count = 0;
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";
count = 0;
int randNumber = rand();
+ //int randNumber = 12345;
dbFileName = toString(randNumber) + ".template.unaligned.fasta";
queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
blastFileName = toString(randNumber) + ".blast";
vector<int> topMatches;
ofstream queryFile;
- m->openOutputFile((queryFileName+seq->getName()), queryFile);
+ int randNumber = rand();
+ m->openOutputFile((queryFileName+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/blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);;
- blastCommand += (" -i " + (queryFileName+seq->getName()) + " -o " + blastFileName+seq->getName());
+ 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));
#else
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());
+ blastCommand += (" -i " + (queryFileName+toString(randNumber)) + " -o " + blastFileName+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(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(randNumber)).c_str());
+ remove((blastFileName+toString(randNumber)).c_str());
return topMatches;
}
Scores.clear();
ofstream queryFile;
-
- m->openOutputFile((queryFileName+seq->getName()), queryFile);
+ int randNumber = rand();
+ //int randNumber = 12345;
+ m->openOutputFile((queryFileName+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+seq->getName()) + " -o " + blastFileName+seq->getName());
+ blastCommand += (" -i " + (queryFileName+toString(randNumber)) + " -o " + blastFileName+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+seq->getName()) + " -o " + blastFileName+seq->getName());
+ blastCommand += (" -i " + (queryFileName+toString(randNumber)) + " -o " + blastFileName+toString(randNumber));
//wrap entire string in ""
blastCommand = "\"" + blastCommand + "\"";
#endif
-
+ //cout << blastCommand << endl;
system(blastCommand.c_str());
ifstream m8FileHandle;
- m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
+ m->openInputFile(blastFileName+toString(randNumber), m8FileHandle, "no error");
string dummy, eScore;
int templateAccession;
//cout << templateAccession << endl;
}
m8FileHandle.close();
- remove((queryFileName+seq->getName()).c_str());
- remove((blastFileName+seq->getName()).c_str());
+ remove((queryFileName+toString(randNumber)).c_str());
+ remove((blastFileName+toString(randNumber)).c_str());
//cout << "\n" ;
return topMatches;
}
#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();