added shared file to make.table

diff --git a/countseqscommand.cpp b/countseqscommand.cpp
index 575ffe844ed0a1134d52ecd0d6aa30531e2fc584..301aff7007c309d18952f04493188b9330b56f55 100644 (file)
--- a/countseqscommand.cpp
+++ b/countseqscommand.cpp
@@ -10,12 +10,14 @@
 #include "countseqscommand.h"
 #include "sharedutilities.h"
 #include "counttable.h"
 #include "countseqscommand.h"
 #include "sharedutilities.h"
 #include "counttable.h"

+#include "inputdata.h"

 
 //**********************************************************************************************************************
 vector<string> CountSeqsCommand::setParameters(){      
        try {
 
 //**********************************************************************************************************************
 vector<string> CountSeqsCommand::setParameters(){      
        try {

-               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","count",false,true,true); parameters.push_back(pname);
-               CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(pgroup);
+        CommandParameter pshared("shared", "InputTypes", "", "", "NameSHared-sharedGroup", "NameSHared", "none","count",false,false,true); parameters.push_back(pshared);
+               CommandParameter pname("name", "InputTypes", "", "", "NameSHared", "NameSHared", "none","count",false,false,true); parameters.push_back(pname);
+               CommandParameter pgroup("group", "InputTypes", "", "", "sharedGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);

         CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
         CommandParameter plarge("large", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(plarge);
                CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
         CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
         CommandParameter plarge("large", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(plarge);
                CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);


@@ -35,7 +37,7 @@ vector<string> CountSeqsCommand::setParameters(){
 string CountSeqsCommand::getHelpString(){      
        try {
                string helpString = "";
 string CountSeqsCommand::getHelpString(){      
        try {
                string helpString = "";

-               helpString += "The count.seqs aka. make.table command reads a name file and outputs a .count_table file.  You may also provide a group file to get the counts broken down by group.\n";
+               helpString += "The count.seqs aka. make.table command reads a name or shared file and outputs a .count_table file.  You may also provide a group with the names file to get the counts broken down by group.\n";

                helpString += "The groups parameter allows you to indicate which groups you want to include in the counts, by default all groups in your groupfile are used.\n";
         helpString += "The large parameter indicates the name and group files are too large to fit in RAM.\n";
                helpString += "When you use the groups parameter and a sequence does not represent any sequences from the groups you specify it is not included in the .count.summary file.\n";
                helpString += "The groups parameter allows you to indicate which groups you want to include in the counts, by default all groups in your groupfile are used.\n";
         helpString += "The large parameter indicates the name and group files are too large to fit in RAM.\n";
                helpString += "When you use the groups parameter and a sequence does not represent any sequences from the groups you specify it is not included in the .count.summary file.\n";


@@ -54,8 +56,7 @@ string CountSeqsCommand::getHelpString(){
 string CountSeqsCommand::getOutputPattern(string type) {
     try {
         string pattern = "";
 string CountSeqsCommand::getOutputPattern(string type) {
     try {
         string pattern = "";

-        
-        if (type == "count") {  pattern = "[filename],count_table"; }
+        if (type == "count") {  pattern = "[filename],count_table-[filename],[distance],count_table"; }

         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
         
         return pattern;
         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
         
         return pattern;


@@ -82,7 +83,8 @@ CountSeqsCommand::CountSeqsCommand(){
 
 CountSeqsCommand::CountSeqsCommand(string option)  {
        try {
 
 CountSeqsCommand::CountSeqsCommand(string option)  {
        try {

-               abort = false; calledHelp = false;   
+               abort = false; calledHelp = false;
+        allLines = 1;

                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }


@@ -126,25 +128,48 @@ CountSeqsCommand::CountSeqsCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["group"] = inputDir + it->second;            }
                                }
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["group"] = inputDir + it->second;            }
                                }

+                
+                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;           }
+                               }

                        }
                        
                        //check for required parameters
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { namefile = ""; abort = true; }
                        }
                        
                        //check for required parameters
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { namefile = ""; abort = true; }

-                       else if (namefile == "not found"){                                      
-                               namefile = m->getNameFile(); 
-                               if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
-                               else {  m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }else { m->setNameFile(namefile); }
-                       
+                       else if (namefile == "not found"){      namefile = ""; }
+            else { m->setNameFile(namefile); }
+            
+            sharedfile = validParameter.validFile(parameters, "shared", true);
+                       if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+                       else if (sharedfile == "not found"){    sharedfile = ""; }
+            else { m->setSharedFile(sharedfile); }
+            

                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") {  groupfile = "";  }        
                        else { m->setGroupFile(groupfile); }
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }
                        else if (groupfile == "not found") {  groupfile = "";  }        
                        else { m->setGroupFile(groupfile); }

-                       
+            
+            if ((namefile == "") && (sharedfile == "")) {
+                namefile = m->getNameFile();
+                               if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
+                               else {
+                    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 namefile or sharedfile and the name or shared parameter is required."); m->mothurOutEndLine(); abort = true;
+                    }
+                }
+                       }
+

                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = "all"; }
                        m->splitAtDash(groups, Groups);
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = "all"; }
                        m->splitAtDash(groups, Groups);

+            m->setGroups(Groups);

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


@@ -154,7 +179,7 @@ CountSeqsCommand::CountSeqsCommand(string option)  {
                        m->mothurConvert(temp, processors);
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        m->mothurConvert(temp, processors);
                        
                        //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(namefile);               }
+                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }

 
                }
                
 
                }
                


@@ -171,20 +196,107 @@ int CountSeqsCommand::execute(){
                
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                

-        map<string, string> variables; 
-        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(namefile));
-               string outputFileName = getOutputFileName("count", variables);
-               
-        int total = 0;
-        int start = time(NULL);
-        if (!large) { total = processSmall(outputFileName); }
-        else { total = processLarge(outputFileName);  }
-        
-               if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
-               
-        m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create a table for " + toString(total) + " sequences.");
-        m->mothurOutEndLine();
-        m->mothurOutEndLine();
+        map<string, string> variables;
+
+        if (namefile != "") {
+            int total = 0;
+            int start = time(NULL);
+            if (outputDir == "") { outputDir = m->hasPath(namefile); }
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(namefile));
+            string outputFileName = getOutputFileName("count", variables);
+            
+            if (!large) { total = processSmall(outputFileName); }
+            else { total = processLarge(outputFileName);  }
+            
+            if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
+            
+            m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create a table for " + toString(total) + " sequences.");
+            m->mothurOutEndLine(); m->mothurOutEndLine();
+            
+            m->mothurOutEndLine();
+            m->mothurOut("Total number of sequences: " + toString(total)); m->mothurOutEndLine();
+ 
+        }else {
+            if (outputDir == "") { outputDir = m->hasPath(sharedfile); }
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+            
+            InputData input(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;
+            
+            //as long as you are not at the end of the file or done wih the lines you want
+            while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+                
+                if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]); } return 0; }
+                
+                if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+                    
+                    m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+                    
+                    processShared(lookup, variables);
+                    
+                    processedLabels.insert(lookup[0]->getLabel());
+                    userLabels.erase(lookup[0]->getLabel());
+                }
+                
+                if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                    string saveLabel = lookup[0]->getLabel();
+                    
+                    for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
+                    lookup = input.getSharedRAbundVectors(lastLabel);
+                    m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+                    
+                    processShared(lookup, variables);
+                    
+                    processedLabels.insert(lookup[0]->getLabel());
+                    userLabels.erase(lookup[0]->getLabel());
+                    
+                    //restore real lastlabel to save below
+                    lookup[0]->setLabel(saveLabel);
+                }
+                
+                lastLabel = lookup[0]->getLabel();
+                //prevent memory leak
+                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
+                
+                if (m->control_pressed) { return 0; }
+                
+                //get next line to process
+                lookup = input.getSharedRAbundVectors();
+            }
+            
+            if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]); }  return 0; }
+            
+            //output error messages about any remaining user labels
+            set<string>::iterator it;
+            bool needToRun = false;
+            for (it = userLabels.begin(); it != userLabels.end(); it++) {
+                m->mothurOut("Your file does not include the label " + *it);
+                if (processedLabels.count(lastLabel) != 1) {
+                    m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+                    needToRun = true;
+                }else {
+                    m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+                }
+            }
+            
+            //run last label if you need to
+            if (needToRun == true)  {
+                for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+                lookup = input.getSharedRAbundVectors(lastLabel);
+                
+                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+                
+                processShared(lookup, variables);
+                
+                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
+            }
+            
+        }

         
         //set rabund file as new current rabundfile
                itTypes = outputTypes.find("count");
         
         //set rabund file as new current rabundfile
                itTypes = outputTypes.find("count");


@@ -193,12 +305,10 @@ int CountSeqsCommand::execute(){
                }
         
         m->mothurOutEndLine();
                }
         
         m->mothurOutEndLine();

-               m->mothurOut("Total number of sequences: " + toString(total)); m->mothurOutEndLine();
-               m->mothurOutEndLine();

                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();

-               m->mothurOut(outputFileName); m->mothurOutEndLine();    
+               for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }

                m->mothurOutEndLine();
                m->mothurOutEndLine();

-               
+        

                return 0;               
        }
        
                return 0;               
        }
        


@@ -209,6 +319,40 @@ int CountSeqsCommand::execute(){
 }
 //**********************************************************************************************************************
 
 }
 //**********************************************************************************************************************
 

+int CountSeqsCommand::processShared(vector<SharedRAbundVector*>& lookup, map<string, string> variables){
+    try {
+        variables["[distance]"] = lookup[0]->getLabel();
+        string outputFileName = getOutputFileName("count", variables);
+        outputNames.push_back(outputFileName); outputTypes["count"].push_back(outputFileName);
+        
+        ofstream out;
+        m->openOutputFile(outputFileName, out);
+        
+        out << "OTU_Label\ttotal\t";
+        for (int i = 0; i < lookup.size(); i++) { out << lookup[i]->getGroup() << '\t'; } out << endl;
+        
+        for (int j = 0; j < lookup[0]->getNumBins(); j++) {
+            if (m->control_pressed) { break; }
+            
+            int total = 0;
+            string output = "";
+            for (int i = 0; i < lookup.size(); i++) {
+                total += lookup[i]->getAbundance(j);
+                output += toString(lookup[i]->getAbundance(j)) + '\t';
+            }
+            out << m->currentSharedBinLabels[j] << '\t' << total << '\t' << output << endl;
+        }
+        out.close();
+        
+        return 0;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "CountSeqsCommand", "processShared");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
+

 int CountSeqsCommand::processSmall(string outputFileName){
        try {
         ofstream out;
 int CountSeqsCommand::processSmall(string outputFileName){
        try {
         ofstream out;

diff --git a/countseqscommand.h b/countseqscommand.h
index a5326d401e870c1878b5d8e7f4c2708bc0c48f04..e91ed08fc1be2200ae85b01a9284419730dbf8c8 100644 (file)
--- a/countseqscommand.h
+++ b/countseqscommand.h
@@ -12,6 +12,7 @@
 
 #include "command.hpp"
 #include "groupmap.h"
 
 #include "command.hpp"
 #include "groupmap.h"

+#include "sharedrabundvector.h"

 
 class CountSeqsCommand : public Command {
        
 
 class CountSeqsCommand : public Command {
        


@@ -28,7 +29,7 @@ public:
        string getHelpString(); 
     string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Count.seqs"; }
        string getHelpString(); 
     string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Count.seqs"; }

-       string getDescription()         { return "counts the number of sequences represented by each unique sequence in a namesfile"; }
+       string getDescription()         { return "makes a count file from a names or shared file"; }

 
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
 
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  


@@ -42,10 +43,11 @@ private:
                linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
        };
     
                linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
        };
     

-       string namefile, groupfile, outputDir, groups;
-       bool abort, large;
+       string namefile, groupfile, outputDir, groups, sharedfile;
+       bool abort, large, allLines;

        vector<string> Groups, outputNames;
     int processors;
        vector<string> Groups, outputNames;
     int processors;

+    set<string> labels;

     
     int processSmall(string);
     int processLarge(string);
     
     int processSmall(string);
     int processLarge(string);


@@ -54,6 +56,8 @@ private:
     
     int createProcesses(GroupMap*&, string);
     int driver(unsigned long long, unsigned long long, string, GroupMap*&);
     
     int createProcesses(GroupMap*&, string);
     int driver(unsigned long long, unsigned long long, string, GroupMap*&);

+    int processShared(vector<SharedRAbundVector*>& lookup, map<string, string> variables);
+

     
 };
 
     
 };
 

diff --git a/shannonrange.cpp b/shannonrange.cpp
index cbcacd8c0a21e8fc635bae96782a3d6e12ee5643..8223fd429a71275301e4b8c0a0fcd6d914a92658 100644 (file)
--- a/shannonrange.cpp
+++ b/shannonrange.cpp
@@ -80,7 +80,7 @@ EstOutput RangeShannon::getValues(SAbundVector* rank){
         //this calc has no data[0], just a lower and upper estimate. set data[0] to lower estimate.
         data[0] = data[1];
         if (data[1] > data[2]) { data[1] = data[2]; data[2] = data[0]; }
         //this calc has no data[0], just a lower and upper estimate. set data[0] to lower estimate.
         data[0] = data[1];
         if (data[1] > data[2]) { data[1] = data[2]; data[2] = data[0]; }

-        data[0] = data[1];
+        data[0] = -1.0; //no value

         
                if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }
                
         
                if (isnan(data[0]) || isinf(data[0])) { data[0] = 0; }