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added phylo.diversity command. added hard parameter to cluster, hcluster and read...
[mothur.git] / removeseqscommand.cpp
diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index c76c7113f237c45df86a91faa523f93163fc6ff8..a61e467e0bd5820060c052acffefe5fe7983294f 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -125,13 +125,13 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
                        
                        if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport or list."); m->mothurOutEndLine(); abort = true; }
                        
-                       int okay = 2;
-                       if (outputDir != "") { okay++; }
-                       if (usedDups != "") { okay++;  }
+                       //int okay = 2;
+                       //if (outputDir != "") { okay++; }
+                       //if (usedDups != "") { okay++;  }
                        
                        if ((usedDups != "") && (namefile == "")) {  m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine();  abort = true; }
                        
-                       if (parameters.size() > okay) { m->mothurOut("You may only enter one of the following: fasta, name, group, alignreport, or list."); m->mothurOutEndLine(); abort = true;  }
+                       //if (parameters.size() > okay) { m->mothurOut("You may only enter one of the following: fasta, name, group, alignreport, or list."); m->mothurOutEndLine(); abort = true;  }
                }
 
        }
@@ -168,12 +168,16 @@ int RemoveSeqsCommand::execute(){
                //get names you want to keep
                readAccnos();
                
+               if (m->control_pressed) { return 0; }
+               
                //read through the correct file and output lines you want to keep
                if (fastafile != "")            {               readFasta();    }
-               else if (namefile != "")        {               readName();             }
-               else if (groupfile != "")       {               readGroup();    }
-               else if (alignfile != "")       {               readAlign();    }
-               else if (listfile != "")        {               readList();             }
+               if (namefile != "")                     {               readName();             }
+               if (groupfile != "")            {               readGroup();    }
+               if (alignfile != "")            {               readAlign();    }
+               if (listfile != "")                     {               readList();             }
+               
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
                
                if (outputNames.size() != 0) {
                        m->mothurOutEndLine();
@@ -192,10 +196,10 @@ int RemoveSeqsCommand::execute(){
 }
 
 //**********************************************************************************************************************
-void RemoveSeqsCommand::readFasta(){
+int RemoveSeqsCommand::readFasta(){
        try {
                if (outputDir == "") {  outputDir += hasPath(fastafile);  }
-               string outputFileName = getRootName(fastafile) + "pick" + getExtension(fastafile);
+               string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "pick" + getExtension(fastafile);
                ofstream out;
                openOutputFile(outputFileName, out);
                
@@ -206,6 +210,8 @@ void RemoveSeqsCommand::readFasta(){
                bool wroteSomething = false;
                
                while(!in.eof()){
+                       if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+                       
                        Sequence currSeq(in);
                        name = currSeq.getName();
                        
@@ -215,7 +221,7 @@ void RemoveSeqsCommand::readFasta(){
                                        wroteSomething = true;
                                        
                                        currSeq.printSequence(out);
-                               }else {         names.erase(name);              }
+                               }//else {               names.erase(name);              }
                        }
                        gobble(in);
                }
@@ -226,7 +232,9 @@ void RemoveSeqsCommand::readFasta(){
                        m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();
                        remove(outputFileName.c_str()); 
                }else { outputNames.push_back(outputFileName); }
-
+               
+               return 0;
+               
        }
        catch(exception& e) {
                m->errorOut(e, "RemoveSeqsCommand", "readFasta");
@@ -234,10 +242,10 @@ void RemoveSeqsCommand::readFasta(){
        }
 }
 //**********************************************************************************************************************
-void RemoveSeqsCommand::readList(){
+int RemoveSeqsCommand::readList(){
        try {
                if (outputDir == "") {  outputDir += hasPath(listfile);  }
-               string outputFileName = getRootName(listfile) + "pick" +  getExtension(listfile);
+               string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + "pick" +  getExtension(listfile);
                ofstream out;
                openOutputFile(outputFileName, out);
                
@@ -256,6 +264,7 @@ void RemoveSeqsCommand::readList(){
                        
                        //for each bin
                        for (int i = 0; i < list.getNumBins(); i++) {
+                               if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
                        
                                //parse out names that are in accnos file
                                string binnames = list.get(i);
@@ -270,10 +279,13 @@ void RemoveSeqsCommand::readList(){
                                }
                        
                                //get last name
-                               if (names.count(binnames) == 0) {  newNames += binnames;  }
+                               if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
 
                                //if there are names in this bin add to new list
-                               if (newNames != "") {  newList.push_back(newNames);     }
+                               if (newNames != "") {  
+                                       newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
+                                       newList.push_back(newNames);    
+                               }
                        }
                                
                        //print new listvector
@@ -291,6 +303,8 @@ void RemoveSeqsCommand::readList(){
                        m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();
                        remove(outputFileName.c_str()); 
                }else { outputNames.push_back(outputFileName); }
+               
+               return 0;
 
        }
        catch(exception& e) {
@@ -299,11 +313,11 @@ void RemoveSeqsCommand::readList(){
        }
 }
 //**********************************************************************************************************************
-void RemoveSeqsCommand::readName(){
+int RemoveSeqsCommand::readName(){
        try {
                if (outputDir == "") {  outputDir += hasPath(namefile);  }
-               string outputFileName = getRootName(namefile) + "pick" + getExtension(namefile);
-               string outputFileName2 = getRootName(namefile) + "dups.accnos";
+               string outputFileName = outputDir + getRootName(getSimpleName(namefile)) + "pick" + getExtension(namefile);
+               string outputFileName2 = outputDir + getRootName(getSimpleName(namefile)) + "dups.accnos";
 
                ofstream out2;
                if (dups) {      openOutputFile(outputFileName2, out2); }
@@ -319,6 +333,7 @@ void 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; }
 
                        in >> firstCol;                         
                        in >> secondCol;                        
@@ -388,6 +403,7 @@ void RemoveSeqsCommand::readName(){
                        remove(outputFileName.c_str()); 
                }else { outputNames.push_back(outputFileName); }
                
+               return 0;
        }
        catch(exception& e) {
                m->errorOut(e, "RemoveSeqsCommand", "readName");
@@ -396,10 +412,10 @@ void RemoveSeqsCommand::readName(){
 }
 
 //**********************************************************************************************************************
-void RemoveSeqsCommand::readGroup(){
+int RemoveSeqsCommand::readGroup(){
        try {
                if (outputDir == "") {  outputDir += hasPath(groupfile);  }
-               string outputFileName = getRootName(groupfile) + "pick" + getExtension(groupfile);
+               string outputFileName = outputDir + getRootName(getSimpleName(groupfile)) + "pick" + getExtension(groupfile);
                ofstream out;
                openOutputFile(outputFileName, out);
 
@@ -410,7 +426,8 @@ void RemoveSeqsCommand::readGroup(){
                bool wroteSomething = false;
                
                while(!in.eof()){
-
+                       if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+                       
                        in >> name;                             //read from first column
                        in >> group;                    //read from second column
                        
@@ -418,7 +435,7 @@ void RemoveSeqsCommand::readGroup(){
                        if (names.count(name) == 0) {
                                wroteSomething = true;
                                out << name << '\t' << group << endl;
-                       }else {         names.erase(name);              }
+                       }//else {               names.erase(name);              }
                                        
                        gobble(in);
                }
@@ -429,7 +446,8 @@ void RemoveSeqsCommand::readGroup(){
                        m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();
                        remove(outputFileName.c_str()); 
                }else { outputNames.push_back(outputFileName); }
-
+               
+               return 0;
        }
        catch(exception& e) {
                m->errorOut(e, "RemoveSeqsCommand", "readGroup");
@@ -439,10 +457,10 @@ void RemoveSeqsCommand::readGroup(){
 
 //**********************************************************************************************************************
 //alignreport file has a column header line then all other lines contain 16 columns.  we just want the first column since that contains the name
-void RemoveSeqsCommand::readAlign(){
+int RemoveSeqsCommand::readAlign(){
        try {
                if (outputDir == "") {  outputDir += hasPath(alignfile);  }
-               string outputFileName = getRootName(getRootName(alignfile)) + "pick.align.report";
+               string outputFileName = outputDir + getRootName(getSimpleName(alignfile)) + "pick.align.report";
                ofstream out;
                openOutputFile(outputFileName, out);
 
@@ -460,7 +478,8 @@ void RemoveSeqsCommand::readAlign(){
                out << endl;
                
                while(!in.eof()){
-
+                       if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+                       
                        in >> name;                             //read from first column
                        
                        //if this name is in the accnos file
@@ -477,7 +496,7 @@ void RemoveSeqsCommand::readAlign(){
                                out << endl;
                                
                        }else {//still read just don't do anything with it
-                               names.erase(name);      
+                               //names.erase(name);    
                                
                                //read rest
                                for (int i = 0; i < 15; i++) {  
@@ -496,6 +515,8 @@ void RemoveSeqsCommand::readAlign(){
                        remove(outputFileName.c_str()); 
                }else { outputNames.push_back(outputFileName); }
                
+               return 0;
+               
        }
        catch(exception& e) {
                m->errorOut(e, "RemoveSeqsCommand", "readAlign");
Mothur--16S microbiota sequencing software; mirror of main repository with my branches