Minor changes to make mtax.cpp more standalone and not rely on files generated by other classes

mtax.cpp

@@ -4,19 +4,27 @@
 #include <vector>
 #include <map>
 
+#include "util.h"
+
 using namespace std;
 
 void separate_fields(string line,vector<string>& fields, char separator);
+void create_genome_names(string path, string bfn);
 
 int main(int argc, char* argv[])
 {
   if(argc<3)
     {
-      cout<<"Wrong use of mtax: ./mtax <path to directory containing genome names> <path to directory containing names.dmp and nodes.dmp>"<<endl;
+      cout<<"Wrong use of mtax: ./mtax <path to main directory> <path to Taxonomy directory containing names.dmp and nodes.dmp>"<<endl;
       exit(1);
     }
 
   string names_file=argv[1];
+  string path,bfn;
+  util u;
+  u.extract_paths(names_file,path,bfn);
+
+  create_genome_names(path,bfn);
   string names_file1=names_file+"/genome_names.txt";
   string tax_dir=argv[2];
 
@@ -295,3 +303,36 @@ void separate_fields(string line,vector<string>& fields, char separator)
       //      cout<<"i="<<fields.at(i)<<endl;
     }
 }
+
+void create_genome_names(string path,string bfn)
+{
+  ofstream gmstream;
+  string gmfile=path+"/"+bfn+"/genome_names.txt";
+  gmstream.open(gmfile.c_str());
+  if(gmstream.fail())
+    {
+      cout<<"Failed to open gmstream to gmfile="<<gmfile<<endl;
+      exit(1);
+    }
+  util u;
+  
+  int main_set_size;
+  int ref_set_size;
+  u.get_mss(path+"/"+bfn+"/"+bfn+"_info.txt",main_set_size);
+  u.get_rss(path+"/"+bfn+"/"+bfn+"_info.txt",ref_set_size);
+
+  for(int i=0; i<main_set_size+ref_set_size; i++)
+    {
+      string tn=u.get_oname(path+"/"+bfn+"/",i);
+      //      string tn=organisms.at(i).get_directory();
+      for(int f=0; f<tn.length(); f++)
+	{
+	  if(tn[f]=='_')
+	    {
+	      tn[f]=' ';
+	    }
+	}
+      gmstream<<tn<<endl;
+    }
+  gmstream.close(); 
+}