//**********************************************************************************************************************
vector<string> MakeContigsCommand::setParameters(){
try {
- CommandParameter pfasta("ffastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter prfasta("rfastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(prfasta);
- CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
- CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
- CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
+ CommandParameter pfasta("ffastq", "InputTypes", "", "", "none", "none", "none","fasta-qfile",false,true,true); parameters.push_back(pfasta);
+ CommandParameter prfasta("rfastq", "InputTypes", "", "", "none", "none", "none","fasta-qfile",false,true,true); parameters.push_back(prfasta);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","group",false,false,true); parameters.push_back(poligos);
+ 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 ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
- CommandParameter palign("align", "Multiple", "needleman-gotoh", "needleman", "", "", "",false,false); parameters.push_back(palign);
- CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pallfiles);
- CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
- CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
- CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
- CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
- CommandParameter pthreshold("threshold", "Number", "", "40", "", "", "",false,false); parameters.push_back(pthreshold);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter palign("align", "Multiple", "needleman-gotoh", "needleman", "", "", "","",false,false); parameters.push_back(palign);
+ CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pallfiles);
+ CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
+ CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
+ CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
+ CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
+ CommandParameter pthreshold("threshold", "Number", "", "40", "", "", "","",false,false); parameters.push_back(pthreshold);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ 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); }
}
}
//**********************************************************************************************************************
-string MakeContigsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string MakeContigsCommand::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 = "contigs.fasta"; }
- else if (type == "qfile") { outputFileName = "contigs.qual"; }
- else if (type == "group") { outputFileName = "groups"; }
- else if (type == "mismatch") { outputFileName = "contigs.mismatch"; }
- 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, "MakeContigsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],[tag],contigs.fasta"; }
+ else if (type == "qfile") { pattern = "[filename],[tag],contigs.qual"; }
+ else if (type == "group") { pattern = "[filename],[tag],groups"; }
+ else if (type == "mismatch") { pattern = "[filename],[tag],contigs.mismatch"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeContigsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
MakeContigsCommand::MakeContigsCommand(){
temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found") { temp = "0"; }
m->mothurConvert(temp, pdiffs);
- // temp = validParameter.validFile(parameters, "ldiffs", false); if (temp == "not found") { temp = "0"; }
+ // temp = validParameter.validFile(parameters, "ldiffs", false); if (temp == "not found") { temp = "0"; }
// m->mothurConvert(temp, ldiffs);
+ ldiffs = 0;
// temp = validParameter.validFile(parameters, "sdiffs", false); if (temp == "not found") { temp = "0"; }
-// m->mothurConvert(temp, sdiffs);
+ // m->mothurConvert(temp, sdiffs);
+ sdiffs = 0;
- temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs; temp = toString(tempTotal); }
+ temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs; temp = toString(tempTotal); }
m->mothurConvert(temp, tdiffs);
if(tdiffs == 0){ tdiffs = bdiffs + pdiffs; } //+ ldiffs + sdiffs;
vector<vector<string> > qualFileNames;
createGroup = false;
string outputGroupFileName;
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(ffastqfile));
+ variables["[tag]"] = "";
if(oligosfile != ""){
createGroup = getOligos(fastaFileNames, qualFileNames);
if (createGroup) {
- outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("group");
+ outputGroupFileName = getOutputFileName("group",variables);
outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
}
}
- string outFastaFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "trim." + getOutputFileNameTag("fasta");
- string outQualFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "trim." + getOutputFileNameTag("qfile");
- string outScrapFastaFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "scrap." + getOutputFileNameTag("fasta");
- string outScrapQualFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "scrap." + getOutputFileNameTag("qfile");
+ variables["[tag]"] = "trim";
+ string outFastaFile = getOutputFileName("fasta",variables);
+ string outQualFile = getOutputFileName("qfile",variables);
+ variables["[tag]"] = "scrap";
+ string outScrapFastaFile = getOutputFileName("fasta",variables);
+ string outScrapQualFile = getOutputFileName("qfile",variables);
- string outMisMatchFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("mismatch");
+ variables["[tag]"] = "";
+ string outMisMatchFile = getOutputFileName("mismatch",variables);
outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
outputNames.push_back(outQualFile); outputTypes["qfile"].push_back(outQualFile);
outputNames.push_back(outScrapFastaFile); outputTypes["fasta"].push_back(outScrapFastaFile);
ofstream out;
string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first));
- thisGroupName += getOutputFileNameTag("group"); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
+ thisGroupName += getOutputFileName("group",variables); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
m->openOutputFile(thisGroupName, out);
while (!in.eof()){