fixed read.tree so that it can read trees generated by fasttree

[mothur.git] / removeseqscommand.cpp

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index da6bc44297d474e75d9866c69ff3d790ae92052a..5f5fe6535d6e159850694204efc83253387b9d4c 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -154,7 +154,7 @@ void RemoveSeqsCommand::help(){
                m->mothurOut("The remove.seqs command reads an .accnos file and at least one of the following file types: fasta, name, group, list, taxonomy or alignreport file.\n");
                m->mothurOut("It outputs a file containing the sequences NOT in the .accnos file.\n");
                m->mothurOut("The remove.seqs command parameters are accnos, fasta, name, group, list, taxonomy, alignreport and dups.  You must provide accnos and at least one of the file parameters.\n");
-               m->mothurOut("The dups parameter allows you to remove the entire line from a name file if you remove any name from the line. default=false. If dups=true, then remove.seqs outputs a new .accnos file containing all the sequences removed. \n");
+               m->mothurOut("The dups parameter allows you to remove the entire line from a name file if you remove any name from the line. default=false. \n");
                m->mothurOut("The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
                m->mothurOut("Example remove.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n");
                m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
@@ -178,8 +178,8 @@ int RemoveSeqsCommand::execute(){
                if (m->control_pressed) { return 0; }
                
                //read through the correct file and output lines you want to keep
-               if (fastafile != "")            {               readFasta();    }
                if (namefile != "")                     {               readName();             }
+               if (fastafile != "")            {               readFasta();    }
                if (groupfile != "")            {               readGroup();    }
                if (alignfile != "")            {               readAlign();    }
                if (listfile != "")                     {               readList();             }
@@ -325,12 +325,7 @@ int RemoveSeqsCommand::readName(){
        try {
                if (outputDir == "") {  outputDir += hasPath(namefile);  }
                string outputFileName = outputDir + getRootName(getSimpleName(namefile)) + "pick" + getExtension(namefile);
-               string outputFileName2 = outputDir + getRootName(getSimpleName(namefile)) + "dups.accnos";
 
-               ofstream out2;
-               if (dups) {      openOutputFile(outputFileName2, out2); }
-               bool wroteDups = false;
-               
                ofstream out;
                openOutputFile(outputFileName, out);
 
@@ -341,7 +336,7 @@ int RemoveSeqsCommand::readName(){
                bool wroteSomething = false;
                
                while(!in.eof()){
-                       if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str()); if (dups) { out2.close(); remove(outputFileName2.c_str()); } return 0; }
+                       if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
 
                        in >> firstCol;                         
                        in >> secondCol;                        
@@ -365,9 +360,8 @@ int RemoveSeqsCommand::readName(){
                                }
                        }
                        
-                       if ((dups) && (validSecond.size() != parsedNames.size())) { 
-                               wroteDups = true;
-                               for (int i = 0; i < parsedNames.size(); i++) {  out2 << parsedNames[i] << endl;  }
+                       if ((dups) && (validSecond.size() != parsedNames.size())) {  //if dups is true and we want to get rid of anyone, get rid of everyone
+                               for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
                        }else {
                                        //if the name in the first column is in the set then print it and any other names in second column also in set
                                if (names.count(firstCol) == 0) {
@@ -401,11 +395,6 @@ int RemoveSeqsCommand::readName(){
                in.close();
                out.close();
                
-               if (dups) { out2.close();  }
-               if (wroteDups == false) {
-                       remove(outputFileName2.c_str()); 
-               }else { outputNames.push_back(outputFileName2); }
-               
                if (wroteSomething == false) {
                        m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();
                        remove(outputFileName.c_str());