get.oturep change and trim.seqs fix

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index fce4763dcb891ef56a57f24644b9574ffa51cd1a..5e0541f9cb954575d39d277cdf4a50d6931c21c2 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -337,7 +337,7 @@ int TrimSeqsCommand::execute(){
                        outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
                        getOligos(fastaFileNames, qualFileNames);
                }
-               cout << fastaFileNames.size() << '\t' << qualFileNames.size() << endl;
+               
                vector<unsigned long int> fastaFilePos;
                vector<unsigned long int> qFilePos;
                
@@ -360,12 +360,11 @@ int TrimSeqsCommand::execute(){
                #endif
                
                if (m->control_pressed) {  return 0; }                  
-               cout << "done with driver " << endl;                                                                    
+                                                                               
                for(int i=0;i<fastaFileNames.size();i++){
-                       cout << fastaFileNames[i] << endl;
                        
-                       if (m->isBlank(fastaFileNames[i])) { cout << fastaFileNames[i] << " was blank" << endl; remove(fastaFileNames[i].c_str());      }
-                       else if (filesToRemove.count(fastaFileNames[i]) > 0) { cout << fastaFileNames[i] << " was on the remove list" << endl; remove(fastaFileNames[i].c_str()); }
+                       if (m->isBlank(fastaFileNames[i])) {  remove(fastaFileNames[i].c_str());        }
+                       else if (filesToRemove.count(fastaFileNames[i]) > 0) {  remove(fastaFileNames[i].c_str()); }
                        else {
                                ifstream inFASTA;
                                string seqName;
@@ -382,7 +381,7 @@ int TrimSeqsCommand::execute(){
                                                if(itCombo->second == i){       thisGroup = itCombo->first;     combos.erase(itCombo);  break;  }
                                        }
                                }else{ thisGroup = groupVector[i]; }
-                               cout << thisGroup << '\t' << i  << '\t' << comboStarts << endl; 
+                                       
                                while(!inFASTA.eof()){
                                        if(inFASTA.get() == '>'){
                                                inFASTA >> seqName;
@@ -394,12 +393,11 @@ int TrimSeqsCommand::execute(){
                                inFASTA.close();
                        }
                }
-       cout << "done with fastaFileNames " << endl;            
+               
                if(qFileName != ""){
                        for(int i=0;i<qualFileNames.size();i++){
-                               cout << qualFileNames[i] << endl;
-                               if (m->isBlank(qualFileNames[i])) { cout << qualFileNames[i] << " was blank" << endl; remove(qualFileNames[i].c_str()); }
-                               else if (filesToRemove.count(qualFileNames[i]) > 0) { cout << qualFileNames[i] << " was on the remove list" << endl; remove(qualFileNames[i].c_str()); }
+                               if (m->isBlank(qualFileNames[i])) {  remove(qualFileNames[i].c_str());  }
+                               else if (filesToRemove.count(qualFileNames[i]) > 0) {  remove(qualFileNames[i].c_str()); }
                                else {
                                        ifstream inQual;
                                        string seqName;
@@ -419,7 +417,7 @@ int TrimSeqsCommand::execute(){
                                }
                        }
                }
-               cout << "done with qualFileNames " << endl;
+               
                
                if (m->control_pressed) { 
                        for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
@@ -460,8 +458,6 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                }
                
                ofstream outGroups;
-               //vector<ofstream*> fastaFileNames;
-               //vector<ofstream*> qualFileNames;
                
                if (oligoFile != "") {          
                        m->openOutputFile(groupFile, outGroups);   
@@ -474,6 +470,19 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                ifstream qFile;
                if(qFileName != "")     {       m->openInputFile(qFileName, qFile);     qFile.seekg(qline->start);  }
                
+               
+               for (int i = 0; i < fastaNames.size(); i++) { //clears old file
+                       ofstream temp;
+                       m->openOutputFile(fastaNames[i], temp);
+                       temp.close();
+               }
+               for (int i = 0; i < qualNames.size(); i++) { //clears old file
+                       ofstream temp;
+                       m->openOutputFile(qualNames[i], temp);
+                       temp.close();
+               }
+               
+                       
                bool done = false;
                int count = 0;
        
@@ -753,7 +762,7 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                }
                        }
                        
-                       if (allFiles) { m->mothurOut("Done with allfile"); m->mothurOutEndLine(); }
+                       if (allFiles) { m->mothurOut("Done with allfiles"); m->mothurOutEndLine(); }
                }
        
                return exitCommand;
@@ -862,7 +871,7 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& out
                //int indexPrimer = 0;
                
                while(!inOligos.eof()){
-                       inOligos >> type;
+                       inOligos >> type; m->gobble(inOligos);
                                        
                        if(type[0] == '#'){
                                while (!inOligos.eof()) {       char c = inOligos.get(); if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
@@ -893,29 +902,29 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& out
                                        map<string, int>::iterator itPrime = primers.find(oligo);
                                        if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
                                        
-                                       primers[oligo]=index; index++;
-                                       groupVector.push_back(group);
+                                               primers[oligo]=index; index++;
+                                               groupVector.push_back(group);
                                        
-                                       if(allFiles){
-                                               outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
-                                               if(qFileName != ""){
-                                                       outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
-                                               }
-                                               if (group == "") { //if there is not a group for this primer, then this file will not get written to, but we add it to keep the indexes correct
-                                                       filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                               if(allFiles){
+                                                       outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
                                                        if(qFileName != ""){
-                                                               filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                               outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                       }
+                                                       if (group == "") { //if there is not a group for this primer, then this file will not get written to, but we add it to keep the indexes correct
+                                                               filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                               if(qFileName != ""){
+                                                                       filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                               }
+                                                       }else {
+                                                               outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                               outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                               if(qFileName != ""){
+                                                                       outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                                       outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                               }                                                       
                                                        }
-                                               }else {
-                                                       outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
-                                                       outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
-                                                       if(qFileName != ""){
-                                                               outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
-                                                               outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
-                                                       }                                                       
                                                }
-                                       }
-
+                                       
                                }
                                else if(type == "REVERSE"){
                                        Sequence oligoRC("reverse", oligo);
@@ -929,19 +938,20 @@ void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& out
                                        map<string, int>::iterator itBar = barcodes.find(oligo);
                                        if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
                                        
-                                       barcodes[oligo]=index; index++;
-                                       groupVector.push_back(group);
+                                               barcodes[oligo]=index; index++;
+                                               groupVector.push_back(group);
+                                               
+                                               if(allFiles){
+                                                       outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                       outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                       outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
+                                                       if(qFileName != ""){
+                                                               outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                               outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                               outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
+                                                       }                                                       
+                                               }
                                        
-                                       if(allFiles){
-                                               outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
-                                               outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
-                                               outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
-                                               if(qFileName != ""){
-                                                       outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
-                                                       outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
-                                                       outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
-                                               }                                                       
-                                       }
                                }else{  m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();  }
                        }
                        m->gobble(inOligos);