/**************************************************************************************************/
-BlastDB::BlastDB(string tag, float gO, float gE, float mm, float mM, string b) : 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;
string pid = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- pid += toString(getpid());
+#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";
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)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
path += "blast/bin/";
#else
path += "blast\\bin\\";
string formatdbCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#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";
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)
+#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";
string megablastCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#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";
}
/**************************************************************************************************/
-BlastDB::BlastDB(string b) : 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 == "") {
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)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
path += "blast/bin/";
#else
path += "blast\\bin\\";
int randNumber = rand();
string pid = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- pid += toString(getpid());
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ pid += getpid();
+#else
+ pid += toString(threadID);
#endif
dbFileName = pid + toString(randNumber) + ".template.unaligned.fasta";
blastFileName = pid + toString(randNumber) + ".blast";
string formatdbCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#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";
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)
+#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";
string megablastCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#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";
ofstream queryFile;
int randNumber = rand();
- string pid = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- pid += toString(getpid());
-#endif
+ string pid = scrubName(seq->getName());
m->openOutputFile((queryFileName+pid+toString(randNumber)), queryFile);
queryFile << '>' << seq->getName() << endl;
// 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 + "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));
ofstream queryFile;
int randNumber = rand();
- string pid = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- pid += toString(getpid());
-#endif
+ string pid = scrubName(seq->getName());
m->openOutputFile((queryFileName+pid+toString(randNumber)), queryFile);
queryFile << '>' << seq->getName() << endl;
// 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)
+ #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
string formatdbCommand;
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #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
}
}
/**************************************************************************************************/
+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);
+ }
+}
+/**************************************************************************************************/
/**************************************************************************************************/