added SequenceCountParser class to parse the count table by group. added count parame...

[mothur.git] / parsefastaqcommand.cpp

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 9509a20af2528392c2df8590aea61fef6a7665b4..1331b7f47f4e131cb5a76913889d275b7ec93121 100644 (file)
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -33,8 +33,10 @@ string ParseFastaQCommand::getHelpString(){
        try {
                string helpString = "";
                helpString += "The fastq.info command reads a fastq file and creates a fasta and quality file.\n";
-               helpString += "The fastq.info command parameter is fastq, and it is required.\n";
+               helpString += "The fastq.info command parameters are fastq, fasta and qfile; fastq is required.\n";
                helpString += "The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n";
+        helpString += "The fasta parameter allows you to indicate whether you want a fasta file generated. Default=T.\n";
+        helpString += "The qfile parameter allows you to indicate whether you want a quality file generated. Default=T.\n";
                helpString += "Example fastq.info(fastaq=test.fastaq).\n";
                helpString += "Note: No spaces between parameter labels (i.e. fastq), '=' and yourFastQFile.\n";
                return helpString;
@@ -44,6 +46,28 @@ string ParseFastaQCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string ParseFastaQCommand::getOutputFileNameTag(string type, string inputName=""){     
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "fasta") {  outputFileName =  "fasta"; }
+            else if (type == "qfile") {  outputFileName =  "qual"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ParseFastaQCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+
 //**********************************************************************************************************************
 ParseFastaQCommand::ParseFastaQCommand(){      
        try {
@@ -130,8 +154,8 @@ int ParseFastaQCommand::execute(){
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //open Output Files
-               string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "fasta";
-               string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "qual";
+               string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + getOutputFileNameTag("fasta");
+               string qualFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + getOutputFileNameTag("qfile");
                ofstream outFasta, outQual;
                
                if (fasta) { m->openOutputFile(fastaFile, outFasta);  outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile);      }
@@ -166,7 +190,7 @@ int ParseFastaQCommand::execute(){
                        
                        //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 (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; }
+                       if (quality.length() != sequence.length()) { m->mothurOut("[ERROR]: Lengths do not match for sequence " + name + ". 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
                        if (fasta) { outFasta << ">" << name << endl << sequence << endl; }
@@ -214,7 +238,7 @@ vector<int> ParseFastaQCommand::convertQual(string qual) {
        try {
                vector<int> qualScores;
                
-               int controlChar = int('!');
+               int controlChar = int('@');
                
                for (int i = 0; i < qual.length(); i++) { 
                        int temp = int(qual[i]);