added relabund parameter to classify.seqs and summary.tax commands

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index 160928f3aa46906900ac5262f198112fb70fda36..f4a551cf59ffc95c587f47ea111081e0cfb6a727 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -544,11 +544,11 @@ int ClassifyOtuCommand::process(ListVector* processList) {
                
                PhyloSummary* taxaSum;
         if (countfile != "") {
                
                PhyloSummary* taxaSum;
         if (countfile != "") {

-            if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, ct);  }
-            else {  taxaSum = new PhyloSummary(ct); }
+            if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, ct,false);  }
+            else {  taxaSum = new PhyloSummary(ct,false); }

                }else {
                }else {

-            if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, groupMap);  }
-            else {  taxaSum = new PhyloSummary(groupMap); }
+            if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, groupMap,false);  }
+            else {  taxaSum = new PhyloSummary(groupMap,false); }

         }
         
         vector<ofstream*> outSums;
         }
         
         vector<ofstream*> outSums;


@@ -574,11 +574,11 @@ int ClassifyOtuCommand::process(ListVector* processList) {
                 
                 PhyloSummary* taxaSumt;
                 if (countfile != "") {
                 
                 PhyloSummary* taxaSumt;
                 if (countfile != "") {

-                    if (refTaxonomy != "") { taxaSumt = new PhyloSummary(refTaxonomy, ct);  }
-                    else {  taxaSumt = new PhyloSummary(ct); }
+                    if (refTaxonomy != "") { taxaSumt = new PhyloSummary(refTaxonomy, ct, false);  }
+                    else {  taxaSumt = new PhyloSummary(ct, false); }

                 }else {
                 }else {

-                    if (refTaxonomy != "") { taxaSumt = new PhyloSummary(refTaxonomy, groupMap);  }
-                    else {  taxaSumt = new PhyloSummary(groupMap); }
+                    if (refTaxonomy != "") { taxaSumt = new PhyloSummary(refTaxonomy, groupMap,false);  }
+                    else {  taxaSumt = new PhyloSummary(groupMap,false); }

                 }
                 taxaSums.push_back(taxaSumt);
             }
                 }
                 taxaSums.push_back(taxaSumt);
             }

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 1b56433073d404e2c7f33513f7362f8306afcb42..30bfd9e486c151572940ce461f14a05ed46e5721 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -34,6 +34,7 @@ vector<string> ClassifySeqsCommand::setParameters(){
                CommandParameter piters("iters", "Number", "", "100", "", "", "","",false,true); parameters.push_back(piters);
                CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
         CommandParameter pshortcuts("shortcuts", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshortcuts);
                CommandParameter piters("iters", "Number", "", "100", "", "", "","",false,true); parameters.push_back(piters);
                CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
         CommandParameter pshortcuts("shortcuts", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshortcuts);

+        CommandParameter prelabund("relabund", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(prelabund);

                CommandParameter pnumwanted("numwanted", "Number", "", "10", "", "", "","",false,true); parameters.push_back(pnumwanted);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                CommandParameter pnumwanted("numwanted", "Number", "", "10", "", "", "","",false,true); parameters.push_back(pnumwanted);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);


@@ -52,7 +53,7 @@ string ClassifySeqsCommand::getHelpString(){
        try {
                string helpString = "";
                helpString += "The classify.seqs command reads a fasta file containing sequences and creates a .taxonomy file and a .tax.summary file.\n";
        try {
                string helpString = "";
                helpString += "The classify.seqs command reads a fasta file containing sequences and creates a .taxonomy file and a .tax.summary file.\n";

-               helpString += "The classify.seqs command parameters are reference, fasta, name, group, count, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted and probs.\n";
+               helpString += "The classify.seqs command parameters are reference, fasta, name, group, count, search, ksize, method, taxonomy, processors, match, mismatch, gapopen, gapextend, numwanted, relabund and probs.\n";

                helpString += "The reference, fasta and taxonomy parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
                helpString += "The search parameter allows you to specify the method to find most similar template.  Your options are: suffix, kmer, blast, align and distance. The default is kmer.\n";
                helpString += "The name parameter allows you add a names file with your fasta file, if you enter multiple fasta files, you must enter matching names files for them.\n";
                helpString += "The reference, fasta and taxonomy parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
                helpString += "The search parameter allows you to specify the method to find most similar template.  Your options are: suffix, kmer, blast, align and distance. The default is kmer.\n";
                helpString += "The name parameter allows you add a names file with your fasta file, if you enter multiple fasta files, you must enter matching names files for them.\n";


@@ -72,6 +73,7 @@ string ClassifySeqsCommand::getHelpString(){
                helpString += "The numwanted parameter allows you to specify the number of sequence matches you want with the knn method.  The default is 10.\n";
                helpString += "The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy.  The default is 0.\n";
                helpString += "The probs parameter shuts off the bootstrapping results for the wang and zap method. The default is true, meaning you want the bootstrapping to be shown.\n";
                helpString += "The numwanted parameter allows you to specify the number of sequence matches you want with the knn method.  The default is 10.\n";
                helpString += "The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy.  The default is 0.\n";
                helpString += "The probs parameter shuts off the bootstrapping results for the wang and zap method. The default is true, meaning you want the bootstrapping to be shown.\n";

+        helpString += "The relabund parameter allows you to indicate you want the summary file values to be relative abundances rather than raw abundances. Default=F. \n";

                helpString += "The iters parameter allows you to specify how many iterations to do when calculating the bootstrap confidence score for your taxonomy with the wang method.  The default is 100.\n";
                //helpString += "The flip parameter allows you shut off mothur's   The default is T.\n";
                helpString += "The classify.seqs command should be in the following format: \n";
                helpString += "The iters parameter allows you to specify how many iterations to do when calculating the bootstrap confidence score for your taxonomy with the wang method.  The default is 100.\n";
                //helpString += "The flip parameter allows you shut off mothur's   The default is T.\n";
                helpString += "The classify.seqs command should be in the following format: \n";


@@ -558,6 +560,9 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                        temp = validParameter.validFile(parameters, "probs", false);            if (temp == "not found"){       temp = "true";                  }
                        probs = m->isTrue(temp);
             
                        temp = validParameter.validFile(parameters, "probs", false);            if (temp == "not found"){       temp = "true";                  }
                        probs = m->isTrue(temp);
             

+            temp = validParameter.validFile(parameters, "relabund", false);            if (temp == "not found"){       temp = "false";                 }
+                       relabund = m->isTrue(temp);
+            

             temp = validParameter.validFile(parameters, "shortcuts", false);   if (temp == "not found"){       temp = "true";                  }
                        writeShortcuts = m->isTrue(temp);
                        
             temp = validParameter.validFile(parameters, "shortcuts", false);   if (temp == "not found"){       temp = "true";                  }
                        writeShortcuts = m->isTrue(temp);
                        


@@ -813,12 +818,12 @@ int ClassifySeqsCommand::execute(){
                 if (hasCount) { 
                     ct = new CountTable();
                     ct->readTable(countfileNames[s], true, false);
                 if (hasCount) { 
                     ct = new CountTable();
                     ct->readTable(countfileNames[s], true, false);

-                    taxaSum = new PhyloSummary(taxonomyFileName, ct);
+                    taxaSum = new PhyloSummary(taxonomyFileName, ct, relabund);

                     taxaSum->summarize(tempTaxonomyFile);
                 }else {
                     if (groupfile != "") {  group = groupfileNames[s]; groupMap = new GroupMap(group); groupMap->readMap(); }
                     
                     taxaSum->summarize(tempTaxonomyFile);
                 }else {
                     if (groupfile != "") {  group = groupfileNames[s]; groupMap = new GroupMap(group); groupMap->readMap(); }
                     

-                    taxaSum = new PhyloSummary(taxonomyFileName, groupMap);
+                    taxaSum = new PhyloSummary(taxonomyFileName, groupMap, relabund);

                     
                     if (m->control_pressed) { outputTypes.clear(); if (ct != NULL) { delete ct; }  if (groupMap != NULL) { delete groupMap; } delete taxaSum; for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);        } delete classify; return 0; }
                     
                     
                     if (m->control_pressed) { outputTypes.clear(); if (ct != NULL) { delete ct; }  if (groupMap != NULL) { delete groupMap; } delete taxaSum; for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);        } delete classify; return 0; }
                     

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 55546f2032af82f9934fb1af4b73891684904cd6..bfc42a9b81c6406caabea9eac68c00eeab5f30ff 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -77,7 +77,7 @@ private:
        string fastaFileName, templateFileName, countfile, distanceFileName, namefile, search, method, taxonomyFileName, outputDir, groupfile;
        int processors, kmerSize, numWanted, cutoff, iters;
        float match, misMatch, gapOpen, gapExtend;
        string fastaFileName, templateFileName, countfile, distanceFileName, namefile, search, method, taxonomyFileName, outputDir, groupfile;
        int processors, kmerSize, numWanted, cutoff, iters;
        float match, misMatch, gapOpen, gapExtend;

-       bool abort, probs, save, flip, hasName, hasCount, writeShortcuts;
+       bool abort, probs, save, flip, hasName, hasCount, writeShortcuts, relabund;

        
        int driver(linePair*, string, string, string, string);
        int createProcesses(string, string, string, string); 
        
        int driver(linePair*, string, string, string, string);
        int createProcesses(string, string, string, string); 

diff --git a/phylosummary.cpp b/phylosummary.cpp
index a9d501e2190a9f68ed79edc8586b4dba2cb03342..89099fff3fcc312b81c033b23fe87af81242d58e 100644 (file)
--- a/phylosummary.cpp
+++ b/phylosummary.cpp
@@ -11,12 +11,13 @@
 #include "referencedb.h"
 /**************************************************************************************************/
 
 #include "referencedb.h"
 /**************************************************************************************************/
 

-PhyloSummary::PhyloSummary(string refTfile, CountTable* c){
+PhyloSummary::PhyloSummary(string refTfile, CountTable* c, bool r){

        try {
                m = MothurOut::getInstance();
                maxLevel = 0;
                ignore = false;
         numSeqs = 0;
        try {
                m = MothurOut::getInstance();
                maxLevel = 0;
                ignore = false;
         numSeqs = 0;

+        relabund = r;

                
                ct = c;
         groupmap = NULL;
                
                ct = c;
         groupmap = NULL;


@@ -44,12 +45,13 @@ PhyloSummary::PhyloSummary(string refTfile, CountTable* c){
 
 /**************************************************************************************************/
 
 
 /**************************************************************************************************/
 

-PhyloSummary::PhyloSummary(CountTable* c){
+PhyloSummary::PhyloSummary(CountTable* c, bool r){

        try {
                m = MothurOut::getInstance();
                maxLevel = 0;
                ignore = true;
         numSeqs = 0;
        try {
                m = MothurOut::getInstance();
                maxLevel = 0;
                ignore = true;
         numSeqs = 0;

+        relabund = r;

                
                ct = c;
         groupmap = NULL;
                
                ct = c;
         groupmap = NULL;


@@ -63,12 +65,13 @@ PhyloSummary::PhyloSummary(CountTable* c){
        }
 }
 /**************************************************************************************************/
        }
 }
 /**************************************************************************************************/

-PhyloSummary::PhyloSummary(string refTfile, GroupMap* g){
+PhyloSummary::PhyloSummary(string refTfile, GroupMap* g, bool r){

        try {
                m = MothurOut::getInstance();
                maxLevel = 0;
                ignore = false;
         numSeqs = 0;
        try {
                m = MothurOut::getInstance();
                maxLevel = 0;
                ignore = false;
         numSeqs = 0;

+        relabund = r;

                
                groupmap = g;
         ct = NULL;
                
                groupmap = g;
         ct = NULL;


@@ -96,12 +99,13 @@ PhyloSummary::PhyloSummary(string refTfile, GroupMap* g){
 
 /**************************************************************************************************/
 
 
 /**************************************************************************************************/
 

-PhyloSummary::PhyloSummary(GroupMap* g){
+PhyloSummary::PhyloSummary(GroupMap* g, bool r){

        try {
                m = MothurOut::getInstance();
                maxLevel = 0;
                ignore = true;
         numSeqs = 0;
        try {
                m = MothurOut::getInstance();
                maxLevel = 0;
                ignore = true;
         numSeqs = 0;

+        relabund = r;

                
                groupmap = g;
         ct = NULL;
                
                groupmap = g;
         ct = NULL;


@@ -377,11 +381,10 @@ void PhyloSummary::assignRank(int index){
        try {
                map<string,int>::iterator it;
                int counter = 1;
        try {
                map<string,int>::iterator it;
                int counter = 1;

-               
+        

                for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
                        tree[it->second].rank = tree[index].rank + '.' + toString(counter);
                        counter++;
                for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
                        tree[it->second].rank = tree[index].rank + '.' + toString(counter);
                        counter++;

-                                                                       

                        assignRank(it->second);
                }
        }
                        assignRank(it->second);
                }
        }


@@ -395,7 +398,7 @@ void PhyloSummary::assignRank(int index){
 void PhyloSummary::print(ofstream& out){
        try {
                
 void PhyloSummary::print(ofstream& out){
        try {
                

-               if (ignore) { assignRank(0); }
+               if (ignore)     {  assignRank(0); }

         vector<string> mGroups;
                //print labels
                out << "taxlevel\t rankID\t taxon\t daughterlevels\t total\t";
         vector<string> mGroups;
                //print labels
                out << "taxlevel\t rankID\t taxon\t daughterlevels\t total\t";


@@ -414,12 +417,10 @@ void PhyloSummary::print(ofstream& out){
                 }
             }
         }
                 }
             }
         }

-               

                out << endl;
                
                int totalChildrenInTree = 0;
                map<string, int>::iterator itGroup;
                out << endl;
                
                int totalChildrenInTree = 0;
                map<string, int>::iterator itGroup;

-               

                map<string,int>::iterator it;
                for(it=tree[0].children.begin();it!=tree[0].children.end();it++){   
                        if (tree[it->second].total != 0)  {   
                map<string,int>::iterator it;
                for(it=tree[0].children.begin();it!=tree[0].children.end();it++){   
                        if (tree[it->second].total != 0)  {   


@@ -435,15 +436,35 @@ void PhyloSummary::print(ofstream& out){
                }
                
                //print root
                }
                
                //print root

-               out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << tree[0].total << "\t";
-               
-               
-               if (groupmap != NULL) {
-                       for (int i = 0; i < mGroups.size(); i++) {  out << tree[0].groupCount[mGroups[i]] << '\t'; }  
-        }else if ( ct != NULL) {
-            if (ct->hasGroupInfo()) { for (int i = 0; i < mGroups.size(); i++) {  out << tree[0].groupCount[mGroups[i]] << '\t'; } }
-        }
-               out << endl;
+        if (relabund) {
+            out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+            out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << (tree[0].total/(double) tree[0].total) << '\t';
+            
+            if (groupmap != NULL) {
+                for (int i = 0; i < mGroups.size(); i++) {
+                    double thisNum = tree[0].groupCount[mGroups[i]];
+                    thisNum /= (double) groupmap->getNumSeqs(mGroups[i]);
+                    out << thisNum << '\t';
+                }
+            }else if ( ct != NULL) {
+                if (ct->hasGroupInfo()) {
+                    for (int i = 0; i < mGroups.size(); i++) {
+                        double thisNum = tree[0].groupCount[mGroups[i]];
+                        thisNum /= (double) ct->getGroupCount(mGroups[i]);
+                        out << thisNum << '\t';
+                    }
+                }
+            }
+            out << endl;
+        }else {
+            out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << tree[0].total << "\t";
+            if (groupmap != NULL) {
+                for (int i = 0; i < mGroups.size(); i++) {  out << tree[0].groupCount[mGroups[i]] << '\t'; }
+            }else if ( ct != NULL) {
+                if (ct->hasGroupInfo()) { for (int i = 0; i < mGroups.size(); i++) {  out << tree[0].groupCount[mGroups[i]] << '\t'; } }
+            }
+            out << endl;
+               }

                
                //print rest
                print(0, out);
                
                //print rest
                print(0, out);


@@ -525,22 +546,37 @@ void PhyloSummary::print(int i, ofstream& out){
                                        if (tree[it2->second].total != 0)  {   totalChildrenInTree++; }
                                }
                 
                                        if (tree[it2->second].total != 0)  {   totalChildrenInTree++; }
                                }
                 

-                               out << tree[it->second].level << "\t" << tree[it->second].rank << "\t" << tree[it->second].name << "\t" << totalChildrenInTree << "\t" << tree[it->second].total << "\t";
-                               
-                               map<string, int>::iterator itGroup;
-                               if (groupmap != NULL) {
-                                       //for (itGroup = tree[it->second].groupCount.begin(); itGroup != tree[it->second].groupCount.end(); itGroup++) {
-                                       //      out << itGroup->second << '\t';
-                                       //}
-                                       vector<string> mGroups = groupmap->getNamesOfGroups();
-                                       for (int i = 0; i < mGroups.size(); i++) {  out << tree[it->second].groupCount[mGroups[i]] << '\t'; }
-                               }else if (ct != NULL) {
-                    if (ct->hasGroupInfo()) {
-                        vector<string> mGroups = ct->getNamesOfGroups();
+                if (relabund) {
+                    out << tree[it->second].level << "\t" << tree[it->second].rank << "\t" << tree[it->second].name << "\t" << totalChildrenInTree << "\t" << (tree[it->second].total/(double) tree[0].total) << "\t";
+                }else {
+                    out << tree[it->second].level << "\t" << tree[it->second].rank << "\t" << tree[it->second].name << "\t" << totalChildrenInTree << "\t" << tree[it->second].total << "\t";
+                               }
+                
+                if (relabund) {
+                    map<string, int>::iterator itGroup;
+                    if (groupmap != NULL) {
+                        vector<string> mGroups = groupmap->getNamesOfGroups();
+                        for (int i = 0; i < mGroups.size(); i++) {  out << (tree[it->second].groupCount[mGroups[i]]/(double)groupmap->getNumSeqs(mGroups[i])) << '\t'; }
+                    }else if (ct != NULL) {
+                        if (ct->hasGroupInfo()) {
+                            vector<string> mGroups = ct->getNamesOfGroups();
+                            for (int i = 0; i < mGroups.size(); i++) {  out << (tree[it->second].groupCount[mGroups[i]]/(double)ct->getGroupCount(mGroups[i])) << '\t'; }
+                        }
+                    }
+                }else {
+                    map<string, int>::iterator itGroup;
+                    if (groupmap != NULL) {
+                        vector<string> mGroups = groupmap->getNamesOfGroups();

                         for (int i = 0; i < mGroups.size(); i++) {  out << tree[it->second].groupCount[mGroups[i]] << '\t'; }
                         for (int i = 0; i < mGroups.size(); i++) {  out << tree[it->second].groupCount[mGroups[i]] << '\t'; }

+                    }else if (ct != NULL) {
+                        if (ct->hasGroupInfo()) {
+                            vector<string> mGroups = ct->getNamesOfGroups();
+                            for (int i = 0; i < mGroups.size(); i++) {  out << tree[it->second].groupCount[mGroups[i]] << '\t'; }
+                        }

                     }
                     }

+ 

                 }
                 }

-                               out << endl;
+                out << endl;

                                
                        }
                        
                                
                        }
                        

diff --git a/phylosummary.h b/phylosummary.h
index bd31173a48647e1bf2ed7b2f7ec95d25e0bfe388..4d3464f70472cdd2d2f8575934fcb96f6efbb3e5 100644 (file)
--- a/phylosummary.h
+++ b/phylosummary.h
@@ -33,10 +33,10 @@ struct rawTaxNode {
 class PhyloSummary {
 
 public:
 class PhyloSummary {
 
 public:

-       PhyloSummary(GroupMap*);
-       PhyloSummary(string, GroupMap*);
-    PhyloSummary(CountTable*);
-       PhyloSummary(string, CountTable*);
+       PhyloSummary(GroupMap*, bool);
+       PhyloSummary(string, GroupMap*, bool);
+    PhyloSummary(CountTable*, bool);
+       PhyloSummary(string, CountTable*, bool);

        ~PhyloSummary() {}
        
        int summarize(string);  //pass it a taxonomy file and a group file and it makes the tree
        ~PhyloSummary() {}
        
        int summarize(string);  //pass it a taxonomy file and a group file and it makes the tree


@@ -55,7 +55,7 @@ private:
        void readTreeStruct(ifstream&);
        GroupMap* groupmap;
     CountTable* ct;
        void readTreeStruct(ifstream&);
        GroupMap* groupmap;
     CountTable* ct;

-       bool ignore;
+       bool ignore, relabund;

        
        int numNodes;
        int numSeqs;
        
        int numNodes;
        int numSeqs;

diff --git a/summarytaxcommand.cpp b/summarytaxcommand.cpp
index 097983e93f24c853cc4d720eb2b1b82a3261b79c..9741e666e8c939d42ad4a6a5ec2001ea8a6004f2 100644 (file)
--- a/summarytaxcommand.cpp
+++ b/summarytaxcommand.cpp
@@ -18,6 +18,8 @@ vector<string> SummaryTaxCommand::setParameters(){
         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
                CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
                CommandParameter preftaxonomy("reftaxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(preftaxonomy);
         CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
                CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
                CommandParameter preftaxonomy("reftaxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(preftaxonomy);

+        CommandParameter prelabund("relabund", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(prelabund);
+

                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                


@@ -35,11 +37,12 @@ string SummaryTaxCommand::getHelpString(){
        try {
                string helpString = "";
                helpString += "The summary.tax command reads a taxonomy file and an optional name file, and summarizes the taxonomy information.\n";
        try {
                string helpString = "";
                helpString += "The summary.tax command reads a taxonomy file and an optional name file, and summarizes the taxonomy information.\n";

-               helpString += "The summary.tax command parameters are taxonomy, count, group and name. taxonomy is required, unless you have a valid current taxonomy file.\n";
+               helpString += "The summary.tax command parameters are taxonomy, count, group, name and relabund. taxonomy is required, unless you have a valid current taxonomy file.\n";

                helpString += "The name parameter allows you to enter a name file associated with your taxonomy file. \n";
                helpString += "The group parameter allows you add a group file so you can have the summary totals broken up by group.\n";
         helpString += "The count parameter allows you add a count file so you can have the summary totals broken up by group.\n";
                helpString += "The reftaxonomy parameter allows you give the name of the reference taxonomy file used when you classified your sequences. It is not required, but providing it will keep the rankIDs in the summary file static.\n";
                helpString += "The name parameter allows you to enter a name file associated with your taxonomy file. \n";
                helpString += "The group parameter allows you add a group file so you can have the summary totals broken up by group.\n";
         helpString += "The count parameter allows you add a count file so you can have the summary totals broken up by group.\n";
                helpString += "The reftaxonomy parameter allows you give the name of the reference taxonomy file used when you classified your sequences. It is not required, but providing it will keep the rankIDs in the summary file static.\n";

+        helpString += "The relabund parameter allows you to indicate you want the summary file values to be relative abundances rather than raw abundances. Default=F. \n";

                helpString += "The summary.tax command should be in the following format: \n";
                helpString += "summary.tax(taxonomy=yourTaxonomyFile) \n";
                helpString += "Note: No spaces between parameter labels (i.e. taxonomy), '=' and parameters (i.e.yourTaxonomyFile).\n"; 
                helpString += "The summary.tax command should be in the following format: \n";
                helpString += "summary.tax(taxonomy=yourTaxonomyFile) \n";
                helpString += "Note: No spaces between parameter labels (i.e. taxonomy), '=' and parameters (i.e.yourTaxonomyFile).\n"; 


@@ -194,6 +197,9 @@ SummaryTaxCommand::SummaryTaxCommand(string option)  {
                                outputDir = ""; 
                                outputDir += m->hasPath(taxfile); //if user entered a file with a path then preserve it 
                        }
                                outputDir = ""; 
                                outputDir += m->hasPath(taxfile); //if user entered a file with a path then preserve it 
                        }

+            
+            string temp = validParameter.validFile(parameters, "relabund", false);             if (temp == "not found"){       temp = "false";                 }
+                       relabund = m->isTrue(temp);

                        
             if (countfile == "") {
                 if (namefile == "") {
                        
             if (countfile == "") {
                 if (namefile == "") {


@@ -228,11 +234,11 @@ int SummaryTaxCommand::execute(){
                
         PhyloSummary* taxaSum;
         if (countfile != "") {
                
         PhyloSummary* taxaSum;
         if (countfile != "") {

-            if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, ct); }
-            else { taxaSum = new PhyloSummary(ct); }
+            if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, ct, relabund); }
+            else { taxaSum = new PhyloSummary(ct, relabund); }

         }else {
         }else {

-            if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, groupMap); }
-            else { taxaSum = new PhyloSummary(groupMap); }
+            if (refTaxonomy != "") { taxaSum = new PhyloSummary(refTaxonomy, groupMap, relabund); }
+            else { taxaSum = new PhyloSummary(groupMap, relabund); }

                }
         
                if (m->control_pressed) { if (groupMap != NULL) { delete groupMap; } if (ct != NULL) { delete ct; } delete taxaSum; return 0; }
                }
         
                if (m->control_pressed) { if (groupMap != NULL) { delete groupMap; } if (ct != NULL) { delete ct; } delete taxaSum; return 0; }

diff --git a/summarytaxcommand.h b/summarytaxcommand.h
index 5f61d13849fbfb332c8927445825bc5447b4ce8f..7716ad0ca41b4dee22f993c95c8955c94e5b4852 100644 (file)
--- a/summarytaxcommand.h
+++ b/summarytaxcommand.h
@@ -34,7 +34,7 @@ class SummaryTaxCommand : public Command {
                void help() { m->mothurOut(getHelpString()); }  
                
        private:
                void help() { m->mothurOut(getHelpString()); }  
                
        private:

-               bool abort;
+               bool abort, relabund;

                string taxfile, outputDir, namefile, groupfile, refTaxonomy, countfile;
                vector<string> outputNames;
                map<string, int> nameMap;
                string taxfile, outputDir, namefile, groupfile, refTaxonomy, countfile;
                vector<string> outputNames;
                map<string, int> nameMap;