From: Sarah Westcott <mothur.westcott@gmail.com>
Date: Mon, 5 Mar 2012 14:59:50 +0000 (-0500)
Subject: fixed classify.seq error message when flip accnos file was blank. Fixed bug with... 
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=a626c629e4d4840cd2ce04d98055dcfef1f8593a

fixed classify.seq error message when flip accnos file was blank. Fixed bug with phylotype command related to the addition of "unknown" classification in phylotree.
---

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 794b961..72acd22 100644
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -905,16 +905,35 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
 		}
 		
 	#endif	
-		
+        vector<string> nonBlankAccnosFiles;
+		if (!(m->isBlank(accnos))) { nonBlankAccnosFiles.push_back(accnos); }
+		else { m->mothurRemove(accnos); } //remove so other files can be renamed to it
+        
 		for(int i=0;i<processIDS.size();i++){
 			appendTaxFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
 			appendTaxFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
-			appendTaxFiles((accnos + toString(processIDS[i]) + ".temp"), accnos);
+            if (!(m->isBlank(accnos + toString(processIDS[i]) + ".temp"))) {
+				nonBlankAccnosFiles.push_back(accnos + toString(processIDS[i]) + ".temp");
+			}else { m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));  }
+
 			m->mothurRemove((m->getFullPathName(taxFileName) + toString(processIDS[i]) + ".temp"));
 			m->mothurRemove((m->getFullPathName(tempTaxFile) + toString(processIDS[i]) + ".temp"));
-			m->mothurRemove((m->getFullPathName(accnos) + toString(processIDS[i]) + ".temp"));
 		}
 		
+        //append accnos files
+		if (nonBlankAccnosFiles.size() != 0) { 
+			rename(nonBlankAccnosFiles[0].c_str(), accnos.c_str());
+			
+			for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
+				appendTaxFiles(nonBlankAccnosFiles[h], accnos);
+				m->mothurRemove(nonBlankAccnosFiles[h]);
+			}
+		}else { //recreate the accnosfile if needed
+			ofstream out;
+			m->openOutputFile(accnos, out);
+			out.close();
+		}
+
 		return num;
 		
 	}
diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index 1d6c391..f402f2a 100644
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -244,13 +244,15 @@ int PhylotypeCommand::execute(){
 					//make the names compatable with listvector
 					string name = "";
 					for (int i = 0; i < names.size(); i++) {  
-						if (namefile != "") {	
-							map<string, string>::iterator itNames = namemap.find(names[i]);  //make sure this name is in namefile
-		
-							if (itNames != namemap.end()) {  name += namemap[names[i]] + ",";   } //you found it in namefile
-							else { m->mothurOut(names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); exit(1);  }
-							
-						}else{   name += names[i] + ",";	}
+                        if (names[i] != "unknown") {
+                            if (namefile != "") {	
+                                map<string, string>::iterator itNames = namemap.find(names[i]);  //make sure this name is in namefile
+                                
+                                if (itNames != namemap.end()) {  name += namemap[names[i]] + ",";   } //you found it in namefile
+                                else { m->mothurOut(names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); exit(1);  }
+                                
+                            }else{   name += names[i] + ",";	}
+                        }
 					}
 					name = name.substr(0, name.length()-1);  //rip off extra ','