queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
blastFileName = toString(randNumber) + ".blast";
+}
+/**************************************************************************************************/
+
+BlastDB::BlastDB() : Database() {
+
+ globaldata = GlobalData::getInstance();
+ count = 0;
+
+ int randNumber = rand();
+ dbFileName = toString(randNumber) + ".template.unaligned.fasta";
+ queryFileName = toString(randNumber) + ".candidate.unaligned.fasta";
+ blastFileName = toString(randNumber) + ".blast";
+
}
/**************************************************************************************************/
}
m8FileHandle.close();
- string root = dbFileName;
- string temp = dbFileName + ".nsq";
- remove(temp.c_str());
- temp = dbFileName + ".nsi";
- remove(temp.c_str());
-
- temp = dbFileName + ".nsd";
- remove(temp.c_str());
-
- temp = dbFileName + ".nin";
- remove(temp.c_str());
-
- temp = dbFileName + ".nhr";
- remove(temp.c_str());
-
-
-
return topMatches;
}
catch(exception& e) {
- errorOut(e, "BlastDB", "findClosestSequences");
+ m->errorOut(e, "BlastDB", "findClosestSequences");
exit(1);
}
system(blastCommand.c_str());
ifstream m8FileHandle;
- openInputFile(blastFileName, m8FileHandle);
+ openInputFile(blastFileName, m8FileHandle, "no error");
string dummy;
int templateAccession;
gobble(m8FileHandle);
topMatches.push_back(templateAccession);
+//cout << templateAccession << endl;
}
m8FileHandle.close();
-
+//cout << "\n\n" ;
return topMatches;
}
catch(exception& e) {
- errorOut(e, "BlastDB", "findClosest");
+ m->errorOut(e, "BlastDB", "findClosest");
exit(1);
}
}
unalignedFastaFile << '>' << count << endl; // sequences, which will be input to formatdb
unalignedFastaFile << seq.getUnaligned() << endl;
unalignedFastaFile.close();
-
+
count++;
}
catch(exception& e) {
- errorOut(e, "BlastDB", "addSequence");
+ m->errorOut(e, "BlastDB", "addSequence");
exit(1);
}
}
void BlastDB::generateDB() {
try {
- //mothurOut("Generating the temporary BLAST database...\t"); cout.flush();
+ //m->mothurOut("Generating the temporary BLAST database...\t"); cout.flush();
path = globaldata->argv;
path = path.substr(0, (path.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
system(formatdbCommand.c_str()); // to get the right sequence names, i think. -p F
// option tells formatdb that seqs are DNA, not prot
- //mothurOut("DONE."); mothurOutEndLine(); mothurOutEndLine(); cout.flush();
+ //m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine(); cout.flush();
}
catch(exception& e) {
- errorOut(e, "BlastDB", "generateDB");
+ m->errorOut(e, "BlastDB", "generateDB");
exit(1);
}
}
+/**************************************************************************************************/
/**************************************************************************************************/