X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitabundcommand.cpp;h=287086a28a3b0b1ecc18b3988f68ef41ec1909dc;hb=0fb6d165c8dc8dc7153a101513a05f457431d0bc;hp=f86891bde47d6817a3d65651b989f24c7533ea30;hpb=2a7d1455e8cfe4f67a7173f3a7249762c5436217;p=mothur.git

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index f86891b..287086a 100644
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -20,7 +20,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
 		
 		else {
 			//valid paramters for this command
-			string Array[] =  {"name","group","label","accnos","groups","fasta","cutoff","outputdir","inputdir"}; //"list",
+			string Array[] =  {"name","group","list","label","accnos","groups","fasta","cutoff","outputdir","inputdir"}; //
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
 			OptionParser parser(option);
@@ -146,7 +146,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
 void SplitAbundCommand::help(){
 	try {
 		m->mothurOut("The split.abund command reads a fasta file and a list or a names file splits the sequences into rare and abundant groups. \n");
-		m->mothurOut("The split.abund command parameters are list, name, cutoff, group, label, groups and accnos.\n");
+		m->mothurOut("The split.abund command parameters are fasta, list, name, cutoff, group, label, groups, cutoff and accnos.\n");
 		m->mothurOut("The fasta and a list or name parameter are required, and you must provide a cutoff value.\n");
 		m->mothurOut("The cutoff parameter is used to qualify what is abundant and rare.\n");
 		m->mothurOut("The group parameter allows you to parse a group file into rare and abundant groups.\n");
@@ -155,8 +155,8 @@ void SplitAbundCommand::help(){
 		m->mothurOut("The groups parameter allows you to parse the files into rare and abundant files by group.  \n");
 		m->mothurOut("For example if you set groups=A-B-C, you will get a .A.abund, .A.rare, .B.abund, .B.rare, .C.abund, .C.rare files.  \n");
 		m->mothurOut("If you want .abund and .rare files for all groups, set groups=all.  \n");
-		m->mothurOut("The split.abund command should be used in the following format: split.abund(list=yourListFile, group=yourGroupFile, label=yourLabels, cutoff=yourCutoff).\n");
-		m->mothurOut("Example: split.abundt(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, cutoff=2).\n");
+		m->mothurOut("The split.abund command should be used in the following format: split.abund(fasta=yourFasta, list=yourListFile, group=yourGroupFile, label=yourLabels, cutoff=yourCutoff).\n");
+		m->mothurOut("Example: split.abund(fasta=abrecovery.fasta, list=abrecovery.fn.list, group=abrecovery.groups, label=0.03, cutoff=2).\n");
 		m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
 
 	}
@@ -278,6 +278,9 @@ int SplitAbundCommand::execute(){
 			
 			for (map<string, bool>::iterator itBool = wroteListFile.begin(); itBool != wroteListFile.end(); itBool++) {
 				string filename = fileroot + itBool->first;
+				if ((itBool->first == "rare") || (itBool->first == "abund")) {
+					filename = fileroot + itBool->first + ".list";
+				}
 				if (itBool->second) { //we wrote to this file
 					outputNames.push_back(filename);
 				}else{
@@ -373,17 +376,17 @@ int SplitAbundCommand::writeList(ListVector* thisList) {
 			ofstream rout;
 			
 			if (rareNames.size() != 0) {
-				string rare = outputDir + getRootName(getSimpleName(listfile))  + ".rare.list";
+				string rare = outputDir + getRootName(getSimpleName(listfile))  + "rare.list";
 				wroteListFile["rare"] = true;
 				openOutputFileAppend(rare, rout);
 				rout << thisList->getLabel() << '\t' << numRareBins << '\t';
 			}
 			
 			if (abundNames.size() != 0) {
-				string abund = outputDir + getRootName(getSimpleName(listfile))  + ".abund.list";
+				string abund = outputDir + getRootName(getSimpleName(listfile))  + "abund.list";
 				wroteListFile["abund"] = true;
 				openOutputFileAppend(abund, aout);
-				rout << thisList->getLabel() << '\t' << numAbundBins << '\t';
+				aout << thisList->getLabel() << '\t' << numAbundBins << '\t';
 			}
 
 			for (int i = 0; i < thisList->getNumBins(); i++) {