candidate.unaligned.fasta";
+ blastFileName = pid + toString(randNumber) + ".blast";
+
+ string formatdbCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ formatdbCommand = path + "formatdb"; // format the database, -o option gives us the ability
+#else
+ formatdbCommand = path + "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."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ string blastCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ blastCommand = path + "blastall"; // format the database, -o option gives us the ability
+#else
+ blastCommand = path + "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."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+
+ string megablastCommand;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ megablastCommand = path + "megablast"; // format the database, -o option gives us the ability
+#else
+ megablastCommand = path + "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."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+
}
catch(exception& e) {
m->errorOut(e, "BlastDB", "BlastDB");
BlastDB::~BlastDB(){
try{
- remove(queryFileName.c_str()); // let's clean stuff up and remove the temp files
- remove(dbFileName.c_str()); // let's clean stuff up and remove the temp files
- remove((dbFileName+".nsq").c_str()); // let's clean stuff up and remove the temp files
- remove((dbFileName+".nsi").c_str()); // let's clean stuff up and remove the temp files
- remove((dbFileName+".nsd").c_str()); // let's clean stuff up and remove the temp files
- remove((dbFileName+".nin").c_str()); // let's clean stuff up and remove the temp files
- remove((dbFileName+".nhr").c_str()); // let's clean stuff up and remove the temp files
- remove(blastFileName.c_str()); // let's clean stuff up and remove the temp files
+ m->mothurRemove(queryFileName); // let's clean stuff up and remove the temp files
+ m->mothurRemove(dbFileName); // let's clean stuff up and remove the temp files
+ m->mothurRemove((dbFileName+".nsq")); // let's clean stuff up and remove the temp files
+ m->mothurRemove((dbFileName+".nsi")); // let's clean stuff up and remove the temp files
+ m->mothurRemove((dbFileName+".nsd")); // let's clean stuff up and remove the temp files
+ m->mothurRemove((dbFileName+".nin")); // let's clean stuff up and remove the temp files
+ m->mothurRemove((dbFileName+".nhr")); // let's clean stuff up and remove the temp files
+ m->mothurRemove(blastFileName.c_str()); // let's clean stuff up and remove the temp files
}
catch(exception& e) {
m->errorOut(e, "BlastDB", "~BlastDB");
vector<int> topMatches;
ofstream queryFile;
- m->openOutputFile((queryFileName+seq->getName()), queryFile);
+ int randNumber = rand();
+ string pid = scrubName(seq->getName());
+
+ m->openOutputFile((queryFileName+pid+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) || (__linux__) || (__unix__) || (__unix)
+
+ blastCommand = path + "blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
+ blastCommand += (" -i " + (queryFileName+pid+toString(randNumber)) + " -o " + blastFileName+pid+toString(randNumber));
+ #else
+ blastCommand = "\"" + path + "blastall\" -p blastn -d " + "\"" + dbFileName + "\"" + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
+ blastCommand += (" -i " + (queryFileName+pid+toString(randNumber)) + " -o " + blastFileName+pid+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+pid+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());
+ m->mothurRemove((queryFileName+pid+toString(randNumber)));
+ m->mothurRemove((blastFileName+pid+toString(randNumber)));
return topMatches;
}
Scores.clear();
ofstream queryFile;
-
- m->openOutputFile((queryFileName+seq->getName()), queryFile);
+ int randNumber = rand();
+ string pid = scrubName(seq->getName());
+
+ m->openOutputFile((queryFileName+pid+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.
//7000004128189528left 0 100 66 0 0 1 66 61 126 1e-31 131
-
- 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());
+ string blastCommand;
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ blastCommand = path + "megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
+ blastCommand += (" -i " + (queryFileName+pid+toString(randNumber)) + " -o " + blastFileName+pid+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 + "megablast\" -e 1e-10 -d " + "\"" + dbFileName + "\"" + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
+ blastCommand += (" -i " + (queryFileName+pid+toString(randNumber)) + " -o " + blastFileName+pid+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+pid+toString(randNumber), m8FileHandle, "no error");
string dummy, eScore;
int templateAccession;
while(!m8FileHandle.eof()){
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;
+// 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; }else{ cout << c; } } //
//cout << templateAccession << endl;
}
m8FileHandle.close();
- remove((queryFileName+seq->getName()).c_str());
- remove((blastFileName+seq->getName()).c_str());
+ m->mothurRemove((queryFileName+pid+toString(randNumber)));
+ m->mothurRemove((blastFileName+pid+toString(randNumber)));
//cout << "\n" ;
return topMatches;
}
try {
//m->mothurOut("Generating the temporary BLAST database...\t"); cout.flush();
+
+ string formatdbCommand;
- 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 = path + "blast/bin/formatdb -p F -o T -i " + dbFileName; // format the database, -o option gives us the ability
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ formatdbCommand = path + "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 + "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();
}
}
/**************************************************************************************************/
+string BlastDB::scrubName(string seqName) {
+ try {
+
+ string cleanName = "";
+
+ for (int i = 0; i < seqName.length(); i++) {
+ if (isalnum(seqName[i])) { cleanName += seqName[i]; }
+ else { cleanName += "_"; }
+ }
+
+ return cleanName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BlastDB", "scrubName");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
/**************************************************************************************************/
projects / mothur.git / blobdiff