X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makebiomcommand.cpp;h=03e7baf2b9888fc7f52cbe6076ea8fdfa472b584;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=41f2316b3a036840208635d3abbacd89e59f6413;hpb=7dab6ac3ae5a5f1ce37dca8cfacaa719881fd5b2;p=mothur.git

diff --git a/makebiomcommand.cpp b/makebiomcommand.cpp
index 41f2316..03e7baf 100644
--- a/makebiomcommand.cpp
+++ b/makebiomcommand.cpp
@@ -112,12 +112,12 @@ vector<string> MakeBiomCommand::setParameters(){
 string MakeBiomCommand::getHelpString(){	
 	try {
 		string helpString = "";
-		helpString += "The make.biom command parameters are shared, groups, matrixtype and label.  shared is required, unless you have a valid current file.\n";
+		helpString += "The make.biom command parameters are shared, contaxonomy, groups, matrixtype and label.  shared is required, unless you have a valid current file.\n";
 		helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n";
 		helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";
 		helpString += "The matrixtype parameter allows you to select what type you would like to make. Choices are sparse and dense, default is sparse.\n";
+        helpString += "The contaxonomy file is the taxonomy file outputted by classify.otu(list=yourListfile, taxonomy=yourTaxonomyFile). Be SURE that the you are the constaxonomy file distance matches the shared file distance.  ie, for *.0.03.cons.taxonomy set label=0.03. Mothur is smart enough to handle shared files that have been subsampled.\n";
 		helpString += "The make.biom command should be in the following format: make.biom(shared=yourShared, groups=yourGroups, label=yourLabels).\n";
-        helpString += "The contaxonomy file is the taxonomy file outputted by classify.otu(list=yourListfile, taxonomy=yourTaxonomyFile). Be SURE that the you are the constaxonomy file distance matches the shared file distance.  ie, for *.0.03.cons.taxonomy set label=0.03. Mothur is smart enough to handle shared files that have been subsampled after the classify.otu command was run on the list and taxonomy file.\n";
 		helpString += "Example make.biom(shared=abrecovery.an.shared, groups=A-B-C).\n";
 		helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
 		helpString += "The make.biom command outputs a .biom file.\n";
@@ -165,10 +165,10 @@ MakeBiomCommand::MakeBiomCommand(string option) {
 			for (it = parameters.begin(); it != parameters.end(); it++) { 
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
-			
+
 			//initialize outputTypes
 			vector<string> tempOutNames;
-			outputTypes["relabund"] = tempOutNames;
+			outputTypes["biom"] = tempOutNames;
 			
 			//if the user changes the input directory command factory will send this info to us in the output parameter 
 			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
@@ -328,6 +328,14 @@ int MakeBiomCommand::execute(){
 		
         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); }  return 0; }     
 		
+        //set sabund file as new current sabundfile
+        string current = "";
+		itTypes = outputTypes.find("biom");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setBiomFile(current); }
+		}
+
+        
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}
@@ -604,7 +612,7 @@ vector<string> MakeBiomCommand::parseTax(string tax, vector<string>& scores) {
                         scores.push_back(confidenceScore);
 					}else{ scores.push_back("null"); }
 				}
-			}
+			}else{ scores.push_back("null"); }
 			
             //strip "" if they are there
             pos = taxon.find("\"");