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changing command name classify.shared to classifyrf.shared
[mothur.git] / splitabundcommand.cpp
diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index 48fada8eb7fc89d858f24c4d54dcc0a64d8a8225..580493b60a1e4d449a71b8689635e8ced4dea397 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -13,17 +13,17 @@
 //**********************************************************************************************************************
 vector<string> SplitAbundCommand::setParameters(){     
        try {           
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-        CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none",false,false); parameters.push_back(pname);
-        CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
-               CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
-               CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter pcutoff("cutoff", "Number", "", "0", "", "", "",false,true); parameters.push_back(pcutoff);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter paccnos("accnos", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(paccnos);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+        CommandParameter pname("name", "InputTypes", "", "", "NameCount", "FNGLT", "none","name",false,false,true); parameters.push_back(pname);
+        CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false); parameters.push_back(pcount);
+               CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false); parameters.push_back(pgroup);
+               CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none","list",false,false,true); parameters.push_back(plist);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               CommandParameter pcutoff("cutoff", "Number", "", "0", "", "", "","",false,true); parameters.push_back(pcutoff);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter paccnos("accnos", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(paccnos);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -58,30 +58,26 @@ string SplitAbundCommand::getHelpString(){
                exit(1);
        }
 }
+
 //**********************************************************************************************************************
-string SplitAbundCommand::getOutputFileNameTag(string type, string inputName=""){      
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string SplitAbundCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //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 == "fasta")            {   outputFileName =  "fasta";   }
-            else if (type == "list")    {   outputFileName =  "list";   }
-            else if (type == "name")        {   outputFileName =  "names";   }
-            else if (type == "count")        {   outputFileName =  "count_table";   }
-            else if (type == "group")       {   outputFileName =  "groups";   }
-            else if (type == "accnos")        {   outputFileName =  "accnos";   }
-            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, "SplitAbundCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "fasta")        {  pattern = "[filename],[tag],[tag2],fasta-[filename],[tag],[group],[tag2],fasta";            } 
+        else if (type == "list")    {   pattern = "[filename],[tag],[tag2],list-[filename],[group],[tag],[tag2],list";            }
+        else if (type == "name")    {   pattern = "[filename],[tag],names-[filename],[group],[tag],names";           }
+        else if (type == "count")   {   pattern = "[filename],[tag],[tag2],count_table-[filename],[tag],count_table";     }
+        else if (type == "group")   {   pattern = "[filename],[tag],[tag2],groups-[filename],[tag],[group],[tag2],groups";          }
+        else if (type == "accnos")  {   pattern = "[filename],[tag],[tag2],accnos-[filename],[tag],[group],[tag2],accnos";          }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "SplitAbundCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 SplitAbundCommand::SplitAbundCommand(){        
@@ -216,7 +212,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                        else if (countfile == "not found") { countfile = "";  } 
                        else {
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile);
+                ct.readTable(countfile, true);
             }
             
             if ((namefile != "") && (countfile != "")) {
@@ -471,7 +467,7 @@ int SplitAbundCommand::splitList(ListVector* thisList) {
                }//end for
 
                
-               string tag = thisList->getLabel() + ".";
+               string tag = thisList->getLabel();
        
                writeList(thisList, tag, numRareBins);
     
@@ -500,11 +496,16 @@ int SplitAbundCommand::writeList(ListVector* thisList, string tag, int numRareBi
                        ofstream aout;
                        ofstream rout;
                        
-                       string rare = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "rare." + getOutputFileNameTag("list");
+            map<string, string> variables; 
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+            variables["[tag]"] = tag;
+            variables["[tag2]"] = "rare";
+                       string rare = getOutputFileName("list",variables);
                        m->openOutputFile(rare, rout);
                        outputNames.push_back(rare); outputTypes["list"].push_back(rare);
                        
-                       string abund = outputDir + m->getRootName(m->getSimpleName(listfile)) + tag + "abund." + getOutputFileNameTag("list");
+            variables["[tag2]"] = "abund";
+                       string abund = getOutputFileName("list",variables);
                        m->openOutputFile(abund, aout);
                        outputNames.push_back(abund); outputTypes["list"].push_back(abund);
 
@@ -548,8 +549,14 @@ int SplitAbundCommand::writeList(ListVector* thisList, string tag, int numRareBi
                                temp2 = new ofstream;
                                filehandles[Groups[i]+".abund"] = temp2;
                                
-                string rareGroupFileName = fileroot + Groups[i] +"."+ tag + "rare." + getOutputFileNameTag("list");
-                string abundGroupFileName = fileroot + Groups[i] +"."+ tag + "abund." + getOutputFileNameTag("list");
+                map<string, string> variables; 
+                variables["[filename]"] = fileroot;
+                variables["[tag]"] = tag;
+                variables["[tag2]"] = "rare";
+                variables["[group]"] = Groups[i];
+                string rareGroupFileName = getOutputFileName("list",variables);
+                variables["[tag2]"] = "abund";
+                string abundGroupFileName = getOutputFileName("list",variables);
                                m->openOutputFile(rareGroupFileName, *(filehandles[Groups[i]+".rare"]));
                                m->openOutputFile(abundGroupFileName, *(filehandles[Groups[i]+".abund"]));
                                outputNames.push_back(rareGroupFileName); outputTypes["list"].push_back(rareGroupFileName);
@@ -759,10 +766,14 @@ int SplitAbundCommand::parseCount(string tag) { //namefile
                map<string, ofstream*> filehandles;
         
                if (Groups.size() == 0) {
-                       string rare = outputDir + m->getRootName(m->getSimpleName(countfile))  + tag + "rare." + getOutputFileNameTag("count");
+            map<string, string> variables; 
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(countfile));
+            variables["[tag]"] = tag;
+            variables["[tag2]"] = "rare";
+                       string rare = getOutputFileName("count",variables);
             outputNames.push_back(rare); outputTypes["count"].push_back(rare);
-                       
-                       string abund = outputDir + m->getRootName(m->getSimpleName(countfile))  + tag + "abund." + getOutputFileNameTag("count");
+                       variables["[tag2]"] = "abund";
+                       string abund = getOutputFileName("count",variables);
                        outputNames.push_back(abund); outputTypes["count"].push_back(abund);
                        
             CountTable rareTable;
@@ -846,7 +857,10 @@ int SplitAbundCommand::parseCount(string tag) { //namefile
                        
                        for (it3 = countTableMap.begin(); it3 != countTableMap.end(); it3++) { 
                 string fileroot =  outputDir + m->getRootName(m->getSimpleName(countfile));
-                string filename = fileroot + it3->first + "." + getOutputFileNameTag("count");
+                map<string, string> variables; 
+                variables["[filename]"] = fileroot;
+                variables["[tag]"] = it3->first;
+                string filename = getOutputFileName("count",variables);
                 outputNames.push_back(filename);  outputTypes["count"].push_back(filename);
                 (it3->second)->printTable(filename);
                                delete it3->second;
@@ -871,11 +885,15 @@ int SplitAbundCommand::writeNames() { //namefile
                        ofstream aout;
                        ofstream rout;
                        
-                       string rare = outputDir + m->getRootName(m->getSimpleName(namefile))  + "rare." + getOutputFileNameTag("name");
+            map<string, string> variables;
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(namefile));
+            variables["[tag]"] = "rare";
+                       string rare = getOutputFileName("name", variables);
                        m->openOutputFile(rare, rout);
                        outputNames.push_back(rare); outputTypes["name"].push_back(rare);
                        
-                       string abund = outputDir + m->getRootName(m->getSimpleName(namefile))  + "abund." + getOutputFileNameTag("name");
+            variables["[tag]"] = "abund";
+                       string abund = getOutputFileName("name", variables);
                        m->openOutputFile(abund, aout);
                        outputNames.push_back(abund); outputTypes["name"].push_back(abund);
                        
@@ -906,8 +924,13 @@ int SplitAbundCommand::writeNames() { //namefile
                                temp2 = new ofstream;
                                filehandles[Groups[i]+".abund"] = temp2;
                                
-                string rareGroupFileName = fileroot + Groups[i] + ".rare." + getOutputFileNameTag("name");
-                string abundGroupFileName = fileroot + Groups[i] + ".abund." + getOutputFileNameTag("name");
+                map<string, string> variables;
+                variables["[filename]"] = fileroot;
+                variables["[tag]"] = "rare";
+                variables["[group]"] = Groups[i];
+                string rareGroupFileName = getOutputFileName("name",variables);
+                variables["[tag]"] = "abund";
+                string abundGroupFileName = getOutputFileName("name",variables);
                                m->openOutputFile(rareGroupFileName, *(filehandles[Groups[i]+".rare"]));
                                m->openOutputFile(abundGroupFileName, *(filehandles[Groups[i]+".abund"]));
                        }
@@ -945,7 +968,10 @@ int SplitAbundCommand::writeNames() { //namefile
                        
                        for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { 
                                (*(filehandles[it3->first])).close();
-                               outputNames.push_back(fileroot + it3->first + "." + getOutputFileNameTag("name"));  outputTypes["name"].push_back(fileroot + it3->first + "." + getOutputFileNameTag("name"));
+                map<string, string> variables;
+                variables["[filename]"] = fileroot;
+                variables["[tag]"] = it3->first;
+                               outputNames.push_back(getOutputFileName("name",variables));  outputTypes["name"].push_back(getOutputFileName("name",variables));
                                delete it3->second;
                        }
                }
@@ -969,8 +995,11 @@ int SplitAbundCommand::writeAccnos(string tag) {
                        ofstream aout;
                        ofstream rout;
                        
-                       
-                       string rare = outputDir + m->getRootName(m->getSimpleName(inputFile))  + tag + "rare." + getOutputFileNameTag("accnos");
+            map<string, string> variables;
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFile));
+            variables["[tag]"] = tag;
+            variables["[tag2]"] = "rare";
+                       string rare = getOutputFileName("accnos",variables);
                        m->openOutputFile(rare, rout);
                        outputNames.push_back(rare); outputTypes["accnos"].push_back(rare); 
                        
@@ -979,7 +1008,8 @@ int SplitAbundCommand::writeAccnos(string tag) {
                        }
                        rout.close();
                
-                       string abund = outputDir + m->getRootName(m->getSimpleName(inputFile)) + tag  + "abund." + getOutputFileNameTag("accnos");
+            variables["[tag2]"] = "abund";
+                       string abund = getOutputFileName("accnos",variables);
                        m->openOutputFile(abund, aout);
                        outputNames.push_back(abund); outputTypes["accnos"].push_back(abund);
                        
@@ -1001,8 +1031,14 @@ int SplitAbundCommand::writeAccnos(string tag) {
                                temp2 = new ofstream;
                                filehandles[Groups[i]+".abund"] = temp2;
                                
-                               m->openOutputFile(fileroot + tag + Groups[i] + ".rare." + getOutputFileNameTag("accnos"), *(filehandles[Groups[i]+".rare"]));
-                               m->openOutputFile(fileroot + tag + Groups[i] + ".abund." + getOutputFileNameTag("accnos"), *(filehandles[Groups[i]+".abund"]));
+                map<string, string> variables;
+                variables["[filename]"] = fileroot;
+                variables["[tag]"] = tag;
+                variables["[tag2]"] = "rare";
+                variables["[group]"] = Groups[i];
+                               m->openOutputFile(getOutputFileName("accnos",variables), *(filehandles[Groups[i]+".rare"]));
+                variables["[tag2]"] = "abund";
+                               m->openOutputFile(getOutputFileName("accnos",variables), *(filehandles[Groups[i]+".abund"]));
                        }
                        
                        //write rare
@@ -1026,7 +1062,11 @@ int SplitAbundCommand::writeAccnos(string tag) {
                        //close files
                        for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { 
                                (*(filehandles[it3->first])).close();
-                               outputNames.push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("accnos"));  outputTypes["accnos"].push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("accnos"));
+                map<string, string> variables;
+                variables["[filename]"] = fileroot;
+                variables["[tag]"] = tag;
+                variables["[tag2]"] = it3->first;
+                               outputNames.push_back(getOutputFileName("accnos",variables));  outputTypes["accnos"].push_back(getOutputFileName("accnos",variables));
                                delete it3->second;
                        }
                }
@@ -1049,11 +1089,16 @@ int SplitAbundCommand::parseGroup(string tag) { //namefile
                        ofstream aout;
                        ofstream rout;
                        
-                       string rare = outputDir + m->getRootName(m->getSimpleName(groupfile))  + tag + "rare." + getOutputFileNameTag("group");
+            map<string, string> variables;
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(groupfile));
+            variables["[tag]"] = tag;
+            variables["[tag2]"] = "rare";
+                       string rare = getOutputFileName("group",variables);
                        m->openOutputFile(rare, rout);
                        outputNames.push_back(rare); outputTypes["group"].push_back(rare);
                
-                       string abund = outputDir + m->getRootName(m->getSimpleName(groupfile))  + tag + "abund." + getOutputFileNameTag("group");
+            variables["[tag2]"] = "abund";
+                       string abund = getOutputFileName("group",variables);
 ;
                        m->openOutputFile(abund, aout);
                        outputNames.push_back(abund); outputTypes["group"].push_back(abund);
@@ -1094,8 +1139,14 @@ int SplitAbundCommand::parseGroup(string tag) { //namefile
                                temp2 = new ofstream;
                                filehandles[Groups[i]+".abund"] = temp2;
                                
-                               m->openOutputFile(fileroot + tag + Groups[i] + ".rare." + getOutputFileNameTag("group"), *(filehandles[Groups[i]+".rare"]));
-                               m->openOutputFile(fileroot + tag + Groups[i] + ".abund." + getOutputFileNameTag("group"), *(filehandles[Groups[i]+".abund"]));
+                map<string, string> variables;
+                variables["[filename]"] = fileroot;
+                variables["[tag]"] = tag;
+                variables["[tag2]"] = "rare";
+                variables["[group]"] = Groups[i];
+                               m->openOutputFile(getOutputFileName("group",variables), *(filehandles[Groups[i]+".rare"]));
+                variables["[tag2]"] = "abund";
+                               m->openOutputFile(getOutputFileName("group",variables), *(filehandles[Groups[i]+".abund"]));
                        }
                        
                        for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {                               
@@ -1121,7 +1172,11 @@ int SplitAbundCommand::parseGroup(string tag) { //namefile
                        
                        for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { 
                                (*(filehandles[it3->first])).close();
-                               outputNames.push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("group"));  outputTypes["group"].push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("group"));
+                map<string, string> variables;
+                variables["[filename]"] = fileroot;
+                variables["[tag]"] = tag;
+                variables["[tag2]"] = it3->first;
+                               outputNames.push_back(getOutputFileName("group",variables));  outputTypes["group"].push_back(getOutputFileName("group",variables));
                                delete it3->second;
                        }
                }
@@ -1144,11 +1199,16 @@ int SplitAbundCommand::parseFasta(string tag) { //namefile
                        ofstream aout;
                        ofstream rout;
                        
-                       string rare = outputDir + m->getRootName(m->getSimpleName(fastafile))  + tag + "rare." + getOutputFileNameTag("fasta");
+            map<string, string> variables;
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+            variables["[tag]"] = tag;
+            variables["[tag2]"] = "rare";
+                       string rare = getOutputFileName("fasta",variables);
                        m->openOutputFile(rare, rout);
                        outputNames.push_back(rare); outputTypes["fasta"].push_back(rare);
                
-                       string abund = outputDir + m->getRootName(m->getSimpleName(fastafile))  + tag + "abund." + getOutputFileNameTag("fasta");
+            variables["[tag2]"] = "abund";
+                       string abund = getOutputFileName("fasta",variables);
                        m->openOutputFile(abund, aout);
                        outputNames.push_back(abund); outputTypes["fasta"].push_back(abund);
                
@@ -1195,8 +1255,14 @@ int SplitAbundCommand::parseFasta(string tag) { //namefile
                                temp2 = new ofstream;
                                filehandles[Groups[i]+".abund"] = temp2;
                                
-                               m->openOutputFile(fileroot + tag + Groups[i] + ".rare." + getOutputFileNameTag("fasta"), *(filehandles[Groups[i]+".rare"]));
-                               m->openOutputFile(fileroot + tag + Groups[i] + ".abund." + getOutputFileNameTag("fasta"), *(filehandles[Groups[i]+".abund"]));
+                map<string, string> variables;
+                variables["[filename]"] = fileroot;
+                variables["[tag]"] = tag;
+                variables["[tag2]"] = "rare";
+                variables["[group]"] = Groups[i];
+                               m->openOutputFile(getOutputFileName("fasta",variables), *(filehandles[Groups[i]+".rare"]));
+                variables["[tag2]"] = "abund";
+                               m->openOutputFile(getOutputFileName("fasta",variables), *(filehandles[Groups[i]+".abund"]));
                        }
                        
                        //open input file
@@ -1249,7 +1315,11 @@ int SplitAbundCommand::parseFasta(string tag) { //namefile
                        
                        for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { 
                                (*(filehandles[it3->first])).close();
-                               outputNames.push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("fasta"));  outputTypes["fasta"].push_back(fileroot + tag + it3->first + "." + getOutputFileNameTag("fasta"));
+                map<string, string> variables;
+                variables["[filename]"] = fileroot;
+                variables["[tag]"] = tag;
+                variables["[tag2]"] = it3->first;
+                               outputNames.push_back(getOutputFileName("fasta",variables));  outputTypes["fasta"].push_back(getOutputFileName("fasta",variables));
                                delete it3->second;
                        }
                }
Mothur--16S microbiota sequencing software; mirror of main repository with my branches