X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=trimflowscommand.cpp;h=cc49755d2ced89f31aa60258de2abc18838e9967;hb=f12174bc43f9e8ad536f2a37fb3a763b1ac90ba9;hp=d45f20cae1f0516c014d42cf7e6afaef57d2a1a2;hpb=f687723a8357916e86a05116978e6869b039ce36;p=mothur.git diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp index d45f20c..cc49755 100644 --- a/trimflowscommand.cpp +++ b/trimflowscommand.cpp @@ -14,24 +14,24 @@ //********************************************************************************************************************** vector 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 myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -57,26 +57,21 @@ string TrimFlowsCommand::getHelpString(){ } } //********************************************************************************************************************** -string TrimFlowsCommand::getOutputFileNameTag(string type, string inputName=""){ - try { - string outputFileName = ""; - map >::iterator it; +string TrimFlowsCommand::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 == "flow") { outputFileName = "flow"; } - else if (type == "fasta") { outputFileName = "flow.fasta"; } - else if (type == "file") { outputFileName = "flow.files"; } - 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, "TrimFlowsCommand", "getOutputFileNameTag"); - exit(1); - } + 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); + } } //********************************************************************************************************************** @@ -248,16 +243,20 @@ int TrimFlowsCommand::execute(){ if (abort == true) { if (calledHelp) { return 0; } return 2; } - string trimFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "trim." + getOutputFileNameTag("flow"); + map 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." + getOutputFileNameTag("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)) + getOutputFileNameTag("fasta"); - if(fasta){ - outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName); - } + vector flowFilePos; #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) @@ -307,7 +306,8 @@ int TrimFlowsCommand::execute(){ if(allFiles){ set namesAlreadyProcessed; - flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("file"); + variables["[tag]"] = ""; + flowFilesFileName = getOutputFileName("file",variables); m->openOutputFile(flowFilesFileName, output); for(int i=0;igetRootName(m->getSimpleName(flowFileName)) + getOutputFileNameTag("file"); + 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 @@ -423,11 +424,9 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN 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'; @@ -443,6 +442,8 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN } + 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'; } @@ -623,9 +624,13 @@ void TrimFlowsCommand::getOligos(vector >& outFlowFileNames){ string comboGroupName = ""; string fileName = ""; + map 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 == ""){ @@ -634,7 +639,8 @@ void TrimFlowsCommand::getOligos(vector >& outFlowFileNames){ 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;