chimeras, fix to sabundvector and sharedsabundvector that caused getRabundVector...

[mothur.git] / removeseqscommand.cpp

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index a8f03e06b29c505d219a8a4f5770999586e182ae..19a4bc032abbcd1a5a7c9f53cdeac1b1be2c5715 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -22,7 +22,7 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta","name", "group", "alignreport", "accnos", "list","outputdir","inputdir" };
+                       string Array[] =  {"fasta","name", "group", "alignreport", "accnos", "list","outputdir","inputdir", "dups" };
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -119,10 +119,17 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option){
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
                        
+                       string usedDups = "true";
+                       string temp = validParameter.validFile(parameters, "dups", false);      if (temp == "not found") { temp = "false"; usedDups = ""; }
+                       dups = isTrue(temp);
+                       
                        if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == ""))  { mothurOut("You must provide one of the following: fasta, name, group, alignreport or list."); mothurOutEndLine(); abort = true; }
                        
                        int okay = 2;
                        if (outputDir != "") { okay++; }
+                       if (usedDups != "") { okay++;  }
+                       
+                       if ((usedDups != "") && (namefile == "")) {  mothurOut("You may only use dups with the name option."); mothurOutEndLine();  abort = true; }
                        
                        if (parameters.size() > okay) { mothurOut("You may only enter one of the following: fasta, name, group, alignreport, or list."); mothurOutEndLine(); abort = true;  }
                }
@@ -139,7 +146,8 @@ void RemoveSeqsCommand::help(){
        try {
                mothurOut("The remove.seqs command reads an .accnos file and one of the following file types: fasta, name, group, list or alignreport file.\n");
                mothurOut("It outputs a file containing the sequences NOT in the .accnos file.\n");
-               mothurOut("The remove.seqs command parameters are accnos, fasta, name, group, list and alignreport.  You must provide accnos and one of the other parameters.\n");
+               mothurOut("The remove.seqs command parameters are accnos, fasta, name, group, list, alignreport and dups.  You must provide accnos and one of the file parameters.\n");
+               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");
                mothurOut("The remove.seqs command should be in the following format: remove.seqs(accnos=yourAccnos, fasta=yourFasta).\n");
                mothurOut("Example remove.seqs(accnos=amazon.accnos, fasta=amazon.fasta).\n");
                mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
@@ -288,7 +296,12 @@ void RemoveSeqsCommand::readName(){
        try {
                if (outputDir == "") {  outputDir += hasPath(namefile);  }
                string outputFileName = getRootName(namefile) + "pick" + getExtension(namefile);
+               string outputFileName2 = getRootName(namefile) + "dups.accnos";
 
+               ofstream out2;
+               if (dups) {      openOutputFile(outputFileName2, out2); }
+               bool wroteDups = false;
+               
                ofstream out;
                openOutputFile(outputFileName, out);
 
@@ -322,38 +335,47 @@ void RemoveSeqsCommand::readName(){
                                }
                        }
                        
-                       //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) {
-                       
-                               wroteSomething = true;
-                               
-                               out << firstCol << '\t';
-                               
-                               //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;
-                       
-                       //make first name in set you come to first column and then add the remaining names to second column
+                       if ((dups) && (validSecond.size() != parsedNames.size())) { 
+                               wroteDups = true;
+                               for (int i = 0; i < parsedNames.size(); i++) {  out2 << parsedNames[i] << endl;  }
                        }else {
-                               
-                               //you want part of this row
-                               if (validSecond.size() != 0) {
-                               
+                                       //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) {
+                                       
                                        wroteSomething = true;
                                        
-                                       out << validSecond[0] << '\t';
-                               
+                                       out << firstCol << '\t';
+                                       
                                        //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;
+                                       
+                                       //make first name in set you come to first column and then add the remaining names to second column
+                               }else {
+                                       
+                                       //you want part of this row
+                                       if (validSecond.size() != 0) {
+                                               
+                                               wroteSomething = true;
+                                               
+                                               out << validSecond[0] << '\t';
+                                               
+                                               //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;
+                                       }
                                }
                        }
-                       
                        gobble(in);
                }
                in.close();
                out.close();
                
+               if (dups) { out2.close();  }
+               if (wroteDups == false) {
+                       remove(outputFileName2.c_str()); 
+               }
+               
                if (wroteSomething == false) {
                        mothurOut("Your file contains only sequences from the .accnos file."); mothurOutEndLine();
                        remove(outputFileName.c_str());