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";
+ string pid = "";
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ pid += toString(getpid());
+#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;
count = 0;
int randNumber = rand();
- //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";
+ string pid = "";
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ pid += toString(getpid());
+#endif
+
+ dbFileName = pid + toString(randNumber) + ".template.unaligned.fasta";
+ queryFileName = pid + toString(randNumber) + ".candidate.unaligned.fasta";
+ blastFileName = pid + toString(randNumber) + ".blast";
//make sure blast exists in the write place
path = m->argv;
ofstream queryFile;
int randNumber = rand();
- m->openOutputFile((queryFileName+toString(getpid())+toString(randNumber)), queryFile);
+ string pid = "";
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ pid += toString(getpid());
+#endif
+
+ m->openOutputFile((queryFileName+pid+toString(randNumber)), queryFile);
queryFile << '>' << seq->getName() << endl;
queryFile << seq->getUnaligned() << endl;
queryFile.close();
#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));
+ 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(getpid())+toString(randNumber)) + " -o " + blastFileName+toString(getpid())+toString(randNumber));
+ 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(getpid())+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(getpid())+toString(randNumber)).c_str());
- remove((blastFileName+toString(getpid())+toString(randNumber)).c_str());
+ remove((queryFileName+pid+toString(randNumber)).c_str());
+ remove((blastFileName+pid+toString(randNumber)).c_str());
return topMatches;
}
ofstream queryFile;
int randNumber = rand();
- //int randNumber = 12345;
- m->openOutputFile((queryFileName+toString(getpid())+toString(randNumber)), queryFile);
+ string pid = "";
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ pid += toString(getpid());
+#endif
+
+ m->openOutputFile((queryFileName+pid+toString(randNumber)), queryFile);
queryFile << '>' << seq->getName() << endl;
queryFile << seq->getUnaligned() << endl;
queryFile.close();
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));
+ 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(getpid())+toString(randNumber)) + " -o " + blastFileName+toString(getpid())+toString(randNumber));
+ blastCommand += (" -i " + (queryFileName+pid+toString(randNumber)) + " -o " + blastFileName+pid+toString(randNumber));
//wrap entire string in ""
blastCommand = "\"" + blastCommand + "\"";
system(blastCommand.c_str());
ifstream m8FileHandle;
- m->openInputFile(blastFileName+toString(getpid())+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(getpid())+toString(randNumber)).c_str());
- remove((blastFileName+toString(getpid())+toString(randNumber)).c_str());
+ remove((queryFileName+pid+toString(randNumber)).c_str());
+ remove((blastFileName+pid+toString(randNumber)).c_str());
//cout << "\n" ;
return topMatches;
}