added remove.seqs command

[mothur.git] / getseqscommand.cpp

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index e58cc883b26a33d2dec9526bb52bcbfb7de7741e..ae242b6f56946c544aff5f389b026c2c93a50bee 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -119,19 +119,30 @@ void GetSeqsCommand::readFasta(){
                openInputFile(fastafile, in);
                string name;
                
+               bool wroteSomething = false;
+               
                while(!in.eof()){
                        Sequence currSeq(in);
                        name = currSeq.getName();
                        
                        //if this name is in the accnos file
                        if (names.count(name) == 1) {
+                               wroteSomething = true;
+                               
                                currSeq.printSequence(out);
+                               
+                               names.erase(name);
                        }
                        
                        gobble(in);
                }
                in.close();     
-               out.close();    
+               out.close();
+               
+               if (wroteSomething == false) {
+                       mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine();
+                       remove(outputFileName.c_str()); 
+               }
 
        }
        catch(exception& e) {
@@ -152,6 +163,8 @@ void GetSeqsCommand::readName(){
                openInputFile(namefile, in);
                string name, firstCol, secondCol;
                
+               bool wroteSomething = false;
+               
                
                while(!in.eof()){
 
@@ -173,22 +186,31 @@ void GetSeqsCommand::readName(){
                        for (int i = 0; i < parsedNames.size(); i++) {
                                if (names.count(parsedNames[i]) == 1) {
                                        validSecond.push_back(parsedNames[i]);
+                                       names.erase(parsedNames[i]);
                                }
                        }
 
                        
                        //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) == 1) {
+                       
+                               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;
+                               
+                               names.erase(firstCol);
                        
                        //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
@@ -202,6 +224,11 @@ void GetSeqsCommand::readName(){
                in.close();
                out.close();
                
+               if (wroteSomething == false) {
+                       mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine();
+                       remove(outputFileName.c_str()); 
+               }
+               
        }
        catch(exception& e) {
                errorOut(e, "GetSeqsCommand", "readName");
@@ -221,6 +248,8 @@ void GetSeqsCommand::readGroup(){
                openInputFile(groupfile, in);
                string name, group;
                
+               bool wroteSomething = false;
+               
                while(!in.eof()){
 
                        in >> name;                             //read from first column
@@ -228,13 +257,22 @@ void GetSeqsCommand::readGroup(){
                        
                        //if this name is in the accnos file
                        if (names.count(name) == 1) {
+                               wroteSomething = true;
+                               
                                out << name << '\t' << group << endl;
+                               
+                               names.erase(name);
                        }
                                        
                        gobble(in);
                }
                in.close();
                out.close();
+               
+               if (wroteSomething == false) {
+                       mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine();
+                       remove(outputFileName.c_str()); 
+               }
 
        }
        catch(exception& e) {
@@ -255,6 +293,8 @@ void GetSeqsCommand::readAlign(){
                openInputFile(alignfile, in);
                string name, junk;
                
+               bool wroteSomething = false;
+               
                //read column headers
                for (int i = 0; i < 16; i++) {  
                        if (!in.eof())  {       in >> junk;      out << junk << '\t';   }
@@ -268,7 +308,8 @@ void GetSeqsCommand::readAlign(){
                        
                        //if this name is in the accnos file
                        if (names.count(name) == 1) {
-
+                               wroteSomething = true;
+                               
                                out << name << '\t';
                                
                                //read rest
@@ -278,6 +319,8 @@ void GetSeqsCommand::readAlign(){
                                }
                                out << endl;
                                
+                               names.erase(name);
+                               
                        }else {//still read just don't do anything with it
                                //read rest
                                for (int i = 0; i < 15; i++) {  
@@ -290,7 +333,11 @@ void GetSeqsCommand::readAlign(){
                }
                in.close();
                out.close();
-
+               
+               if (wroteSomething == false) {
+                       mothurOut("Your file does not contain any sequence from the .accnos file."); mothurOutEndLine();
+                       remove(outputFileName.c_str()); 
+               }
                
        }
        catch(exception& e) {