X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyseqscommand.cpp;h=a95f436dd7ffdf4403d316be77a1f8ab580f21f5;hb=9013e13ecfb2fda3c2664a76f76cc99b8c7fa74c;hp=0635fdeb4cd9a72de87d786d6a0aa30056b99a7d;hpb=cd4c86f68cb53017f0f98a82dd2c2e56a64c67bd;p=mothur.git

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 0635fde..a95f436 100644
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -399,10 +399,15 @@ int ClassifySeqsCommand::execute(){
 		
 			m->mothurOut("Classifying sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 			
+			string RippedTaxName = getRootName(getSimpleName(taxonomyFileName));
+			RippedTaxName = getExtension(RippedTaxName.substr(0, RippedTaxName.length()-1));
+			if (RippedTaxName[0] == '.') { RippedTaxName = RippedTaxName.substr(1, RippedTaxName.length()); }
+			RippedTaxName +=  "."; 
+		
 			if (outputDir == "") { outputDir += hasPath(fastaFileNames[s]); }
-			string newTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + getRootName(getSimpleName(taxonomyFileName)) + "taxonomy";
+			string newTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + RippedTaxName + "taxonomy";
 			string tempTaxonomyFile = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + "taxonomy.temp";
-			string taxSummary = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + getRootName(getSimpleName(taxonomyFileName)) + "tax.summary";
+			string taxSummary = outputDir + getRootName(getSimpleName(fastaFileNames[s])) + RippedTaxName + "tax.summary";
 			
 			outputNames.push_back(newTaxonomyFile);
 			outputNames.push_back(taxSummary);