added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / getgroupscommand.cpp

diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index d3470f16ad990d7285e51e534ad059666a03d097..432894b06fe9d5ffa6982fdaaa49474a44c403e0 100644 (file)
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -16,12 +16,12 @@
 //**********************************************************************************************************************
 vector<string> GetGroupsCommand::setParameters(){      
        try {
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
-               CommandParameter pshared("shared", "InputTypes", "", "", "none", "FNGLT-sharedGroup", "none",false,false); parameters.push_back(pshared);
-               CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname);
-               CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT-sharedGroup", "none",false,false); parameters.push_back(pgroup);
-               CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
-               CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(pfasta);
+               CommandParameter pshared("shared", "InputTypes", "", "", "none", "sharedGroup", "none",false,false); parameters.push_back(pshared);
+               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+               CommandParameter pgroup("group", "InputTypes", "", "", "none", "sharedGroup", "FNGLT",false,false); parameters.push_back(pgroup);
+               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(plist);
+               CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "FNGLT",false,false); parameters.push_back(ptaxonomy);
                CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
                CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
@@ -180,22 +180,27 @@ GetGroupsCommand::GetGroupsCommand(string option)  {
                        else { m->setAccnosFile(accnosfile); }
                        
                        fastafile = validParameter.validFile(parameters, "fasta", true);
-                       if (fastafile == "not open") { abort = true; }
+                       if (fastafile == "not open") { fastafile = ""; abort = true; }
                        else if (fastafile == "not found") {  fastafile = "";  }
                        else { m->setFastaFile(fastafile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
-                       if (namefile == "not open") { abort = true; }
+                       if (namefile == "not open") { namefile = ""; abort = true; }
                        else if (namefile == "not found") {  namefile = "";  }  
                        else { m->setNameFile(namefile); }
                        
+                       groupfile = validParameter.validFile(parameters, "group", true);
+                       if (groupfile == "not open") { groupfile = ""; abort = true; }
+                       else if (groupfile == "not found") {  groupfile = "";                   }
+                       else { m->setGroupFile(groupfile); }    
+                       
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
                        else { m->setListFile(listfile); }
                        
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
-                       if (taxfile == "not open") { abort = true; }
+                       if (taxfile == "not open") { taxfile = ""; abort = true; }
                        else if (taxfile == "not found") {  taxfile = "";  }
                        else { m->setTaxonomyFile(taxfile); }
                        
@@ -203,7 +208,7 @@ GetGroupsCommand::GetGroupsCommand(string option)  {
                        if (groups == "not found") { groups = ""; }
                        else {
                                m->splitAtDash(groups, Groups);
-                               m->Groups = Groups;
+                               m->setGroups(Groups);
                        }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
@@ -248,6 +253,10 @@ GetGroupsCommand::GetGroupsCommand(string option)  {
                        if ((fastafile == "") && (namefile == "") && (groupfile == "")  && (sharedfile == "") && (listfile == "") && (taxfile == ""))  { m->mothurOut("You must provide at least one of the following: fasta, name, taxonomy, group, shared or list."); m->mothurOutEndLine(); abort = true; }
                        if ((groupfile == "") && ((namefile != "") || (fastafile != "") || (listfile != "") || (taxfile != "")))  { m->mothurOut("If using a fasta, name, taxonomy, group or list, then you must provide a group file."); m->mothurOutEndLine(); abort = true; }
 
+                       if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){
+                               vector<string> files; files.push_back(fastafile); files.push_back(taxfile);
+                               parser.getNameFile(files);
+                       }
                }
                
        }
@@ -273,7 +282,9 @@ int GetGroupsCommand::execute(){
                        //make sure groups are valid
                        //takes care of user setting groupNames that are invalid or setting groups=all
                        SharedUtil* util = new SharedUtil();
-                       util->setGroups(Groups, groupMap->namesOfGroups);
+                       vector<string> gNamesOfGroups = groupMap->getNamesOfGroups();
+                       util->setGroups(Groups, gNamesOfGroups);
+                       groupMap->setNamesOfGroups(gNamesOfGroups);
                        delete util;
                        
                        //fill names with names of sequences that are from the groups we want to remove 
@@ -373,6 +384,15 @@ int GetGroupsCommand::readFasta(){
                                        
                                        currSeq.printSequence(out);
                                        selectedCount++;
+                               }else{
+                                       //if you are not in the accnos file check if you are a name that needs to be changed
+                                       map<string, string>::iterator it = uniqueToRedundant.find(name);
+                                       if (it != uniqueToRedundant.end()) {
+                                               wroteSomething = true;
+                                               currSeq.setName(it->second);
+                                               currSeq.printSequence(out);
+                                               selectedCount++;
+                                       }
                                }
                        }
                        m->gobble(in);
@@ -488,10 +508,26 @@ int GetGroupsCommand::readList(){
                                        
                                        //if that name is in the .accnos file, add it
                                        if (names.count(name) != 0) {  newNames += name + ",";  selectedCount++;  }
+                                       else{
+                                               //if you are not in the accnos file check if you are a name that needs to be changed
+                                               map<string, string>::iterator it = uniqueToRedundant.find(name);
+                                               if (it != uniqueToRedundant.end()) {
+                                                       newNames += it->second + ",";
+                                                       selectedCount++;
+                                               }
+                                       }
                                }
                                
                                //get last name
                                if (names.count(binnames) != 0) {  newNames += binnames + ",";  selectedCount++;  }
+                               else{
+                                       //if you are not in the accnos file check if you are a name that needs to be changed
+                                       map<string, string>::iterator it = uniqueToRedundant.find(binnames);
+                                       if (it != uniqueToRedundant.end()) {
+                                               newNames += it->second + ",";
+                                               selectedCount++;
+                                       }
+                               }
                                
                                //if there are names in this bin add to new list
                                if (newNames != "") {  
@@ -583,6 +619,7 @@ int GetGroupsCommand::readName(){
                                        //you know you have at least one valid second since first column is valid
                                        for (int i = 0; i < validSecond.size()-1; i++) {  out << validSecond[i] << ',';  }
                                        out << validSecond[validSecond.size()-1] << endl;
+                                       uniqueToRedundant[firstCol] = validSecond[0];
                                }
                        }
                        
@@ -676,6 +713,13 @@ int GetGroupsCommand::readTax(){
                        if (names.count(name) != 0) {
                                wroteSomething = true;
                                out << name << '\t' << tax << endl;
+                       }else{
+                               //if you are not in the accnos file check if you are a name that needs to be changed
+                               map<string, string>::iterator it = uniqueToRedundant.find(name);
+                               if (it != uniqueToRedundant.end()) {
+                                       wroteSomething = true;
+                                       out << it->second << '\t' << tax << endl;
+                               }
                        }
                        
                        m->gobble(in);
@@ -711,7 +755,7 @@ void GetGroupsCommand::readAccnos(){
                }
                in.close();             
                
-               m->Groups = Groups;
+               m->setGroups(Groups);
                
        }
        catch(exception& e) {