//**********************************************************************************************************************
vector<string> TrimFlowsCommand::setParameters(){
try {
- CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pflow);
- CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
- CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "",false,false); parameters.push_back(pmaxhomop);
- CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pmaxflows);
- CommandParameter pminflows("minflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pminflows);
- 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 pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter psignal("signal", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(psignal);
- CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pnoise);
- CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "",false,false); parameters.push_back(pallfiles);
- CommandParameter porder("order", "String", "", "", "", "", "",false,false); parameters.push_back(porder);
- CommandParameter pfasta("fasta", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfasta);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","flow",false,true,true); parameters.push_back(pflow);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(poligos);
+ CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "","",false,false); parameters.push_back(pmaxhomop);
+ CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "","",false,false); parameters.push_back(pmaxflows);
+ CommandParameter pminflows("minflows", "Number", "", "450", "", "", "","",false,false); parameters.push_back(pminflows);
+ CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
+ CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); 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 pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter psignal("signal", "Number", "", "0.50", "", "", "","",false,false); parameters.push_back(psignal);
+ CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "","",false,false); parameters.push_back(pnoise);
+ CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(pallfiles);
+ CommandParameter porder("order", "String", "", "TACG", "", "", "","",false,false); parameters.push_back(porder);
+ CommandParameter pfasta("fasta", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfasta);
+ 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); }
exit(1);
}
}
-
+//**********************************************************************************************************************
+string TrimFlowsCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "flow") { pattern = "[filename],[tag],flow"; }
+ else if (type == "fasta") { pattern = "[filename],flow.fasta"; }
+ else if (type == "file") { pattern = "[filename],flow.files"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "TrimFlowsCommand", "getOutputPattern");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
TrimFlowsCommand::TrimFlowsCommand(){
vector<string> tempOutNames;
outputTypes["flow"] = tempOutNames;
outputTypes["fasta"] = tempOutNames;
+ outputTypes["file"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
vector<string> tempOutNames;
outputTypes["flow"] = tempOutNames;
outputTypes["fasta"] = tempOutNames;
+ outputTypes["file"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- string trimFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "trim.flow";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
+ string fastaFileName = getOutputFileName("fasta",variables);
+ if(fasta){ outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName); }
+
+ variables["[tag]"] = "trim";
+ string trimFlowFileName = getOutputFileName("flow",variables);
outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
- string scrapFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "scrap.flow";
+ variables["[tag]"] = "scrap";
+ string scrapFlowFileName = getOutputFileName("flow",variables);
outputNames.push_back(scrapFlowFileName); outputTypes["flow"].push_back(scrapFlowFileName);
- string fastaFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.fasta";
- if(fasta){
- outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName);
- }
+
vector<unsigned long long> flowFilePos;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
if(allFiles){
set<string> namesAlreadyProcessed;
- flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
+ variables["[tag]"] = "";
+ flowFilesFileName = getOutputFileName("file",variables);
m->openOutputFile(flowFilesFileName, output);
for(int i=0;i<barcodePrimerComboFileNames.size();i++){
output.close();
}
else{
- flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
+ variables["[tag]"] = "";
+ flowFilesFileName = getOutputFileName("file",variables);
m->openOutputFile(flowFilesFileName, output);
output << m->getFullPathName(trimFlowFileName) << endl;
output.close();
}
- outputTypes["flow.files"].push_back(flowFilesFileName);
+ outputTypes["file"].push_back(flowFilesFileName);
outputNames.push_back(flowFilesFileName);
// set fasta file as new current fastafile
string trashCode = "";
flowData.getNext(flowFile);
- //cout << "driver good bit " << flowFile.good() << endl;
flowData.capFlows(maxFlows);
Sequence currSeq = flowData.getSequence();
-
if(!flowData.hasMinFlows(minFlows)){ //screen to see if sequence is of a minimum number of flows
success = 0;
trashCode += 'l';
}
+ if (m->debug) { m->mothurOut("[DEBUG]: " + currSeq.getName() + " " + currSeq.getUnaligned() + "\n"); }
+
if(barcodes.size() != 0){
success = trimOligos.stripBarcode(currSeq, barcodeIndex);
if(success > bdiffs) { trashCode += 'b'; }
string comboGroupName = "";
string fileName = "";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
+
if(primerName == ""){
comboGroupName = barcodeNameVector[itBar->second];
- fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
+ variables["[tag]"] = comboGroupName;
+ fileName = getOutputFileName("flow", variables);
}
else{
if(barcodeName == ""){
else{
comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
}
- fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
+ variables["[tag]"] = comboGroupName;
+ fileName = getOutputFileName("flow", variables);
}
outFlowFileNames[itBar->second][itPrimer->second] = fileName;