fixed bug in phylo.diversity rooting. added filename patterns and create filename...

[mothur.git] / parsefastaqcommand.cpp

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index e6d7ce6d1aa30da836bb88f2833bd666ae11bd85..63ed3144ad2a2b86ed33c6f9449b8d8143d38204 100644 (file)
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -13,11 +13,12 @@
 //**********************************************************************************************************************
 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);
+               CommandParameter pfastq("fastq", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pfastq);
+               CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "","fasta",false,false); parameters.push_back(pfasta);
+               CommandParameter pqual("qfile", "Boolean", "", "T", "", "", "","qfile",false,false); parameters.push_back(pqual);
+               CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa", "sanger", "", "", "","",false,false,true); parameters.push_back(pformat);
+        CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -33,8 +34,9 @@ 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 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 fastq.info command parameters are fastq, fasta, qfile and format; fastq is required.\n";
+        helpString += "The fastq.info command should be in the following format: fastq.info(fastaq=yourFastaQFile).\n";
+               helpString += "The format parameter is used to indicate whether your sequences are sanger, solexa or illumina, default=sanger.\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";
@@ -47,6 +49,22 @@ string ParseFastaQCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string ParseFastaQCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "fasta") {  pattern = "[filename],fasta"; } 
+        else if (type == "qfile") {  pattern = "[filename],qual"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ParseFastaQCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 ParseFastaQCommand::ParseFastaQCommand(){      
        try {
                abort = true; calledHelp = true; 
@@ -116,6 +134,13 @@ ParseFastaQCommand::ParseFastaQCommand(string option){
                        temp = validParameter.validFile(parameters, "qfile", false);    if(temp == "not found"){        temp = "T";     }
                        qual = m->isTrue(temp); 
                        
+            format = validParameter.validFile(parameters, "format", false);            if (format == "not found"){     format = "sanger";      }
+            
+            if ((format != "sanger") && (format != "illumina") && (format != "solexa"))  { 
+                               m->mothurOut(format + " is not a valid format. Your format choices are sanger, solexa and illumina, aborting." ); m->mothurOutEndLine();
+                               abort=true;
+                       }
+
                        if ((!fasta) && (!qual)) { m->mothurOut("[ERROR]: no outputs selected. Aborting."); m->mothurOutEndLine(); abort=true; }
 
                }               
@@ -132,8 +157,10 @@ 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";
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaQFile));
+               string fastaFile = getOutputFileName("fasta",variables);
+               string qualFile = getOutputFileName("qfile",variables);
                ofstream outFasta, outQual;
                
                if (fasta) { m->openOutputFile(fastaFile, outFasta);  outputNames.push_back(fastaFile); outputTypes["fasta"].push_back(fastaFile);      }
@@ -141,6 +168,12 @@ int ParseFastaQCommand::execute(){
                
                ifstream in;
                m->openInputFile(fastaQFile, in);
+        
+        //fill convert table - goes from solexa to sanger. Used fq_all2std.pl as a reference.
+        for (int i = -64; i < 65; i++) { 
+            char temp = (char) ((int)(33 + 10*log(1+pow(10,(i/10.0)))/log(10)+0.499));
+            convertTable.push_back(temp);
+        }
                
                while (!in.eof()) {
                        
@@ -216,12 +249,18 @@ vector<int> ParseFastaQCommand::convertQual(string qual) {
        try {
                vector<int> qualScores;
                
-               int controlChar = int('!');
-               
                for (int i = 0; i < qual.length(); i++) { 
-                       int temp = int(qual[i]);
-                       temp -= controlChar;
-                       
+            
+            int temp = 0;
+            temp = int(qual[i]);
+            if (format == "illumina") {
+                temp -= 64; //char '@'
+            }else if (format == "solexa") {
+                temp = int(convertTable[temp]); //convert to sanger
+                temp -= int('!'); //char '!'
+            }else {
+                temp -= int('!'); //char '!'
+            }
                        qualScores.push_back(temp);
                }