From: Kathryn Iverson <kd.iverson@gmail.com>
Date: Wed, 11 Jul 2012 15:10:56 +0000 (-0400)
Subject: merged mgcluster. kw files added, but not working in this commit!
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=bfc3401db792f7630a5bfe7aea44b4eb5bae6e6f;hp=ce8794490ab1d83adcdb2b92e0302a1e43e17adf;p=mothur.git

merged mgcluster. kw files added, but not working in this commit!
---

diff --git a/kruskalwalliscommand.cpp b/kruskalwalliscommand.cpp
new file mode 100644
index 0000000..474e82c
--- /dev/null
+++ b/kruskalwalliscommand.cpp
@@ -0,0 +1,265 @@
+/* 
+ * File:   kruskalwalliscommand.cpp
+ * Author: kiverson
+ *
+ * Created on June 26, 2012, 11:06 AM
+ */
+
+#include "kruskalwalliscommand.h"
+
+//**********************************************************************************************************************
+vector<string> KruskalWallisCommand::setParameters(){	
+	try {
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+        CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+        CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);	
+		
+		vector<string> myArray;
+		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "KruskalWallisCommand", "setParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+string KruskalWallisCommand::getHelpString(){	
+	try {
+		string helpString = "";
+		helpString += "The kruskalwallis command parameter options are \n";
+        helpString += "Kruskal–Wallis one-way analysis of variance is a non-parametric method for testing whether samples originate from the same distribution.";
+		return helpString;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "KruskalWallisCommand", "getHelpString");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+string KruskalWallisCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "summary") {  outputFileName =  "cooccurence.summary"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "KruskalWallisCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+KruskalWallisCommand::KruskalWallisCommand(){	
+	try {
+		abort = true; calledHelp = true; 
+		setParameters();
+        vector<string> tempOutNames;
+		outputTypes["summary"] = tempOutNames;
+
+	}
+	catch(exception& e) {
+		m->errorOut(e, "KruskalWallisCommand", "KruskalWallisCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+KruskalWallisCommand::KruskalWallisCommand(string option) {
+	try {
+		abort = false; calledHelp = false;   
+				
+		//allow user to run help
+		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+		
+		else {
+			vector<string> myArray = setParameters();
+			
+			OptionParser parser(option);
+			map<string,string> parameters = parser.getParameters();
+			map<string,string>::iterator it;
+			
+			ValidParameters validParameter;
+			
+			//check to make sure all parameters are valid for command
+			for (it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+			}
+            
+            //get shared file
+			sharedfile = validParameter.validFile(parameters, "shared", true);
+			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
+			else if (sharedfile == "not found") { 
+				//if there is a current shared file, use it
+				sharedfile = m->getSharedFile(); 
+				if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+				else { 	m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
+			}else { m->setSharedFile(sharedfile); }
+            
+            //if the user changes the output directory command factory will send this info to us in the output parameter 
+			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = m->hasPath(sharedfile);		}
+                    
+            groups = validParameter.validFile(parameters, "groups", false);   
+            if (groups == "not found") { groups = "";   }
+            else { 
+            m->splitAtDash(groups, Groups); 
+            }   
+            m->setGroups(Groups);
+				
+			//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);		
+			if (inputDir == "not found"){	inputDir = "";		}
+			else {
+				string path;
+				it = parameters.find("shared");
+				//user has given a template file
+				if(it != parameters.end()){ 
+					path = m->hasPath(it->second);
+					//if the user has not given a path then, add inputdir. else leave path alone.
+					if (path == "") {	parameters["shared"] = inputDir + it->second;		}
+				}
+			}
+		
+            vector<string> tempOutNames;
+            outputTypes["summary"] = tempOutNames;
+
+
+		}
+
+	}
+	catch(exception& e) {
+		m->errorOut(e, "KruskalWallisCommand", "KruskalWallisCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+int KruskalWallisCommand::execute(){
+	try {
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
+        
+        InputData* input = new InputData(sharedfile, "sharedfile");
+        vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
+		string lastLabel = lookup[0]->getLabel();
+        
+	
+		//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 = labels;
+
+        ofstream out;
+		string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("summary");
+        m->openOutputFile(outputFileName, out);
+        outputNames.push_back(outputFileName);  outputTypes["summary"].push_back(outputFileName);
+        out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+        out << "H\tpvalue\n";
+        
+        //math goes here
+        
+        int N = m->getNumGroups();
+        double H;
+        double tmp = 0.0;
+        vector<groupRank> vec;
+        vector<string> groups = m->getGroups();
+        string group;
+        int count;
+        double sum;
+                
+        //merge all groups into a vector
+        
+        
+        
+        //rank function here
+        assignRank(vec);
+        
+        //populate counts and ranSums vectors
+        for (int i=0;i<N;i++) {
+            count = 0;
+            sum = 0;
+            group = groups[i];
+            for(int j;j<vec.size();j++) {
+                if (vec[j].group == group) {
+                    count++;
+                    sum = sum + vec[j].rank;
+                }
+            }
+            counts[i] = count;
+            rankSums[i] = sum;
+        }
+        
+        //test statistic
+        for (int i=0;i<N;i++) { tmp = tmp + (pow(rankSums[i],2) / counts[i]); }
+        
+        H = (12 / (N*(N+1))) * tmp - (3*(N+1));
+        
+        //ss = tmp - pow(accumulate(rankSums.begin(), rankSums.end(), 0), 2);
+        
+        //H = ss / ( (N * (N + 1))/12 );
+        
+        //correction for ties?
+        
+        //p-value calculation
+        
+		return 0;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "KruskalWallisCommand", "execute");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+void KruskalWallisCommand::assignRank(vector<groupRank> &vec) {
+    try {
+        double rank = 1;
+        double numRanks, avgRank, j;
+        vector<groupRank>::iterator it, oldit;
+
+        sort (vec.begin(), vec.end(), comparevalue);
+
+        it = vec.begin();
+
+        while ( it != vec.end() ) {
+            j = rank;
+            oldit = it;
+            if (!equalvalue(*it, *(it+1))) {
+                (*it).rank = rank; 
+                rank = rank+1; 
+                it++; }
+            else {
+                while(equalrank(*it, *(it+1))) {
+                    j = j + (j+1);
+                    rank++;
+                    it++;
+                }
+                numRanks = double (distance(oldit, it));
+                avgRank = j / numRanks;
+                while(oldit != it) {
+                    (*oldit).rank = avgRank;
+                    oldit++;
+                }
+            }
+
+        }
+        
+
+    }
+    catch(exception& e) {
+		m->errorOut(e, "KruskalWallisCommand", "getRank");
+		exit(1);
+	}
+    
+}
+//**********************************************************************************************************************
+void KruskalWallisCommand::assignValue(vector<groupRank> &vec) {
+    
+}
+//**********************************************************************************************************************
+//**********************************************************************************************************************
+//**********************************************************************************************************************
\ No newline at end of file
diff --git a/kruskalwalliscommand.h b/kruskalwalliscommand.h
new file mode 100644
index 0000000..da1166e
--- /dev/null
+++ b/kruskalwalliscommand.h
@@ -0,0 +1,64 @@
+/* 
+ * File:   kruskalwalliscommand.h
+ * Author: kiverson
+ *
+ * Created on June 26, 2012, 11:07 AM
+ */
+
+#ifndef KRUSKALWALLISCOMMAND_H
+#define	KRUSKALWALLISCOMMAND_H
+
+#include "command.hpp"
+#include "inputdata.h"
+#include "sharedrabundvector.h"
+
+
+class KruskalWallisCommand : public Command {
+   
+public:
+	    
+	KruskalWallisCommand(string);	
+	KruskalWallisCommand();
+	~KruskalWallisCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "kruskalwallis";			}
+	string getCommandCategory()		{ return "Hypothesis Testing";	}
+	string getOutputFileNameTag(string, string);
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/kruskalwallis"; }
+	string getDescription()		{ return "Non-parametric method for testing whether samples originate from the same distribution."; }
+    
+    struct groupRank {
+        string group;
+        double value;
+        double rank;        
+    };
+    
+    int execute(); 
+	void help() { m->mothurOut(getHelpString()); }
+    void assignRank(vector<groupRank>&);
+    void assignValue(vector<groupRank>&);
+    
+    
+private:
+    string outputDir, sharedfile, groups;
+    bool abort;
+    set<string> labels;
+    vector<string> outputNames, Groups;
+    vector<int> counts;
+    vector<double> rankSums;
+    vector<double> rankMeans;
+    
+  
+        
+    static bool comparevalue(const groupRank &a, const groupRank &b) { return a.value < b.value; }
+    static bool equalvalue(const groupRank &a, const groupRank &b) { return a.value == b.value; }
+    static bool comparerank(const groupRank &a, const groupRank &b) { return a.rank < b.rank; }
+    static bool equalrank(const groupRank &a, const groupRank &b) { return a.rank == b.rank; }
+    static bool equalgroup(const groupRank &a, const groupRank &b) { return a.group == b.group; }
+    
+};
+
+#endif	/* KRUSKALWALLISCOMMAND_H */
+
diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 2143495..cffb80f 100644
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -14,7 +14,8 @@ vector<string> MGClusterCommand::setParameters(){
 	try {
 		CommandParameter pblast("blast", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pblast);
 		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
-        CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge);
+        CommandParameter pcount("count", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcount);
+        //CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge);
 		CommandParameter plength("length", "Number", "", "5", "", "", "",false,false); parameters.push_back(plength);
 		CommandParameter ppenalty("penalty", "Number", "", "0.10", "", "", "",false,false); parameters.push_back(ppenalty);
 		CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pcutoff);
@@ -165,6 +166,13 @@ MGClusterCommand::MGClusterCommand(string option) {
 			if (namefile == "not open") { abort = true; }	
 			else if (namefile == "not found") { namefile = ""; }
 			else { m->setNameFile(namefile); }
+            
+            countfile = validParameter.validFile(parameters, "count", true);
+			if (countfile == "not open") { abort = true; }	
+			else if (countfile == "not found") { countfile = ""; }
+            else { m->setCountTableFile(countfile); }
+            
+            if (countfile != "" && namefile != "") { m->mothurOut("Cannot have both a name file and count file. Please use one or the other."); m->mothurOutEndLine(); abort = true; }
 			
 			if ((blastfile == "")) { m->mothurOut("When executing a mgcluster command you must provide a blastfile."); m->mothurOutEndLine(); abort = true; }
 			
@@ -237,9 +245,11 @@ int MGClusterCommand::execute(){
         list = new ListVector(nameMap->getListVector());
         RAbundVector* rabund = NULL;
         
-        if(large) {
-            map<string, int> nameMapCounts = m->readNames(namefile);
-            createRabund(nameMapCounts);
+        if(countfile != "") {
+            //map<string, int> nameMapCounts = m->readNames(namefile);
+            ct = new CountTable();
+            ct->readTable(countfile);
+            createRabund(ct, list);
             rabund = &rav;
         }else {
             rabund = new RAbundVector(list->getRAbundVector());
@@ -714,8 +724,25 @@ void MGClusterCommand::sortHclusterFiles(string unsortedDist, string unsortedOve
 
 //**********************************************************************************************************************
 
-void MGClusterCommand::createRabund(map<string, int> nameMapCounts){
+void MGClusterCommand::createRabund(CountTable* ct, ListVector* list){
     try {
+        //vector<string> names = ct.getNamesOfSeqs();
+
+        //for ( int i; i < ct.getNumGroups(); i++ ) {    rav.push_back( ct.getNumSeqs(names[i]) );    }
+        //return rav;
+        
+        for(int i = 0; i < list->getNumBins(); i++) { 
+           vector<string> binNames;
+           string bin = list->get(i);
+           m->splitAtComma(bin, binNames);
+           int total = 0;
+           for (int j = 0; j < binNames.size(); j++) { 
+               total += ct->getNumSeqs(binNames[j]);
+           }
+           rav.push_back(total);   
+       }
+        
+        
     }
     catch(exception& e) {
 		m->errorOut(e, "MGClusterCommand", "createRabund");
diff --git a/mgclustercommand.h b/mgclustercommand.h
index ce3ffec..0626b86 100644
--- a/mgclustercommand.h
+++ b/mgclustercommand.h
@@ -18,6 +18,7 @@
 #include "hcluster.h"
 #include "rabundvector.hpp"
 #include "sabundvector.hpp"
+#include "counttable.h"
 
 /**********************************************************************/
 
@@ -46,12 +47,13 @@ private:
 	Cluster* cluster;
 	HCluster* hcluster;
 	ListVector* list;
+    CountTable* ct;
 	ListVector oldList;
     RAbundVector rav;
 	vector<seqDist> overlapMatrix;
 	vector<string> outputNames;
 	
-	string blastfile, method, namefile, overlapFile, distFile, outputDir;
+	string blastfile, method, namefile, countfile, overlapFile, distFile, outputDir;
 	ofstream sabundFile, rabundFile, listFile;
 	double cutoff;
 	float penalty;
@@ -62,7 +64,7 @@ private:
 	ListVector* mergeOPFs(map<string, int>, float);
 	void sortHclusterFiles(string, string);
 	vector<seqDist> getSeqs(ifstream&);
-    void createRabund(map<string, int>);
+    void createRabund(CountTable*, ListVector*);
 
 };