modified split.groups to use sequenceParser

diff --git a/splitgroupscommand.cpp b/splitgroupscommand.cpp
index 530df68d972cbf70f1b99b867780de5f28a70a4d..113439c9220429f4d9466a72a579c5aa2caa10ae 100644 (file)
--- a/splitgroupscommand.cpp
+++ b/splitgroupscommand.cpp
@@ -9,6 +9,7 @@
 
 #include "splitgroupscommand.h"
 #include "sharedutilities.h"
+#include "sequenceparser.h"
 
 //**********************************************************************************************************************
 vector<string> SplitGroupCommand::setParameters(){     
@@ -164,16 +165,40 @@ int SplitGroupCommand::execute(){
        
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               groupMap = new GroupMap(groupfile);
-               groupMap->readMap();
+               SequenceParser* parser;
                
-               vector<string> namesGroups = groupMap->getNamesOfGroups();
+               if (namefile == "") {   parser = new SequenceParser(groupfile, fastafile);                              }
+               else                            {       parser = new SequenceParser(groupfile, fastafile, namefile);    }
+               
+               if (m->control_pressed) { delete parser; return 0; }
+
+               vector<string> namesGroups = parser->getNamesOfGroups();
                SharedUtil util;  util.setGroups(Groups, namesGroups);  
                
-               if (namefile != "") {  readNames();  }
-               splitFasta();
+               string fastafileRoot = outputDir + m->getRootName(m->getSimpleName(fastafile));
+               string namefileRoot = outputDir + m->getRootName(m->getSimpleName(namefile));
                
-               delete groupMap;
+               m->mothurOutEndLine();
+               for (int i = 0; i < Groups.size(); i++) {
+                       
+                       m->mothurOut("Processing group: " + Groups[i]); m->mothurOutEndLine();
+                       
+                       string newFasta = fastafileRoot + Groups[i] + ".fasta";
+                       string newName = namefileRoot + Groups[i] + ".names";
+                       
+                       parser->getSeqs(Groups[i], newFasta, false);
+                       outputNames.push_back(newFasta); outputTypes["fasta"].push_back(newFasta);
+                       if (m->control_pressed) { delete parser; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]);        } return 0; }
+
+                       if (namefile != "") { 
+                               parser->getNameMap(Groups[i], newName); 
+                               outputNames.push_back(newName); outputTypes["name"].push_back(newName);
+                       }
+                       
+                       if (m->control_pressed) { delete parser; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]);        } return 0; }
+               }
+               
+               delete parser;
                
                if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } return 0; }
                
@@ -200,147 +225,6 @@ int SplitGroupCommand::execute(){
                exit(1);
        }
 }
-/**********************************************************************************************************************/
-int SplitGroupCommand::readNames() { 
-       try {
-               //open input file
-               ifstream in;
-               m->openInputFile(namefile, in);
-               
-               while (!in.eof()) {
-                       if (m->control_pressed) { break; }
-                       
-                       string firstCol, secondCol;
-                       in >> firstCol >> secondCol; m->gobble(in);
-                       
-                       vector<string> names;
-                       m->splitAtComma(secondCol, names);
-                       
-                       nameMap[firstCol] = names;
-               }
-               in.close();
-                               
-               return 0;
-
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SplitGroupCommand", "readNames");
-               exit(1);
-       }
-}
-
-/**********************************************************************************************************************/
-int SplitGroupCommand::splitFasta() { 
-       try {
-               
-               string filerootFasta =  outputDir + m->getRootName(m->getSimpleName(fastafile));
-               string filerootName =  outputDir + m->getRootName(m->getSimpleName(namefile));
-               ofstream* temp;
-               ofstream* temp2;
-               map<string, ofstream*> filehandles;
-               map<string, ofstream*>::iterator it3;
-
-               for (int i=0; i<Groups.size(); i++) {
-                       temp = new ofstream;
-                       filehandles[Groups[i]+"fasta"] = temp;
-                       m->openOutputFile(filerootFasta + Groups[i] + ".fasta", *(filehandles[Groups[i]+"fasta"]));
-                       outputNames.push_back(filerootFasta + Groups[i] + ".fasta"); outputTypes["fasta"].push_back(filerootFasta + Groups[i] + ".fasta");
-                       
-                       if (namefile != "") {
-                               temp2 = new ofstream;
-                               filehandles[Groups[i]+"name"] = temp2;
-                               m->openOutputFile(filerootName + Groups[i] + ".names", *(filehandles[Groups[i]+"name"]));
-                               outputNames.push_back(filerootName + Groups[i] + ".names"); outputTypes["name"].push_back(filerootFasta + Groups[i] + ".names");
-                       }
-               }
-                       
-               //open input file
-               ifstream in;
-               m->openInputFile(fastafile, in);
-       
-               while (!in.eof()) {
-                       if (m->control_pressed) { break; }
-               
-                       Sequence seq(in); m->gobble(in);
-                               
-                       if (seq.getName() != "") { 
-                               
-                               itNames = nameMap.find(seq.getName());
-                               
-                               if (itNames == nameMap.end()) {
-                                       if (namefile != "") {  m->mothurOut(seq.getName() + " is not in your namesfile, ignoring."); m->mothurOutEndLine();  }
-                                       else { //no names file given
-                                               string group = groupMap->getGroup(seq.getName());
-                                               
-                                               if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
-                                                       seq.printSequence(*(filehandles[group+"fasta"]));
-                                               }else if(group == "not found") {
-                                                       m->mothurOut(seq.getName() + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
-                                               }
-                                       }
-                               }else{
-                                       vector<string> names = itNames->second;
-                                       map<string, string> group2Names;
-                                       map<string, string>::iterator it;
-                                       
-                                       for (int i = 0; i < names.size(); i++) {  //build strings for new group names file, will select rep below
-                                               string group = groupMap->getGroup(names[i]);
-                                               
-                                               if (m->inUsersGroups(group, Groups)) { //only add if this is in a group we want
-                                                       it = group2Names.find(group);
-                                                       if (it == group2Names.end()) {
-                                                               group2Names[group] = names[i] + ",";
-                                                       }else{
-                                                               group2Names[group] += names[i] + ",";
-                                                       }
-                                               }else if(group == "not found") {
-                                                       m->mothurOut(names[i] + " is not in your groupfile. Ignoring."); m->mothurOutEndLine();
-                                               }
-                                       }
-                               
-                                       for (map<string, string>::iterator itGroups = group2Names.begin(); itGroups != group2Names.end(); itGroups++) {
-                                               //edit names string, by grabbing the first guy as the rep and removing the last comma
-                                               string newNames = itGroups->second;
-                                               newNames = newNames.substr(0, newNames.length()-1); 
-                                               string repName = "";
-                                               
-                                               int pos = newNames.find_first_of(',');
-                                               if (pos == newNames.npos) { //only one sequence so it represents itself
-                                                       repName = newNames;
-                                               }else{
-                                                       repName = newNames.substr(0, pos);
-                                               }
-                                               
-                                               *(filehandles[itGroups->first+"name"]) << repName << '\t' << newNames << endl;
-                                               *(filehandles[itGroups->first+"fasta"]) << ">" << repName << endl << seq.getAligned() << endl;
-                                       }
-                               }
-                       }
-               }
-                       
-               in.close();
-                       
-               for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { 
-                       (*(filehandles[it3->first])).close();
-                       delete it3->second;
-               }
-               
-               vector<string> newOutputNames;
-               //remove blank files
-               for (int i = 0; i < outputNames.size(); i++) {
-                       if (m->isBlank(outputNames[i])) {
-                               m->mothurRemove(outputNames[i]);
-                       }else { newOutputNames.push_back(outputNames[i]); }
-               }
-               outputNames = newOutputNames;
-                               
-               return 0;
+//**********************************************************************************************************************
 
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SplitGroupCommand", "splitFasta");
-               exit(1);
-       }
-}
-/**********************************************************************************************************************/
 

diff --git a/splitgroupscommand.h b/splitgroupscommand.h
index f8bdca17e2a06877a81d4d5eca2fcabd64cef52a..a6b8854752f406a2bcaf82d5094c9abe023c2a46 100644 (file)
--- a/splitgroupscommand.h
+++ b/splitgroupscommand.h
@@ -39,14 +39,8 @@ public:
        void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       int readNames(); 
-       int splitFasta(); 
-       
        vector<string> outputNames;
-       map<string, vector<string> > nameMap;
-       map<string, vector<string> >::iterator itNames;
-       GroupMap* groupMap;
-       
+               
        string outputDir, namefile, groupfile, groups, fastafile;
        vector<string> Groups;
        bool abort;