added an alignreport option to screen seqs

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 132cc6b767956e2c5b522adb4facb9904fc30a78..e616b744b2ec04d52639eca24cef8fb2af65e783 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -78,16 +78,19 @@ TrimSeqsCommand::TrimSeqsCommand(string option){
                        
                        temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found") { temp = "F"; }
                        allFiles = isTrue(temp);
-
+                       
                        if(allFiles && oligoFile == ""){
                                cout << "You selected allfiles, but didn't enter an oligos file.  Ignoring the allfiles request." << endl;
                        }
-                       
+                       if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
+                               cout << "You didn't provide a quality file name, quality criteria will be ignored." << endl;
+                               qAverage=0;
+                               qThreshold=0;
+                       }
                        if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){               
                                cout << "You didn't set any options... quiting command." << endl;
                                abort = true;
                        }
-                       
                }
 
        }
@@ -141,21 +144,21 @@ int TrimSeqsCommand::execute(){
        try{
        
                if (abort == true) { return 0; }
-       
-               vector<ofstream*> groupFileNames;
-               vector<ofstream*> fastaFileNames;
-               if(oligoFile != "")     {       getOligos(fastaFileNames, groupFileNames);      }
 
                ifstream inFASTA;
                openInputFile(fastaFile, inFASTA);
-
+               
                ofstream outFASTA;
                string trimSeqFile = getRootName(fastaFile) + "trim.fasta";
                openOutputFile(trimSeqFile, outFASTA);
                
                ofstream outGroups;
-               string groupFile = getRootName(fastaFile) + "groups"; 
-               openOutputFile(groupFile, outGroups);
+               vector<ofstream*> fastaFileNames;
+               if(oligoFile != ""){
+                       string groupFile = getRootName(fastaFile) + "groups"; 
+                       openOutputFile(groupFile, outGroups);
+                       getOligos(fastaFileNames);
+               }
                
                ofstream scrapFASTA;
                string scrapSeqFile = getRootName(fastaFile) + "scrap.fasta";
@@ -210,7 +213,6 @@ int TrimSeqsCommand::execute(){
                                        outGroups << currSeq.getName() << '\t' << groupVector[group] << endl;
                                        
                                        if(allFiles){
-                                               *groupFileNames[group] << currSeq.getName() << '\t' << groupVector[group] << endl;                                      
                                                currSeq.printSequence(*fastaFileNames[group]);                                  
                                        }
                                }
@@ -227,14 +229,29 @@ int TrimSeqsCommand::execute(){
                scrapFASTA.close();
                outGroups.close();
                
-               for(int i=0;i<groupFileNames.size();i++){
-                       groupFileNames[i]->close();
-                       delete groupFileNames[i];
-
+               for(int i=0;i<fastaFileNames.size();i++){
                        fastaFileNames[i]->close();
                        delete fastaFileNames[i];
+               }               
+               
+               for(int i=0;i<fastaFileNames.size();i++){
+                       string seqName;
+                       openInputFile(getRootName(fastaFile) + groupVector[i] + ".fasta", inFASTA);
+                       ofstream outGroups;
+                       openOutputFile(getRootName(fastaFile) + groupVector[i] + ".groups", outGroups);
+                       
+                       while(!inFASTA.eof()){
+                               if(inFASTA.get() == '>'){
+                                       inFASTA >> seqName;
+                                       outGroups << seqName << '\t' << groupVector[i] << endl;
+                               }
+                               while (!inFASTA.eof())  {       char c = inFASTA.get(); if (c == 10 || c == 13){        break;  }       }
+                       }
+                       outGroups.close();
+                       inFASTA.close();
                }
                
+               
                return 0;               
        }
        catch(exception& e) {
@@ -249,7 +266,7 @@ int TrimSeqsCommand::execute(){
 
 //***************************************************************************************************************
 
-void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec, vector<ofstream*>& outGroupsVec){
+void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec){
        
        ifstream inOligos;
        openInputFile(oligoFile, inOligos);
@@ -258,10 +275,10 @@ void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec, vector<ofstream*
        
        string type, oligo, group;
        int index=0;
-       
+
        while(!inOligos.eof()){
                inOligos >> type;
-               
+
                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
                }
@@ -286,7 +303,6 @@ void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec, vector<ofstream*
                                        
                                if(allFiles){
                                        outFASTAVec.push_back(new ofstream((getRootName(fastaFile) + group + ".fasta").c_str(), ios::ate));
-                                       outGroupsVec.push_back(new ofstream((getRootName(fastaFile) + group + ".groups").c_str(), ios::ate));
                                }
                        }
                }