/**************************************************************************************************/
-BlastDB::BlastDB(string tag, float gO, float gE, float mm, float mM) : Database(),
+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;
- dbFileName = tag + toString(randNumber) + ".template.unaligned.fasta";
- queryFileName = tag + toString(randNumber) + ".candidate.unaligned.fasta";
- blastFileName = tag + toString(randNumber) + ".blast";
+ 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
- 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 (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)
- formatdbCommand = path + "blast/bin/formatdb"; // format the database, -o option gives us the ability
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ formatdbCommand = path + "formatdb"; // format the database, -o option gives us the ability
#else
- formatdbCommand = path + "blast\\bin\\formatdb";
- //wrap entire string in ""
- formatdbCommand = "\"" + formatdbCommand + "\"";
+ 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 to be in the ./blast/bin folder relative to the mothur.exe location."); m->mothurOutEndLine(); m->control_pressed = true; }
+ 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)
- blastCommand = path + "blast/bin/blastall"; // format the database, -o option gives us the ability
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ blastCommand = path + "blastall"; // format the database, -o option gives us the ability
#else
- blastCommand = path + "blast\\bin\\blastall";
+ blastCommand = path + "blastall.exe";
//wrap entire string in ""
- blastCommand = "\"" + blastCommand + "\"";
+ //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; }
+ 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)
- megablastCommand = path + "blast/bin/megablast"; // format the database, -o option gives us the ability
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ megablastCommand = path + "megablast"; // format the database, -o option gives us the ability
#else
- megablastCommand = path + "blast\\bin\\megablast";
- //wrap entire string in ""
- megablastCommand = "\"" + blastCommmegablastCommandand + "\"";
+ 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 to be in the ./blast/bin folder relative to the mothur.exe location."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + megablastCommand + " file does not exist. mothur requires megablast.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
}
catch(exception& e) {
}
/**************************************************************************************************/
-BlastDB::BlastDB() : Database() {
+BlastDB::BlastDB(string b, int tid) : Database() {
try {
count = 0;
-
- int randNumber = rand();
- //int randNumber = 12345;
- dbFileName = toString(randNumber) + ".template.unaligned.fasta";
- queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
- blastFileName = toString(randNumber) + ".blast";
+
+ path = b;
+ threadID = tid;
//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')));
+ 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();
+ 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)
- formatdbCommand = path + "blast/bin/formatdb"; // format the database, -o option gives us the ability
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ formatdbCommand = path + "formatdb"; // format the database, -o option gives us the ability
#else
- formatdbCommand = path + "blast\\bin\\formatdb";
+ formatdbCommand = path + "formatdb.exe";
//wrap entire string in ""
- formatdbCommand = "\"" + formatdbCommand + "\"";
+ //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; }
+ 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)
- blastCommand = path + "blast/bin/blastall"; // format the database, -o option gives us the ability
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ blastCommand = path + "blastall"; // format the database, -o option gives us the ability
#else
- blastCommand = path + "blast\\bin\\blastall";
+ blastCommand = path + "blastall.exe";
//wrap entire string in ""
- blastCommand = "\"" + blastCommand + "\"";
+ //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; }
+ 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)
- megablastCommand = path + "blast/bin/megablast"; // format the database, -o option gives us the ability
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ megablastCommand = path + "megablast"; // format the database, -o option gives us the ability
#else
- megablastCommand = path + "blast\\bin\\megablast";
+ megablastCommand = path + "megablast.exe";
//wrap entire string in ""
- megablastCommand = "\"" + blastCommmegablastCommandand + "\"";
+ //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; }
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + megablastCommand + " file does not exist. mothur requires megablast.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
}
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");
ofstream queryFile;
int randNumber = rand();
- m->openOutputFile((queryFileName+toString(randNumber)), queryFile);
+ string pid = scrubName(seq->getName());
+
+ m->openOutputFile((queryFileName+pid+toString(randNumber)), queryFile);
queryFile << '>' << seq->getName() << endl;
queryFile << seq->getUnaligned() << endl;
queryFile.close();
// long. With this setting, it seems comparable in speed to the suffix tree approach.
string blastCommand;
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
- blastCommand += (" -i " + (queryFileName+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
+ 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 + "blast\\bin\\blastall\" -p blastn -d " + "\"" + dbFileName + "\"" + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);
- blastCommand += (" -i " + (queryFileName+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
+ 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+toString(randNumber), m8FileHandle, "no error");
+ m->openInputFile(blastFileName+pid+toString(randNumber), m8FileHandle, "no error");
string dummy;
int templateAccession;
topMatches.push_back(templateAccession);
}
m8FileHandle.close();
- remove((queryFileName+toString(randNumber)).c_str());
- remove((blastFileName+toString(randNumber)).c_str());
+ m->mothurRemove((queryFileName+pid+toString(randNumber)));
+ m->mothurRemove((blastFileName+pid+toString(randNumber)));
return topMatches;
}
ofstream queryFile;
int randNumber = rand();
- //int randNumber = 12345;
- m->openOutputFile((queryFileName+toString(randNumber)), queryFile);
+ string pid = scrubName(seq->getName());
+
+ m->openOutputFile((queryFileName+pid+toString(randNumber)), queryFile);
queryFile << '>' << seq->getName() << endl;
queryFile << seq->getUnaligned() << endl;
queryFile.close();
// 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;
- #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(randNumber)) + " -o " + blastFileName+toString(randNumber));
+ #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 + "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
- //cout << blastCommand << endl;
system(blastCommand.c_str());
ifstream m8FileHandle;
- m->openInputFile(blastFileName+toString(randNumber), m8FileHandle, "no error");
+ m->openInputFile(blastFileName+pid+toString(randNumber), m8FileHandle, "no error");
string dummy, eScore;
int templateAccession;
//cout << templateAccession << endl;
}
m8FileHandle.close();
- remove((queryFileName+toString(randNumber)).c_str());
- remove((blastFileName+toString(randNumber)).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();
-
- 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 -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 + "blast\\bin\\formatdb\" -p F -o T -i " + "\"" + dbFileName + "\"";
+ formatdbCommand = "\"" + path + "formatdb\" -p F -o T -i " + "\"" + dbFileName + "\"";
//wrap entire string in ""
formatdbCommand = "\"" + formatdbCommand + "\"";
#endif
}
}
/**************************************************************************************************/
+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);
+ }
+}
+/**************************************************************************************************/
/**************************************************************************************************/