Changes group name error to warning

Adjusts filenames

source/commands/command.hpp

@@ -87,7 +87,13 @@ class Command {
                                                 if (filename.length() > 0) { //rip off last "."
                                                     filename = filename.substr(0, filename.length()-1);
                                                 }
-                                                filename += it->second + "."; 
+                                                filename += it->second + ".";
+                                            }else if ((it->first == "[group]") || (it->first == "[tag]")) {
+                                                string group = it->second;
+                                                for (int j = 0; j < group.length(); j++) {
+                                                    if (group[j] == '-') { group[j] = '_'; }
+                                                }
+                                                filename += group + ".";
                                             }else { filename += it->second + "."; }
                                         }
                                     }

source/commands/getotuscommand.h

@@ -1,55 +0,0 @@
-#ifndef GETOTUSCOMMAND_H
-#define GETOTUSCOMMAND_H
-
-/*
- *  getotuscommand.h
- *  Mothur
- *
- *  Created by westcott on 11/10/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-
-
-#include "command.hpp"
-#include "groupmap.h"
-#include "listvector.hpp"
-
-class GetOtusCommand : public Command {
-	
-public:
-	
-	GetOtusCommand(string);	
-	GetOtusCommand();
-	~GetOtusCommand(){}
-	
-	vector<string> setParameters();
-	string getCommandName()			{ return "get.otus";				}
-	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	
-	string getHelpString();	
-    string getOutputPattern(string);	
-	string getCitation() { return "http://www.mothur.org/wiki/Get.otus"; }
-	string getDescription()		{ return "outputs a new list file containing the otus containing sequences from the groups specified"; }
-
-	
-	int execute(); 
-	void help() { m->mothurOut(getHelpString()); }	
-	
-	
-private:
-	string accnosfile, groupfile, listfile, outputDir, groups, label;
-	bool abort;
-	vector<string> outputNames, Groups;
-	GroupMap* groupMap;
-	
-	int readListGroup();
-	int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);
-	
-};
-
-#endif
-
-
-

source/commands/parselistscommand.cpp

@@ -324,14 +324,7 @@ int ParseListCommand::execute(){
 /**********************************************************************************************************************/
 int ParseListCommand::parse(ListVector* thisList) {
 	try {
-        map<string, string> files;
-        map<string, string>::iterator it3;
-        
-        //set fileroot
-		map<string, string> variables;
-        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
-        variables["[distance]"] = thisList->getLabel();
-		
+
 		//fill filehandles with neccessary ofstreams
 		vector<string> gGroups;
         if (groupfile != "") { gGroups = groupMap->getNamesOfGroups(); }
@@ -342,11 +335,18 @@ int ParseListCommand::parse(ListVector* thisList) {
         map<string, string>::iterator itGroup;
         map<string, int> groupNumBins;
         
+        map<string, string> files;
+        
+        //set fileroot
+        map<string, string> variables;
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+        variables["[distance]"] = thisList->getLabel();
+        
 		for (int i=0; i<gGroups.size(); i++) {
             variables["[group]"] = gGroups[i];
 			string filename = getOutputFileName("list",variables);
 			ofstream temp;
-            m->openOutputFile(filename, temp);
+            m->openOutputFile(filename, temp); temp.close();
             files[gGroups[i]] = filename;
             outputNames.push_back(filename); outputTypes["list"].push_back(filename);
             groupNumBins[gGroups[i]] = 0;
@@ -404,9 +404,10 @@ int ParseListCommand::parse(ListVector* thisList) {
 		}
         
 		//end list vector
-		for (it3 = files.begin(); it3 != files.end(); it3++) {
+		for (map<string, string>::iterator it3 = files.begin(); it3 != files.end(); it3++) {
             ofstream out;
-            m->openOutputFileAppend(files[it3->second], out);
+            string filename = it3->second;
+            m->openOutputFileAppend(filename, out);
             out << groupLabels[it3->first] << endl;
 			out << thisList->getLabel() << '\t' << groupNumBins[it3->first] << groupVector[it3->first] << endl;  // label numBins  listvector for that group
             out.close();

source/commands/removeotuscommand.h

@@ -1,52 +0,0 @@
-#ifndef REMOVEOTUSCOMMAND_H
-#define REMOVEOTUSCOMMAND_H
-
-/*
- *  removeotuscommand.h
- *  Mothur
- *
- *  Created by westcott on 11/12/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "groupmap.h"
-#include "listvector.hpp"
-
-class RemoveOtusCommand : public Command {
-	
-public:
-	
-	RemoveOtusCommand(string);	
-	RemoveOtusCommand();
-	~RemoveOtusCommand(){}
-	
-	vector<string> setParameters();
-	string getCommandName()			{ return "remove.otus";				}
-	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	
-	string getHelpString();	
-    string getOutputPattern(string);	
-	string getCitation() { return "http://www.mothur.org/wiki/Remove.otus"; }
-	string getDescription()		{ return "outputs a new list file containing the otus NOT containing sequences from the groups specified"; }
-
-	int execute(); 
-	void help() { m->mothurOut(getHelpString()); }	
-	
-private:
-	string accnosfile, groupfile, listfile, outputDir, groups, label;
-	bool abort;
-	vector<string> outputNames, Groups;
-	GroupMap* groupMap;
-	
-	int readListGroup();
-	int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);
-	
-};
-
-#endif
-
-
-
-

source/commands/sracommand.cpp

@@ -1327,15 +1327,19 @@ int SRACommand::mapGroupToFile(map<string, vector<string> >& files, vector<strin
 	try {
         for (int i = 0; i < Groups.size(); i++) {
             
+            //correct filename issues if group name contains '-' characters
+            string thisGroup = Groups[i];
+            for (int k = 0; k < thisGroup.length(); k++) { if (thisGroup[k] == '-') { thisGroup[k] = '_'; } }
+            
             for (int j = 0; j < theseFiles.size(); j++) {
                 
                 string tempName = m->getSimpleName(theseFiles[j]);
                 //if ((tempName == "GZGO5KL01.F006D146.sff") || (tempName == "G3BMWHG01.F008D021.sff") || (tempName == "GO2JXTW01.M002D125.sff") || (tempName == "GO5715J01.M003D125.sff")) { cout << Groups[i] << '\t' << theseFiles[j] << endl; }
                 //cout << i << '\t' << j << '\t' << Groups[i] << '\t' << theseFiles[j] << endl;
-                int pos = theseFiles[j].find(Groups[i]);
+                int pos = theseFiles[j].find(thisGroup);
                 if (pos != string::npos) { //you have a potential match, make sure you dont have a case of partial name
-                    if (theseFiles[j][pos+Groups[i].length()] == '.') { //final.soil.sff vs final.soil2.sff both would match soil.
-                        map<string, vector<string> >::iterator it = files.find(Groups[i]);
+                    if (theseFiles[j][pos+thisGroup.length()] == '.') { //final.soil.sff vs final.soil2.sff both would match soil.
+                        map<string, vector<string> >::iterator it = files.find(thisGroup);
                         if (it == files.end()) {
                             vector<string> temp; temp.push_back(theseFiles[j]);
                             files[Groups[i]] = temp;
@@ -1346,6 +1350,7 @@ int SRACommand::mapGroupToFile(map<string, vector<string> >& files, vector<strin
                 }
             }
         }
+        
         return 0;
     }
 	catch(exception& e) {

source/datastructures/counttable.h

@@ -50,8 +50,7 @@ class CountTable {
         //reads and creates smart enough to eliminate groups with zero counts 
         int createTable(set<string>&, map<string, string>&, set<string>&); //seqNames, seqName->group, groupNames 
         int createTable(string, string, bool); //namefile, groupfile, createGroup
-
-        int readTable(string, bool, bool); //file, readGroups, mothurRunning
+        int readTable(string, bool, bool); //filename, readGroups, mothurRunning
     
         int printTable(string);
         int printHeaders(ofstream&);

source/mothurout.cpp

@@ -2993,7 +2993,7 @@ bool MothurOut::checkGroupName(string name) {
         }
         
         if (!goodName) {
-            mothurOut("\n[ERROR]: group " + name + " contains illegal characters in the name. Group names cannot include :, -, or / characters.  The ':' character is a special character used in trees. Using ':' will result in your tree being unreadable by tree reading software.  The '-' character is a special character used by mothur to parse group names.  Using the '-' character will prevent you from selecting groups. The '/' character will created unreadable filenames when mothur includes the group in an output filename. Quitting. \n\n"); control_pressed = true;
+            mothurOut("\n[WARNING]: group " + name + " contains illegal characters in the name. Group names should not include :, -, or / characters.  The ':' character is a special character used in trees. Using ':' will result in your tree being unreadable by tree reading software.  The '-' character is a special character used by mothur to parse group names.  Using the '-' character will prevent you from selecting groups. The '/' character will created unreadable filenames when mothur includes the group in an output filename.  \n\n");
         }
         
         return goodName;