//**********************************************************************************************************************
vector<string> PcrSeqsCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
- CommandParameter poligos("oligos", "InputTypes", "", "", "ecolioligos", "none", "none",false,false); parameters.push_back(poligos);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
- CommandParameter ptax("taxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptax);
- CommandParameter pecoli("ecoli", "InputTypes", "", "", "ecolioligos", "none", "none",false,false); parameters.push_back(pecoli);
- CommandParameter pstart("start", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pstart);
- CommandParameter pend("end", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pend);
- CommandParameter pnomatch("nomatch", "Multiple", "reject-keep", "reject", "", "", "",false,false); parameters.push_back(pnomatch);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter pkeepprimer("keepprimer", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkeepprimer);
- CommandParameter pkeepdots("keepdots", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pkeepdots);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+ CommandParameter poligos("oligos", "InputTypes", "", "", "ecolioligos", "none", "none","",false,false,true); parameters.push_back(poligos);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false,true); parameters.push_back(pgroup);
+ CommandParameter ptax("taxonomy", "InputTypes", "", "", "none", "none", "none","taxonomy",false,false,true); parameters.push_back(ptax);
+ CommandParameter pecoli("ecoli", "InputTypes", "", "", "ecolioligos", "none", "none","",false,false); parameters.push_back(pecoli);
+ CommandParameter pstart("start", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pstart);
+ CommandParameter pend("end", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pend);
+ CommandParameter pnomatch("nomatch", "Multiple", "reject-keep", "reject", "", "", "","",false,false); parameters.push_back(pnomatch);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter pkeepprimer("keepprimer", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pkeepprimer);
+ CommandParameter pkeepdots("keepdots", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pkeepdots);
+ 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 PcrSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string PcrSeqsCommand::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 = "pcr.fasta"; }
- else if (type == "taxonomy") { outputFileName = "pcr" + m->getExtension(inputName); }
- else if (type == "group") { outputFileName = "pcr" + m->getExtension(inputName); }
- else if (type == "name") { outputFileName = "pcr" + m->getExtension(inputName); }
- else if (type == "count") { outputFileName = "pcr" + m->getExtension(inputName); }
- else if (type == "accnos") { outputFileName = "bad.accnos"; }
- 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, "PcrSeqsCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],pcr,[extension]-[filename],[tag],pcr,[extension]"; }
+ else if (type == "taxonomy") { pattern = "[filename],pcr,[extension]"; }
+ else if (type == "name") { pattern = "[filename],pcr,[extension]"; }
+ else if (type == "group") { pattern = "[filename],pcr,[extension]"; }
+ else if (type == "count") { pattern = "[filename],pcr,[extension]"; }
+ else if (type == "accnos") { pattern = "[filename],bad.accnos"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PcrSeqsCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string trimSeqFile = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[extension]"] = m->getExtension(fastafile);
+ string trimSeqFile = getOutputFileName("fasta",variables);
outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
-
- string badSeqFile = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "scrap." + getOutputFileNameTag("fasta");
+ variables["[tag]"] = "scrap";
+ string badSeqFile = getOutputFileName("fasta",variables);
length = 0;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("accnos");
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ string outputFileName = getOutputFileName("accnos",variables);
outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
ofstream out;
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+ variables["[extension]"] = m->getExtension(namefile);
+ string outputFileName = getOutputFileName("name", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string outputFileName = getOutputFileName("group", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
+ variables["[extension]"] = m->getExtension(taxfile);
+ string outputFileName = getOutputFileName("taxonomy", variables);
+
ofstream out;
m->openOutputFile(outputFileName, out);
m->openInputFile(countfile, in);
set<string>::iterator it;
- string goodCountFile = outputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string goodCountFile = getOutputFileName("count", variables);
+
outputNames.push_back(goodCountFile); outputTypes["count"].push_back(goodCountFile);
ofstream goodCountOut; m->openOutputFile(goodCountFile, goodCountOut);