From: westcott <westcott>
Date: Wed, 3 Jun 2009 12:37:21 +0000 (+0000)
Subject: added get.rabund and get.sabund command and fixed bug introduced by line by line... 
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=0024441c1ff9a98467ba53cc7420a37c98f32e86

added get.rabund and get.sabund command and fixed bug introduced by line by line optimization
---

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 245ed55..34dacfa 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -35,6 +35,8 @@
 		3746107E0F4064D100460C57 /* weighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746107D0F4064D100460C57 /* weighted.cpp */; };
 		374610830F40652400460C57 /* unweighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374610820F40652400460C57 /* unweighted.cpp */; };
 		3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */; };
+		3749271D0FD58C840031C06B /* getsabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3749271C0FD58C840031C06B /* getsabundcommand.cpp */; };
+		3749273F0FD5956B0031C06B /* getrabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */; };
 		37519A6B0F80E6EB00FED5E8 /* sharedanderbergs.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */; };
 		37519AA10F810D0200FED5E8 /* venncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519AA00F810D0200FED5E8 /* venncommand.cpp */; };
 		37519AB50F810FAE00FED5E8 /* venn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519AB40F810FAE00FED5E8 /* venn.cpp */; };
@@ -67,6 +69,8 @@
 		379294700F2E191800B9034A /* parsimonycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3792946F0F2E191800B9034A /* parsimonycommand.cpp */; };
 		3792948A0F2E258500B9034A /* parsimony.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379294890F2E258500B9034A /* parsimony.cpp */; };
 		379643ED0FB9B5A80081FDB6 /* readseqs.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379643EB0FB9B5A80081FDB6 /* readseqs.cpp */; };
+		3799A9500FD6A58C00E33EDE /* distancedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3799A94C0FD6A58C00E33EDE /* distancedb.cpp */; };
+		3799A9510FD6A58C00E33EDE /* seqsummarycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */; };
 		37AD4CE40F28AEA300AA2D49 /* sharedlistvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */; };
 		37AD4DBB0F28E2FE00AA2D49 /* tree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */; };
 		37AD4DCA0F28F3DD00AA2D49 /* readtree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */; };
@@ -145,7 +149,6 @@
 		7E412F490F8D21B600381DD0 /* slibshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E412F480F8D21B600381DD0 /* slibshuff.cpp */; };
 		7E412FEA0F8D3E2C00381DD0 /* libshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */; };
 		7E4130F80F8E58FA00381DD0 /* dlibshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */; };
-		7E9214820FD2081200699BF3 /* seqsummarycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E9214810FD2081200699BF3 /* seqsummarycommand.cpp */; };
 		7EC3D4550FA0FFF900338DA5 /* coverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7EC3D4500FA0FFF900338DA5 /* coverage.cpp */; };
 		7EC3D4560FA0FFF900338DA5 /* whittaker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */; };
 		8DD76F6A0486A84900D96B5E /* Mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6859E8B029090EE04C91782 /* Mothur.1 */; };
@@ -230,6 +233,10 @@
 		374610820F40652400460C57 /* unweighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unweighted.cpp; sourceTree = SOURCE_ROOT; };
 		3746109B0F40657600460C57 /* unifracunweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracunweightedcommand.h; sourceTree = SOURCE_ROOT; };
 		3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracunweightedcommand.cpp; sourceTree = SOURCE_ROOT; };
+		3749271B0FD58C840031C06B /* getsabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsabundcommand.h; sourceTree = "<group>"; };
+		3749271C0FD58C840031C06B /* getsabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsabundcommand.cpp; sourceTree = "<group>"; };
+		3749273D0FD5956B0031C06B /* getrabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getrabundcommand.h; sourceTree = "<group>"; };
+		3749273E0FD5956B0031C06B /* getrabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getrabundcommand.cpp; sourceTree = "<group>"; };
 		37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderbergs.h; sourceTree = SOURCE_ROOT; };
 		37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedanderbergs.cpp; sourceTree = SOURCE_ROOT; };
 		37519A9F0F810D0200FED5E8 /* venncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venncommand.h; sourceTree = SOURCE_ROOT; };
@@ -298,6 +305,10 @@
 		3792948D0F2E271100B9034A /* treecalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treecalculator.h; sourceTree = SOURCE_ROOT; };
 		379643EB0FB9B5A80081FDB6 /* readseqs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readseqs.cpp; sourceTree = SOURCE_ROOT; };
 		379643EC0FB9B5A80081FDB6 /* readseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readseqs.h; sourceTree = SOURCE_ROOT; };
+		3799A94C0FD6A58C00E33EDE /* distancedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancedb.cpp; sourceTree = "<group>"; };
+		3799A94D0FD6A58C00E33EDE /* distancedb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = distancedb.hpp; sourceTree = "<group>"; };
+		3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqsummarycommand.cpp; sourceTree = "<group>"; };
+		3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqsummarycommand.h; sourceTree = "<group>"; };
 		37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlistvector.h; sourceTree = SOURCE_ROOT; };
 		37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlistvector.cpp; sourceTree = SOURCE_ROOT; };
 		37AD4DB90F28E2FE00AA2D49 /* tree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tree.h; sourceTree = SOURCE_ROOT; };
@@ -469,8 +480,6 @@
 		7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuff.cpp; sourceTree = SOURCE_ROOT; };
 		7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dlibshuff.cpp; sourceTree = SOURCE_ROOT; };
 		7E4130F70F8E58FA00381DD0 /* dlibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dlibshuff.h; sourceTree = SOURCE_ROOT; };
-		7E9214800FD2081200699BF3 /* seqsummarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqsummarycommand.h; sourceTree = "<group>"; };
-		7E9214810FD2081200699BF3 /* seqsummarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqsummarycommand.cpp; sourceTree = "<group>"; };
 		7EC3D4500FA0FFF900338DA5 /* coverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = coverage.cpp; sourceTree = SOURCE_ROOT; };
 		7EC3D4510FA0FFF900338DA5 /* coverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = coverage.h; sourceTree = SOURCE_ROOT; };
 		7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderberg.h; sourceTree = SOURCE_ROOT; };
@@ -747,8 +756,6 @@
 		37D928A90F2133E5001D4494 /* commands */ = {
 			isa = PBXGroup;
 			children = (
-				7E9214800FD2081200699BF3 /* seqsummarycommand.h */,
-				7E9214810FD2081200699BF3 /* seqsummarycommand.cpp */,
 				37D927CD0F21331F001D4494 /* command.hpp */,
 				378DC5CD0FBDE1C8003B8607 /* aligncommand.h */,
 				378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */,
@@ -778,6 +785,10 @@
 				A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
 				370B88050F8A4EE4005AB382 /* getoturepcommand.h */,
 				370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */,
+				3749273D0FD5956B0031C06B /* getrabundcommand.h */,
+				3749273E0FD5956B0031C06B /* getrabundcommand.cpp */,
+				3749271B0FD58C840031C06B /* getsabundcommand.h */,
+				3749271C0FD58C840031C06B /* getsabundcommand.cpp */,
 				375873F10F7D64800040F377 /* heatmapcommand.h */,
 				375873F00F7D64800040F377 /* heatmapcommand.cpp */,
 				37D927E40F21331F001D4494 /* helpcommand.h */,
@@ -804,6 +815,8 @@
 				372E126F0F26365B0095CF7E /* readotucommand.cpp */,
 				37E5F4900F2A3DA800F8D827 /* readtreecommand.h */,
 				37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */,
+				3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */,
+				3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */,
 				37D928270F21331F001D4494 /* sharedcommand.h */,
 				37D928260F21331F001D4494 /* sharedcommand.cpp */,
 				37D928470F21331F001D4494 /* summarycommand.h */,
@@ -834,6 +847,8 @@
 				37D927D40F21331F001D4494 /* database.hpp */,
 				37D927D30F21331F001D4494 /* database.cpp */,
 				37D927D50F21331F001D4494 /* datavector.hpp */,
+				3799A94C0FD6A58C00E33EDE /* distancedb.cpp */,
+				3799A94D0FD6A58C00E33EDE /* distancedb.hpp */,
 				37D927DC0F21331F001D4494 /* fastamap.h */,
 				37D927DB0F21331F001D4494 /* fastamap.cpp */,
 				375873EA0F7D64520040F377 /* fullmatrix.h */,
@@ -1098,7 +1113,10 @@
 				373C699C0FC1E63600137ACD /* solow.cpp in Sources */,
 				EB72FE260FC1F5CA0051AC11 /* shen.cpp in Sources */,
 				21E859D80FC4632E005E1A48 /* matrixoutputcommand.cpp in Sources */,
-				7E9214820FD2081200699BF3 /* seqsummarycommand.cpp in Sources */,
+				3749271D0FD58C840031C06B /* getsabundcommand.cpp in Sources */,
+				3749273F0FD5956B0031C06B /* getrabundcommand.cpp in Sources */,
+				3799A9500FD6A58C00E33EDE /* distancedb.cpp in Sources */,
+				3799A9510FD6A58C00E33EDE /* seqsummarycommand.cpp in Sources */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
 		};
diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index c217578..8f0bb9f 100644
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -77,9 +77,10 @@ int BinSeqCommand::execute(){
 		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 		set<string> processedLabels;
 		set<string> userLabels = globaldata->labels;
+		set<int> userLines = globaldata->lines;
 
 				
-		while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+		while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 			
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(list->getLabel()) == 1){
 				
@@ -88,7 +89,7 @@ int BinSeqCommand::execute(){
 							
 				processedLabels.insert(list->getLabel());
 				userLabels.erase(list->getLabel());
-
+				userLines.erase(count);
 			}
 			
 			if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp
index 2835061..9ffd2b7 100644
--- a/bootstrapsharedcommand.cpp
+++ b/bootstrapsharedcommand.cpp
@@ -104,6 +104,7 @@ int BootSharedCommand::execute(){
 		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 		set<string> processedLabels;
 		set<string> userLabels = globaldata->labels;
+		set<int> userLines = globaldata->lines;
 				
 		//set users groups
 		util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "treegroup");
@@ -120,7 +121,7 @@ int BootSharedCommand::execute(){
 		tmap->makeSim(globaldata->gGroupmap);
 		globaldata->gTreemap = tmap;
 			
-		while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+		while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 		
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){			
 				
@@ -129,10 +130,10 @@ int BootSharedCommand::execute(){
 				
 				processedLabels.insert(order->getLabel());
 				userLabels.erase(order->getLabel());
-				
-			//you have a label the user want that is smaller than this line and the last line has not already been processed 
+				userLines.erase(count);
 			}
 			
+			//you have a label the user want that is smaller than this line and the last line has not already been processed
 			if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
 											
 				cout << lastOrder->getLabel() << '\t' << count << endl;
diff --git a/collectcommand.cpp b/collectcommand.cpp
index 01f2fff..3d7f1b0 100644
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -133,8 +133,9 @@ int CollectCommand::execute(){
 		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 		set<string> processedLabels;
 		set<string> userLabels = globaldata->labels;
+		set<int> userLines = globaldata->lines;
 		
-		while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+		while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 		
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 				
@@ -145,6 +146,7 @@ int CollectCommand::execute(){
 				cout << order->getLabel() << '\t' << count << endl;
 				processedLabels.insert(order->getLabel());
 				userLabels.erase(order->getLabel());
+				userLines.erase(count);
 			
 			//you have a label the user want that is smaller than this line and the last line has not already been processed 
 			}
diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index fd28e84..d2333d7 100644
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -140,12 +140,13 @@ int CollectSharedCommand::execute(){
 		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 		set<string> processedLabels;
 		set<string> userLabels = globaldata->labels;
+		set<int> userLines = globaldata->lines;
 				
 		//set users groups
 		util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "collect");
 		util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
 
-		while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+		while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 				
@@ -157,6 +158,7 @@ int CollectSharedCommand::execute(){
 				cout << order->getLabel() << '\t' << count << endl;
 				processedLabels.insert(order->getLabel());
 				userLabels.erase(order->getLabel());
+				userLines.erase(count);
 
 			//you have a label the user want that is smaller than this line and the last line has not already been processed 
 			}
diff --git a/commandfactory.cpp b/commandfactory.cpp
index 0edb024..9b64118 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -43,8 +43,11 @@
 #include "distancecommand.h"
 #include "aligncommand.h"
 #include "matrixoutputcommand.h"
+#include "getsabundcommand.h"
+#include "getrabundcommand.h"
 #include "seqsummarycommand.h"
 
+
 /***********************************************************/
 
 /***********************************************************/
@@ -85,6 +88,8 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "get.group")             {   command = new GetgroupCommand();			}
 		else if(commandName == "get.label")             {   command = new GetlabelCommand();			}
 		else if(commandName == "get.line")              {   command = new GetlineCommand();				}
+		else if(commandName == "get.sabund")            {   command = new GetSAbundCommand();			}
+		else if(commandName == "get.rabund")            {   command = new GetRAbundCommand();			}
 		else if(commandName == "libshuff")              {   command = new LibShuffCommand();			}
 		else if(commandName == "heatmap")				{   command = new HeatMapCommand();				}
 		else if(commandName == "filter.seqs")			{   command = new FilterSeqsCommand();          }
diff --git a/errorchecking.cpp b/errorchecking.cpp
index 39fb17e..0652492 100644
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -246,10 +246,18 @@ bool ErrorCheck::checkInput(string input) {
 			else {cout << "Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average." << endl; return false; }
 		}
 		
-		if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){ 
+		if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")){ 
 			if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the collect.single, rarefaction.single or summary.single commands." << endl; return false; }
 		}
 		
+		if (commandName == "get.rabund") {
+			if (globaldata->getListFile() == "") { cout << "You must read a listfile before you can use the get.rabund command." << endl; return false; }
+		}
+		
+		if (commandName == "get.sabund") {
+			if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { cout << "You must read a list or rabund before you can use the get.sabund command." << endl; return false; }
+		}
+		
 		if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")){ 
 			if (globaldata->getSharedFile() == "") {
 				if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared, summary.shared, tree.shared, bootstrap.shared or dist.shared commands." << endl; return false; }
diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index acb9372..eb88fbf 100644
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -99,9 +99,10 @@ int GetOTURepCommand::execute(){
 		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 		set<string> processedLabels;
 		set<string> userLabels = globaldata->labels;
+		set<int> userLines = globaldata->lines;
 
 		
-		while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+		while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 			
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(list->getLabel()) == 1){
 					cout << list->getLabel() << '\t' << count << endl;
@@ -110,6 +111,7 @@ int GetOTURepCommand::execute(){
 					
 					processedLabels.insert(list->getLabel());
 					userLabels.erase(list->getLabel());
+					userLines.erase(count);
 			}
 			
 			if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
new file mode 100644
index 0000000..b0f7a92
--- /dev/null
+++ b/getrabundcommand.cpp
@@ -0,0 +1,128 @@
+/*
+ *  getrabundcommand.cpp
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 6/2/09.
+ *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "getrabundcommand.h"
+
+//**********************************************************************************************************************
+
+GetRAbundCommand::GetRAbundCommand(){
+	try {
+		globaldata = GlobalData::getInstance();
+		filename = getRootName(globaldata->inputFileName) + "rabund";
+		
+		openOutputFile(filename, out);
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the GetRAbundCommand class Function GetRAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the GetRAbundCommand class function GetRAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+			
+}
+
+//**********************************************************************************************************************
+
+GetRAbundCommand::~GetRAbundCommand(){
+}
+
+//**********************************************************************************************************************
+
+int GetRAbundCommand::execute(){
+	try {
+		int count = 1;
+		
+		//read first line
+		read = new ReadOTUFile(globaldata->inputFileName);	
+		read->read(&*globaldata); 
+			
+		input = globaldata->ginput;
+		list = globaldata->gListVector;
+		ListVector* lastList = list;
+		
+		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+		set<string> processedLabels;
+		set<string> userLabels = globaldata->labels;
+		set<int> userLines = globaldata->lines;
+
+		
+		while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+			
+			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(list->getLabel()) == 1){
+					cout << list->getLabel() << '\t' << count << endl;
+					rabund = new RAbundVector();
+					*rabund = (list->getRAbundVector());
+					rabund->print(out);
+					delete rabund;
+															
+					processedLabels.insert(list->getLabel());
+					userLabels.erase(list->getLabel());
+					userLines.erase(count);
+			}
+			
+			if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
+					cout << lastList->getLabel() << '\t' << count << endl;
+					rabund = new RAbundVector();
+					*rabund = (lastList->getRAbundVector());
+					rabund->print(out);
+					delete rabund;
+
+					processedLabels.insert(lastList->getLabel());
+					userLabels.erase(lastList->getLabel());
+			}
+			
+			if (count != 1) { delete lastList; }
+			lastList = list;			
+			
+			list = input->getListVector();
+			count++;
+		}
+		
+		//output error messages about any remaining user labels
+		set<string>::iterator it;
+		bool needToRun = false;
+		for (it = userLabels.begin(); it != userLabels.end(); it++) {  
+			cout << "Your file does not include the label "<< *it; 
+			if (processedLabels.count(lastList->getLabel()) != 1) {
+				cout << ". I will use " << lastList->getLabel() << "." << endl;
+				needToRun = true;
+			}else {
+				cout << ". Please refer to " << lastList->getLabel() << "." << endl;
+			}
+		}
+		
+		//run last line if you need to
+		if (needToRun == true)  {
+			cout << lastList->getLabel() << '\t' << count << endl;
+			rabund = new RAbundVector();
+			*rabund = (lastList->getRAbundVector());
+			rabund->print(out);
+			delete rabund;
+		}
+		delete lastList;
+
+		out.close(); 
+		return 0;		
+	}
+
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the GetRAbundCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the GetRAbundCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
+
+//**********************************************************************************************************************
+
+
diff --git a/getrabundcommand.h b/getrabundcommand.h
new file mode 100644
index 0000000..66a3211
--- /dev/null
+++ b/getrabundcommand.h
@@ -0,0 +1,38 @@
+#ifndef GETRABUNDCOMMAND_H
+#define GETRABUNDCOMMAND_H
+
+/*
+ *  getrabundcommand.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 6/2/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "inputdata.h"
+#include "readotu.h"
+#include "listvector.hpp"
+
+class GlobalData;
+
+class GetRAbundCommand : public Command {
+public:
+	GetRAbundCommand();
+	~GetRAbundCommand();
+	int execute();
+	
+private:
+	GlobalData* globaldata;
+	string filename;
+	ofstream out;
+	ReadOTUFile* read;
+	InputData* input;
+	ListVector* list;
+	RAbundVector* rabund;
+};
+
+#endif
+
diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
new file mode 100644
index 0000000..8c7f07c
--- /dev/null
+++ b/getsabundcommand.cpp
@@ -0,0 +1,128 @@
+/*
+ *  getsabundcommand.cpp
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 6/2/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "getsabundcommand.h"
+
+//**********************************************************************************************************************
+
+GetSAbundCommand::GetSAbundCommand(){
+	try {
+		globaldata = GlobalData::getInstance();
+		filename = getRootName(globaldata->inputFileName) + "sabund";
+		
+		openOutputFile(filename, out);
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function GetSAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the GetSAbundCommand class function GetSAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+			
+}
+
+//**********************************************************************************************************************
+
+GetSAbundCommand::~GetSAbundCommand(){
+}
+
+//**********************************************************************************************************************
+
+int GetSAbundCommand::execute(){
+	try {
+		int count = 1;
+		
+		//using order vector so you don't have to distinguish between the list and rabund files
+		read = new ReadOTUFile(globaldata->inputFileName);	
+		read->read(&*globaldata); 
+		
+		order = globaldata->gorder;
+		lastOrder = order;
+		input = globaldata->ginput;
+						
+		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+		set<string> processedLabels;
+		set<string> userLabels = globaldata->labels;
+		set<int> userLines = globaldata->lines;
+
+		
+		while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+			
+			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+					cout << order->getLabel() << '\t' << count << endl;
+					sabund = new SAbundVector();
+					*sabund = (order->getSAbundVector());
+					sabund->print(out);
+					delete sabund;
+
+					processedLabels.insert(order->getLabel());
+					userLabels.erase(order->getLabel());
+					userLines.erase(count);
+			}
+			
+			if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
+					cout << lastOrder->getLabel() << '\t' << count << endl;
+					sabund = new SAbundVector();
+					*sabund = (lastOrder->getSAbundVector());
+					sabund->print(out);
+					delete sabund;
+
+					processedLabels.insert(lastOrder->getLabel());
+					userLabels.erase(lastOrder->getLabel());
+			}
+			
+			if (count != 1) { delete lastOrder; }
+			lastOrder = order;	
+					
+			order = (input->getOrderVector());
+			count++;
+		}
+		
+		//output error messages about any remaining user labels
+		set<string>::iterator it;
+		bool needToRun = false;
+		for (it = userLabels.begin(); it != userLabels.end(); it++) {  
+			cout << "Your file does not include the label "<< *it; 
+			if (processedLabels.count(lastOrder->getLabel()) != 1) {
+				cout << ". I will use " << lastOrder->getLabel() << "." << endl;
+				needToRun = true;
+			}else {
+				cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
+			}
+		}
+		
+		//run last line if you need to
+		if (needToRun == true)  {
+			cout << lastOrder->getLabel() << '\t' << count << endl;
+			sabund = new SAbundVector();
+			*sabund = (lastOrder->getSAbundVector());
+			sabund->print(out);
+			delete sabund;
+		}
+		delete lastOrder;
+
+		out.close();
+		return 0;		
+	}
+
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the GetSAbundCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
+
+//**********************************************************************************************************************
+
+
diff --git a/getsabundcommand.h b/getsabundcommand.h
new file mode 100644
index 0000000..27d25c2
--- /dev/null
+++ b/getsabundcommand.h
@@ -0,0 +1,38 @@
+#ifndef GETSABUNDCOMMAND_H
+#define GETSABUNDCOMMAND_H
+
+/*
+ *  getsabundcommand.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 6/2/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "inputdata.h"
+#include "readotu.h"
+#include "sabundvector.hpp"
+
+class GlobalData;
+
+class GetSAbundCommand : public Command {
+public:
+	GetSAbundCommand();
+	~GetSAbundCommand();
+	int execute();
+	
+private:
+	GlobalData* globaldata;
+	string filename, format;
+	ofstream out;
+	ReadOTUFile* read;
+	OrderVector* order;
+	OrderVector* lastOrder;
+	InputData* input;
+	SAbundVector* sabund;
+};
+
+#endif
diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index c9f6ae5..e99537d 100644
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -64,11 +64,12 @@ int HeatMapCommand::execute(){
 		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 		set<string> processedLabels;
 		set<string> userLabels = globaldata->labels;
+		set<int> userLines = globaldata->lines;
 
 		if (format != "list") {	
 		
 			//as long as you are not at the end of the file or done wih the lines you want
-			while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+			while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 		
 				if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){			
 	
@@ -77,6 +78,7 @@ int HeatMapCommand::execute(){
 					
 					processedLabels.insert(lookup[0]->getLabel());
 					userLabels.erase(lookup[0]->getLabel());
+					userLines.erase(count);
 				}
 				
 				if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
@@ -122,7 +124,7 @@ int HeatMapCommand::execute(){
 			
 		}else{
 		
-			while((rabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+			while((rabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 
 				if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(rabund->getLabel()) == 1){			
 	
@@ -131,6 +133,7 @@ int HeatMapCommand::execute(){
 					
 					processedLabels.insert(rabund->getLabel());
 					userLabels.erase(rabund->getLabel());
+					userLines.erase(count);
 				}
 				
 				if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastRAbund->getLabel()) != 1)) {
diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 3ecf6df..6602bf9 100644
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -94,13 +94,14 @@ int MatrixOutputCommand::execute(){
 		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 		set<string> processedLabels;
 		set<string> userLabels = globaldata->labels;
+		set<int> userLines = globaldata->lines;
 				
 		if (lookup.size() < 2) { cout << "You have not provided enough valid groups.  I cannot run the command." << endl; return 0;}
 		
 		numGroups = globaldata->Groups.size();
 				
 		//as long as you are not at the end of the file or done wih the lines you want
-		while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+		while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 		
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){			
 				cout << lookup[0]->getLabel() << '\t' << count << endl;
@@ -108,6 +109,7 @@ int MatrixOutputCommand::execute(){
 				
 				processedLabels.insert(lookup[0]->getLabel());
 				userLabels.erase(lookup[0]->getLabel());
+				userLines.erase(count);
 			}
 			
 			if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
diff --git a/parselistcommand.cpp b/parselistcommand.cpp
index 20f92f7..c0622f2 100644
--- a/parselistcommand.cpp
+++ b/parselistcommand.cpp
@@ -99,6 +99,7 @@ int ParseListCommand::execute(){
 			//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 			set<string> processedLabels;
 			set<string> userLabels = globaldata->labels;
+			set<int> userLines = globaldata->lines;
 
 			//read in group map info.
 			groupMap = new GroupMap(globaldata->getGroupFile());
@@ -112,7 +113,7 @@ int ParseListCommand::execute(){
 						
 			//parses and sets each groups listvector
 			//as long as you are not at the end of the file or done wih the lines you want
-			while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+			while((list != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 								
 				if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(list->getLabel()) == 1){
 					cout << list->getLabel() << '\t' << count << endl;
@@ -120,6 +121,7 @@ int ParseListCommand::execute(){
 					
 					processedLabels.insert(list->getLabel());
 					userLabels.erase(list->getLabel());
+					userLines.erase(count);
 				}
 				
 				if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index 752ff62..114c8d0 100644
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -104,9 +104,10 @@ int RareFactCommand::execute(){
 		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 		set<string> processedLabels;
 		set<string> userLabels = globaldata->labels;
+		set<int> userLines = globaldata->lines;
 	
 		//as long as you are not at the end of the file or done wih the lines you want
-		while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+		while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 			
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
 			
@@ -117,6 +118,7 @@ int RareFactCommand::execute(){
 				cout << order->getLabel() << '\t' << count << endl;
 				processedLabels.insert(order->getLabel());
 				userLabels.erase(order->getLabel());
+				userLines.erase(count);
 			}
 			
 			if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index efcbe84..c930025 100644
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -83,9 +83,10 @@ int RareFactSharedCommand::execute(){
 		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 		set<string> processedLabels;
 		set<string> userLabels = globaldata->labels;
+		set<int> userLines = globaldata->lines;
 	
 		//as long as you are not at the end of the file or done wih the lines you want
-		while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+		while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 			
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
 				
@@ -96,6 +97,7 @@ int RareFactSharedCommand::execute(){
 				cout << lookup[0]->getLabel() << '\t' << count << endl;
 				processedLabels.insert(lookup[0]->getLabel());
 				userLabels.erase(lookup[0]->getLabel());
+				userLines.erase(count);
 			}
 			
 			if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index b4de07b..22dc2e9 100644
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -49,10 +49,11 @@ int SharedCommand::execute(){
 		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 		set<string> processedLabels;
 		set<string> userLabels = globaldata->labels;
+		set<int> userLines = globaldata->lines;
 		
 		shared = new Shared();
 		
-		while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+		while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 			
 						
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
@@ -62,6 +63,7 @@ int SharedCommand::execute(){
 				
 					processedLabels.insert(SharedList->getLabel());
 					userLabels.erase(SharedList->getLabel());
+					userLines.erase(count);
 			}
 			
 			if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
diff --git a/summarycommand.cpp b/summarycommand.cpp
index e7fda2e..9bc0c0f 100644
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -144,14 +144,16 @@ int SummaryCommand::execute(){
 		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 		set<string> processedLabels;
 		set<string> userLabels = globaldata->labels;
+		set<int> userLines = globaldata->lines;
 		
-		while((sabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+		while((sabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 			
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){			
 	
 				cout << sabund->getLabel() << '\t' << count << endl;
 				processedLabels.insert(sabund->getLabel());
 				userLabels.erase(sabund->getLabel());
+				userLines.erase(count);
 
 				
 				outputFileHandle << sabund->getLabel();
diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index fafc290..0a742ea 100644
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -169,9 +169,10 @@ int SummarySharedCommand::execute(){
 		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 		set<string> processedLabels;
 		set<string> userLabels = globaldata->labels;
+		set<int> userLines = globaldata->lines;
 		
 		//as long as you are not at the end of the file or done wih the lines you want
-		while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+		while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 		
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){			
 				cout << lookup[0]->getLabel() << '\t' << count << endl;
@@ -179,6 +180,7 @@ int SummarySharedCommand::execute(){
 				
 				processedLabels.insert(lookup[0]->getLabel());
 				userLabels.erase(lookup[0]->getLabel());
+				userLines.erase(count);
 			}
 			
 			if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 7f97ef3..850df46 100644
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -329,9 +329,10 @@ void TreeGroupCommand::makeSimsShared() {
 		
 		set<string> processedLabels;
 		set<string> userLabels = globaldata->labels;
+		set<int> userLines = globaldata->lines;
 
 		//as long as you are not at the end of the file or done wih the lines you want
-		while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+		while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 		
 			if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){			
 				cout << lookup[0]->getLabel() << '\t' << count << endl;
@@ -339,6 +340,7 @@ void TreeGroupCommand::makeSimsShared() {
 				
 				processedLabels.insert(lookup[0]->getLabel());
 				userLabels.erase(lookup[0]->getLabel());
+				userLines.erase(count);
 			}
 			
 			if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
diff --git a/validcommands.cpp b/validcommands.cpp
index 544933c..6439e9b 100644
--- a/validcommands.cpp
+++ b/validcommands.cpp
@@ -39,6 +39,8 @@ ValidCommands::ValidCommands() {
 		commands["get.group"]           = "get.group";
 		commands["get.label"]           = "get.label";
 		commands["get.line"]            = "get.line";
+		commands["get.sabund"]          = "get.sabund";
+		commands["get.rabund"]          = "get.rabund";
 		commands["bootstrap.shared"]	= "bootstrap.shared";
 		commands["concensus"]			= "concensus";
 		commands["help"]				= "help"; 
diff --git a/validparameter.cpp b/validparameter.cpp
index 6069a4f..547d4dc 100644
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -239,6 +239,12 @@ void ValidParameters::initCommandParameters() {
 
 		string getlineArray[] =  {};
 		commandParameters["get.line"] = addParameters(getlineArray, sizeof(getlineArray)/sizeof(string));
+		
+		string getsabundArray[] =  {"line", "label"};
+		commandParameters["get.sabund"] = addParameters(getsabundArray, sizeof(getsabundArray)/sizeof(string));
+		
+		string getrabundArray[] =  {"line", "label"};
+		commandParameters["get.rabund"] = addParameters(getrabundArray, sizeof(getrabundArray)/sizeof(string));
 
 		string rarefactionsingleArray[] =  {"iters","freq","line","label","calc","abund"};
 		commandParameters["rarefaction.single"] = addParameters(rarefactionsingleArray, sizeof(rarefactionsingleArray)/sizeof(string));
diff --git a/venncommand.cpp b/venncommand.cpp
index 519e6cb..bb3762c 100644
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -115,16 +115,18 @@ int VennCommand::execute(){
 		//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 		set<string> processedLabels;
 		set<string> userLabels = globaldata->labels;
+		set<int> userLines = globaldata->lines;
 		
 		if (format != "list") {	
 			
 			//as long as you are not at the end of the file or done wih the lines you want
-			while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+			while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 		
 				if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){			
 					cout << lookup[0]->getLabel() << '\t' << count << endl;
 					processedLabels.insert(lookup[0]->getLabel());
 					userLabels.erase(lookup[0]->getLabel());
+					userLines.erase(count);
 					
 					if (lookup.size() > 4) {
 						cout << "Error: Too many groups chosen.  You may use up to 4 groups with the venn command.  I will use the first four groups in your groupfile." << endl;
@@ -184,7 +186,7 @@ int VennCommand::execute(){
 			
 		}else{
 		
-			while((sabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+			while((sabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 		
 				if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){			
 	
@@ -193,6 +195,7 @@ int VennCommand::execute(){
 					
 					processedLabels.insert(sabund->getLabel());
 					userLabels.erase(sabund->getLabel());
+					userLines.erase(count);
 				}
 				
 				if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastSAbund->getLabel()) != 1)) {