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added end of file character to some type type reads. fixes while testing.
[mothur.git] / sffinfocommand.cpp
diff --git a/sffinfocommand.cpp b/sffinfocommand.cpp
index c50255aeb2ae9c202074b78d89d460651cefdc43..911009982a3ed7a3e5da2845094a82b1338b74a3 100644 (file)
--- a/sffinfocommand.cpp
+++ b/sffinfocommand.cpp
@@ -16,21 +16,21 @@
 //**********************************************************************************************************************
 vector<string> SffInfoCommand::setParameters(){        
        try {           
-               CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psff);
-        CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
-               CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
-               CommandParameter psfftxt("sfftxt", "String", "", "", "", "", "",false,false); parameters.push_back(psfftxt);
-               CommandParameter pflow("flow", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pflow);
-               CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(ptrim);
-               CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pfasta);
-               CommandParameter pqfile("name", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pqfile);
-        CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
-               CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
-        CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
-               CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
-        CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(psff);
+        CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(poligos);
+               CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
+               CommandParameter psfftxt("sfftxt", "String", "", "", "", "", "","",false,false); parameters.push_back(psfftxt);
+               CommandParameter pflow("flow", "Boolean", "", "T", "", "", "","flow",false,false); parameters.push_back(pflow);
+               CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(ptrim);
+               CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "","fasta",false,false); parameters.push_back(pfasta);
+               CommandParameter pqfile("qfile", "Boolean", "", "T", "", "", "","qfile",false,false); parameters.push_back(pqfile);
+        CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ppdiffs);
+               CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pbdiffs);
+        CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs);
+               CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs);
+        CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
+               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);          }
@@ -70,32 +70,26 @@ string SffInfoCommand::getHelpString(){
                exit(1);
        }
 }
+
 //**********************************************************************************************************************
-string SffInfoCommand::getOutputFileNameTag(string type, string inputName=""){ 
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string SffInfoCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //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 == "flow")    {   outputFileName =  "flow";   }
-            else if (type == "sfftxt")        {   outputFileName =  "sff.txt";   }
-            else if (type == "sff")        {   outputFileName =  "sff";   }
-            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, "SffInfoCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "fasta")            {   pattern =  "[filename],fasta-[filename],[tag],fasta";   }
+        else if (type == "flow")    {   pattern =  "[filename],flow";   }
+        else if (type == "sfftxt")        {   pattern =  "[filename],sff.txt";   }
+        else if (type == "sff")        {   pattern =  "[filename],[group],sff";   }
+        else if (type == "qfile")       {   pattern =  "[filename],qual-[filename],[tag],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, "SffInfoCommand", "getOutputPattern");
+        exit(1);
+    }
 }
-
-
 //**********************************************************************************************************************
 SffInfoCommand::SffInfoCommand(){      
        try {
@@ -504,16 +498,14 @@ int SffInfoCommand::extractSffInfo(string input, string accnos, string oligos){
         string rootName = outputDir + m->getRootName(m->getSimpleName(input));
         if(rootName.find_last_of(".") == rootName.npos){ rootName += "."; }
         
-               string sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + getOutputFileNameTag("sfftxt");
-               string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + getOutputFileNameTag("flow");
-               if (trim) {
-                       outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + getOutputFileNameTag("fasta");
-                       outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + getOutputFileNameTag("qfile");
-               }else{
-                       outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw." + getOutputFileNameTag("fasta");
-                       outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw." + getOutputFileNameTag("qfile");
-               }
-               
+        map<string, string> variables; 
+               variables["[filename]"] = rootName;
+               string sfftxtFileName = getOutputFileName("sfftxt",variables);
+               string outFlowFileName = getOutputFileName("flow",variables);
+               if (!trim) { variables["[tag]"] = "raw"; }
+               outFastaFileName = getOutputFileName("fasta",variables);
+        outQualFileName = getOutputFileName("qfile",variables);
+        
                if (sfftxt) { m->openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint);  outputNames.push_back(sfftxtFileName);  outputTypes["sfftxt"].push_back(sfftxtFileName); }
                if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
                if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName);  }
@@ -1047,7 +1039,11 @@ int SffInfoCommand::findGroup(Header header, seqRead read, int& barcode, int& pr
         
         if (trim) {
             if(header.clipQualRight < header.clipQualLeft){
-                seq = "NNNN";
+                if (header.clipQualRight == 0) { //don't trim right
+                    seq = seq.substr(header.clipQualLeft-1);
+                }else {
+                    seq = "NNNN";
+                }
             }
             else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
                 seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
@@ -1268,7 +1264,11 @@ int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& head
                
         if (trim) {
                        if(header.clipQualRight < header.clipQualLeft){
-                               seq = "NNNN";
+                               if (header.clipQualRight == 0) { //don't trim right
+                    seq = seq.substr(header.clipQualLeft-1);
+                }else {
+                    seq = "NNNN";
+                }
                        }
                        else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
                                seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
@@ -1304,8 +1304,13 @@ int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& heade
                
                if (trim) {
                        if(header.clipQualRight < header.clipQualLeft){
-                               out << ">" << header.name << " xy=" << header.xy << endl;
-                               out << "0\t0\t0\t0";
+                if (header.clipQualRight == 0) { //don't trim right
+                    out << ">" << header.name << " xy=" << header.xy << " length=" << (read.qualScores.size()-header.clipQualLeft) << endl;
+                    for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';      }       
+                }else {
+                    out << ">" << header.name << " xy=" << header.xy << endl;
+                    out << "0\t0\t0\t0";
+                }
                        }
                        else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
                                out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
@@ -1333,6 +1338,8 @@ int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& heade
 //**********************************************************************************************************************
 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
        try {
+        if (header.clipQualRight == 0) { header.clipQualRight = read.flowgram.size(); }
+        
                if(header.clipQualRight > header.clipQualLeft){
                        
                        int rightIndex = 0;
@@ -1396,14 +1403,13 @@ int SffInfoCommand::parseSffTxt() {
                        fileRoot = m->getRootName(fileRoot);
                }
                
-               string outFlowFileName = outputDir + fileRoot + getOutputFileNameTag("flow");
-               if (trim) {
-                       outFastaFileName = outputDir + fileRoot + getOutputFileNameTag("fasta");
-                       outQualFileName = outputDir + fileRoot + getOutputFileNameTag("qfile");
-               }else{
-                       outFastaFileName = outputDir + fileRoot + "raw." + getOutputFileNameTag("fasta");
-                       outQualFileName = outputDir + fileRoot + "raw." + getOutputFileNameTag("qfile");
-               }
+        map<string, string> variables; 
+               variables["[filename]"] = fileRoot;
+               string sfftxtFileName = getOutputFileName("sfftxt",variables);
+               string outFlowFileName = getOutputFileName("flow",variables);
+               if (!trim) { variables["[tag]"] = "raw"; }
+               outFastaFileName = getOutputFileName("fasta",variables);
+        outQualFileName = getOutputFileName("qfile",variables);
                
                if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
                if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName);  }
@@ -1650,7 +1656,7 @@ bool SffInfoCommand::readOligos(string oligoFile){
                                        // get rest of line in case there is a primer name
                                        while (!inOligos.eof()) {       
                                                char c = inOligos.get(); 
-                                               if (c == 10 || c == 13){        break;  }
+                                               if (c == 10 || c == 13 || c == -1){     break;  }
                                                else if (c == 32 || c == 9){;} //space or tab
                                                else {  group += c;  }
                                        } 
@@ -1731,7 +1737,10 @@ bool SffInfoCommand::readOligos(string oligoFile){
                                        }
                                        
                                        ofstream temp;
-                                       string thisFilename = outputDir + m->getRootName(m->getSimpleName(currentFileName)) + comboGroupName + "." + getOutputFileNameTag("sff");
+                    map<string, string> variables; 
+                    variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(currentFileName));
+                    variables["[group]"] = comboGroupName;
+                                       string thisFilename = getOutputFileName("sff",variables);
                                        if (uniqueNames.count(thisFilename) == 0) {
                                                outputNames.push_back(thisFilename);
                                                outputTypes["sff"].push_back(thisFilename);
@@ -1746,7 +1755,10 @@ bool SffInfoCommand::readOligos(string oligoFile){
                numFPrimers = primers.size();
         numLinkers = linker.size();
         numSpacers = spacer.size();
-               noMatchFile = outputDir + m->getRootName(m->getSimpleName(currentFileName)) + "scrap." + getOutputFileNameTag("sff");
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(currentFileName));
+        variables["[group]"] = "scrap";
+               noMatchFile = getOutputFileName("sff",variables);
         m->mothurRemove(noMatchFile);
         
                bool allBlank = true;
Mothur--16S microbiota sequencing software; mirror of main repository with my branches