exit(1);
}
}
+//**********************************************************************************************************************
+string SffInfoCommand::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 == "flow") { outputFileName = "flow"; }
+ else if (type == "sfftxt") { outputFileName = "sff.txt"; }
+ 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);
+ }
+}
//**********************************************************************************************************************
int start = time(NULL);
+ filenames[s] = m->getFullPathName(filenames[s]);
m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
string accnos = "";
string rootName = outputDir + m->getRootName(m->getSimpleName(input));
if(rootName.find_last_of(".") == rootName.npos){ rootName += "."; }
- string sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "sff.txt";
- string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "flow";
+ 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)) + "fasta";
- outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "qual";
+ 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.fasta";
- outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.qual";
+ outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw." + getOutputFileNameTag("fasta");
+ outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw." + getOutputFileNameTag("qfile");
}
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); }
fileRoot = m->getRootName(fileRoot);
}
- string outFlowFileName = outputDir + fileRoot + "flow";
+ string outFlowFileName = outputDir + fileRoot + getOutputFileNameTag("flow");
if (trim) {
- outFastaFileName = outputDir + fileRoot + "fasta";
- outQualFileName = outputDir + fileRoot + "qual";
+ outFastaFileName = outputDir + fileRoot + getOutputFileNameTag("fasta");
+ outQualFileName = outputDir + fileRoot + getOutputFileNameTag("qfile");
}else{
- outFastaFileName = outputDir + fileRoot + "raw.fasta";
- outQualFileName = outputDir + fileRoot + "raw.qual";
+ outFastaFileName = outputDir + fileRoot + "raw." + getOutputFileNameTag("fasta");
+ outQualFileName = outputDir + fileRoot + "raw." + getOutputFileNameTag("qfile");
}
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["qual"].push_back(outQualFileName); }
+ if (qual) { m->openOutputFile(outQualFileName, outQual); outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName); }
if (flow) { m->openOutputFile(outFlowFileName, outFlow); outputNames.push_back(outFlowFileName); outFlow.setf(ios::fixed, ios::floatfield); outFlow.setf(ios::showpoint); outputTypes["flow"].push_back(outFlowFileName); }
//read common header