}
}
-
}
catch(exception& e) {
m->errorOut(e, "ClassifySeqsCommand", "ClassifySeqsCommand");
int ClassifySeqsCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
+
if(method == "bayesian"){ classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip); }
else if(method == "knn"){ classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted, rand()); }
else {
string RippedTaxName = m->getRootName(m->getSimpleName(baseTName));
RippedTaxName = m->getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1));
if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); }
- RippedTaxName += ".";
-
+ if (RippedTaxName != "") { RippedTaxName += "."; }
+
if (outputDir == "") { outputDir += m->hasPath(fastaFileNames[s]); }
string newTaxonomyFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "taxonomy";
string newaccnosFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + RippedTaxName + "flip.accnos";