rewrote metastats command in c++, added mothurRemove function to handle ~ error....

[mothur.git] / getseqscommand.cpp

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 71a2db9723c32a39ea8e158074fbfac8a29de1ca..5eba5ccc67b02436fbe39e09cc8fca52a2ea89cc 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -279,9 +279,8 @@ int GetSeqsCommand::execute(){
                if (qualfile != "")                     {               readQual();                     }
                if (accnosfile2 != "")          {               compareAccnos();        }
                
-               if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str());  } return 0; }
+               if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);  } return 0; }
                
-               m->mothurOut("Selected " + toString(names.size()) + " sequences."); m->mothurOutEndLine();
                
                if (outputNames.size() != 0) {
                        m->mothurOutEndLine();
@@ -347,10 +346,11 @@ int GetSeqsCommand::readFasta(){
                string name;
                
                bool wroteSomething = false;
+               int selectedCount = 0;
                
                while(!in.eof()){
                
-                       if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
                        
                        Sequence currSeq(in);
                        name = currSeq.getName();
@@ -361,6 +361,7 @@ int GetSeqsCommand::readFasta(){
                                        wroteSomething = true;
                                        
                                        currSeq.printSequence(out);
+                                       selectedCount++;
                                }
                        }
                        m->gobble(in);
@@ -372,6 +373,8 @@ int GetSeqsCommand::readFasta(){
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
                outputNames.push_back(outputFileName);  outputTypes["fasta"].push_back(outputFileName); 
                
+               m->mothurOut("Selected " + toString(selectedCount) + " sequences from your fasta file."); m->mothurOutEndLine();
+               
                return 0;
 
        }
@@ -395,6 +398,7 @@ int GetSeqsCommand::readQual(){
                string name;
                
                bool wroteSomething = false;
+               int selectedCount = 0;
                
                
                while(!in.eof()){       
@@ -426,6 +430,7 @@ int GetSeqsCommand::readQual(){
                                wroteSomething = true;
                                                
                                out << name << endl << scores;
+                               selectedCount++;
                        }
                        
                        m->gobble(in);
@@ -437,6 +442,9 @@ int GetSeqsCommand::readQual(){
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
                outputNames.push_back(outputFileName);  outputTypes["qfile"].push_back(outputFileName); 
                
+               m->mothurOut("Selected " + toString(selectedCount) + " sequences from your quality file."); m->mothurOutEndLine();
+
+               
                return 0;
                
        }
@@ -458,10 +466,11 @@ int GetSeqsCommand::readList(){
                m->openInputFile(listfile, in);
                
                bool wroteSomething = false;
+               int selectedCount = 0;
                
                while(!in.eof()){
                        
-                       if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
                        //read in list vector
                        ListVector list(in);
@@ -482,11 +491,11 @@ int GetSeqsCommand::readList(){
                                        binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
                                        
                                        //if that name is in the .accnos file, add it
-                                       if (names.count(name) != 0) {  newNames += name + ",";  }
+                                       if (names.count(name) != 0) {  newNames += name + ",";  selectedCount++; }
                                }
                        
                                //get last name
-                               if (names.count(binnames) != 0) {  newNames += binnames + ",";  }
+                               if (names.count(binnames) != 0) {  newNames += binnames + ",";  selectedCount++; }
 
                                //if there are names in this bin add to new list
                                if (newNames != "") { 
@@ -509,6 +518,8 @@ int GetSeqsCommand::readList(){
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
                outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
                
+               m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine();
+               
                return 0;
 
        }
@@ -532,11 +543,11 @@ int GetSeqsCommand::readName(){
                string name, firstCol, secondCol;
                
                bool wroteSomething = false;
-               
+               int selectedCount = 0;
                
                while(!in.eof()){
                
-                       if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
                        in >> firstCol;                         
                        in >> secondCol;
@@ -558,7 +569,10 @@ int GetSeqsCommand::readName(){
                                for (int i = 0; i < parsedNames.size(); i++) {  names.insert(parsedNames[i]);  }
                                out << firstCol << '\t' << hold << endl;
                                wroteSomething = true;
+                               selectedCount += parsedNames.size();
                        }else {
+                               selectedCount += validSecond.size();
+                               
                                //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) {
                                
@@ -594,6 +608,8 @@ int GetSeqsCommand::readName(){
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
                outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
                
+               m->mothurOut("Selected " + toString(selectedCount) + " sequences from your name file."); m->mothurOutEndLine();
+               
                return 0;
                
        }
@@ -618,10 +634,11 @@ int GetSeqsCommand::readGroup(){
                string name, group;
                
                bool wroteSomething = false;
+               int selectedCount = 0;
                
                while(!in.eof()){
 
-                       if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
 
                        in >> name;                             //read from first column
@@ -632,6 +649,7 @@ int GetSeqsCommand::readGroup(){
                                wroteSomething = true;
                                
                                out << name << '\t' << group << endl;
+                               selectedCount++;
                        }
                                        
                        m->gobble(in);
@@ -642,6 +660,9 @@ int GetSeqsCommand::readGroup(){
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
                outputNames.push_back(outputFileName);  outputTypes["group"].push_back(outputFileName);
                
+               m->mothurOut("Selected " + toString(selectedCount) + " sequences from your group file."); m->mothurOutEndLine();
+
+               
                return 0;
 
        }
@@ -664,10 +685,11 @@ int GetSeqsCommand::readTax(){
                string name, tax;
                
                bool wroteSomething = false;
+               int selectedCount = 0;
                
                while(!in.eof()){
 
-                       if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
                        in >> name;                             //read from first column
                        in >> tax;                      //read from second column
@@ -677,6 +699,7 @@ int GetSeqsCommand::readTax(){
                                wroteSomething = true;
                                
                                out << name << '\t' << tax << endl;
+                               selectedCount++;
                        }
                                        
                        m->gobble(in);
@@ -686,6 +709,8 @@ int GetSeqsCommand::readTax(){
                
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
                outputNames.push_back(outputFileName);  outputTypes["taxonomy"].push_back(outputFileName);
+               
+               m->mothurOut("Selected " + toString(selectedCount) + " sequences from your taxonomy file."); m->mothurOutEndLine();
                        
                return 0;
 
@@ -711,6 +736,7 @@ int GetSeqsCommand::readAlign(){
                string name, junk;
                
                bool wroteSomething = false;
+               int selectedCount = 0;
                
                //read column headers
                for (int i = 0; i < 16; i++) {  
@@ -721,7 +747,7 @@ int GetSeqsCommand::readAlign(){
                
                while(!in.eof()){
                
-                       if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
 
                        in >> name;                             //read from first column
@@ -729,6 +755,7 @@ int GetSeqsCommand::readAlign(){
                        //if this name is in the accnos file
                        if (names.count(name) != 0) {
                                wroteSomething = true;
+                               selectedCount++;
                                
                                out << name << '\t';
                                
@@ -755,6 +782,8 @@ int GetSeqsCommand::readAlign(){
                if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
                outputNames.push_back(outputFileName);  outputTypes["alignreport"].push_back(outputFileName);
                
+               m->mothurOut("Selected " + toString(selectedCount) + " sequences from your alignreport file."); m->mothurOutEndLine();
+               
                return 0;
                
        }