fixed bug with shhh.flow from file path name in write functions, added "smart" featur...

[mothur.git] / parsefastaqcommand.cpp

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 9cba70b9d2772edba281cd5f03459d1fdc32a966..9509a20af2528392c2df8590aea61fef6a7665b4 100644 (file)
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -14,6 +14,8 @@
 vector<string> ParseFastaQCommand::setParameters(){    
        try {
                CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfastq);
+               CommandParameter pfasta("fasta", "Bool", "", "T", "", "", "",false,false); parameters.push_back(pfasta);
+               CommandParameter pqual("qfile", "Bool", "", "T", "", "", "",false,false); parameters.push_back(pqual);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
                
@@ -104,6 +106,15 @@ ParseFastaQCommand::ParseFastaQCommand(string option){
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);   if (outputDir == "not found"){  outputDir = m->hasPath(fastaQFile);     }
+                       
+                       string temp;
+                       temp = validParameter.validFile(parameters, "fasta", false);    if(temp == "not found"){        temp = "T";     }
+                       fasta = m->isTrue(temp); 
+
+                       temp = validParameter.validFile(parameters, "qfile", false);    if(temp == "not found"){        temp = "T";     }
+                       qual = m->isTrue(temp); 
+                       
+                       if ((!fasta) && (!qual)) { m->mothurOut("[ERROR]: no outputs selected. Aborting."); m->mothurOutEndLine(); abort=true; }
 
                }               
        }
@@ -122,13 +133,16 @@ int ParseFastaQCommand::execute(){
                string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "fasta";
                string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "qual";
                ofstream outFasta, outQual;
-               m->openOutputFile(fastaFile, outFasta);  outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile);
-               m->openOutputFile(qualFile, outQual);   outputNames.push_back(qualFile);  outputTypes["qfile"].push_back(qualFile);
+               
+               if (fasta) { m->openOutputFile(fastaFile, outFasta);  outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile);      }
+               if (qual) { m->openOutputFile(qualFile, outQual);       outputNames.push_back(qualFile);  outputTypes["qfile"].push_back(qualFile);             }
                
                ifstream in;
                m->openInputFile(fastaQFile, in);
                
                while (!in.eof()) {
+                       
+                       if (m->control_pressed) { break; }
                
                        //read sequence name
                        string name = m->getline(in); m->gobble(in);
@@ -147,27 +161,27 @@ int ParseFastaQCommand::execute(){
                        else { name2 = name2.substr(1);  }
                        
                        //read quality scores
-                       string qual = m->getline(in); m->gobble(in);
-                       if (qual == "") {  m->mothurOut("[ERROR]: missing quality for " + name2); m->mothurOutEndLine(); m->control_pressed = true; break; }
+                       string quality = m->getline(in); m->gobble(in);
+                       if (quality == "") {  m->mothurOut("[ERROR]: missing quality for " + name2); m->mothurOutEndLine(); m->control_pressed = true; break; }
                        
                        //sanity check sequence length and number of quality scores match
                        if (name2 != "") { if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; break; } }
-                       if (qual.length() != sequence.length()) { m->mothurOut("[ERROR]: lengths do not match. read " + toString(sequence.length()) + " characters for fasta and " + toString(qual.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; }
-                       
-                       //convert quality scores
-                       vector<int> qualScores = convertQual(qual);
+                       if (quality.length() != sequence.length()) { m->mothurOut("[ERROR]: lengths do not match. read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; break; }
                        
                        //print sequence info to files
-                       outFasta << ">" << name << endl << sequence << endl;
+                       if (fasta) { outFasta << ">" << name << endl << sequence << endl; }
                        
-                       outQual << ">" << name << endl;
-                       for (int i = 0; i < qualScores.size(); i++) { outQual << qualScores[i] << " "; }
-                       outQual << endl;
+                       if (qual) { 
+                               vector<int> qualScores = convertQual(quality);
+                               outQual << ">" << name << endl;
+                               for (int i = 0; i < qualScores.size(); i++) { outQual << qualScores[i] << " "; }
+                               outQual << endl;
+                       }
                }
                
                in.close();
-               outFasta.close();
-               outQual.close();
+               if (fasta)      { outFasta.close();     }
+               if (qual)       { outQual.close();      }
                
                if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(fastaFile); m->mothurRemove(qualFile); return 0; }