//**********************************************************************************************************************
vector<string> SubSampleCommand::setParameters(){
try {
- CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(pfasta);
- 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 plist("list", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(plist);
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(pshared);
- CommandParameter prabund("rabund", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(prabund);
- CommandParameter psabund("sabund", "InputTypes", "", "", "none", "FLSSR", "none",false,false); parameters.push_back(psabund);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
- CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppersample);
- 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", "FLSSR", "none","fasta",false,false,true); parameters.push_back(pfasta);
+ 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 plist("list", "InputTypes", "", "", "none", "FLSSR", "none","list",false,false,true); parameters.push_back(plist);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "FLSSR", "none","shared",false,false,true); parameters.push_back(pshared);
+ CommandParameter prabund("rabund", "InputTypes", "", "", "none", "FLSSR", "none","rabund",false,false); parameters.push_back(prabund);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "none", "FLSSR", "none","sabund",false,false); parameters.push_back(psabund);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter psize("size", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(psize);
+ CommandParameter ppersample("persample", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(ppersample);
+ 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 SubSampleCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string SubSampleCommand::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 = "subsample" + m->getExtension(inputName); }
- else if (type == "sabund") { outputFileName = "subsample" + m->getExtension(inputName); }
- else if (type == "name") { outputFileName = "subsample" + m->getExtension(inputName); }
- else if (type == "count") { outputFileName = "subsample" + m->getExtension(inputName); }
- else if (type == "group") { outputFileName = "subsample" + m->getExtension(inputName); }
- else if (type == "list") { outputFileName = "subsample" + m->getExtension(inputName); }
- else if (type == "rabund") { outputFileName = "subsample" + m->getExtension(inputName); }
- else if (type == "shared") { outputFileName = "subsample" + m->getExtension(inputName); }
- 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, "SubSampleCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "fasta") { pattern = "[filename],subsample,[extension]"; }
+ else if (type == "sabund") { pattern = "[filename],subsample,[extension]"; }
+ else if (type == "name") { pattern = "[filename],subsample,[extension]"; }
+ else if (type == "group") { pattern = "[filename],subsample,[extension]"; }
+ else if (type == "count") { pattern = "[filename],subsample,[extension]"; }
+ else if (type == "list") { pattern = "[filename],subsample,[extension]"; }
+ else if (type == "shared") { pattern = "[filename],[distance],subsample,[extension]"; }
+ else if (type == "rabund") { pattern = "[filename],subsample,[extension]"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSampleCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
SubSampleCommand::SubSampleCommand(){
try {
string countOutputDir = outputDir;
if (outputDir == "") { countOutputDir += m->hasPath(countfile); }
- string countOutputFileName = countOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+ map<string, string> variables;
+ variables["[filename]"] = countOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string countOutputFileName = getOutputFileName("count", variables);
outputTypes["count"].push_back(countOutputFileName); outputNames.push_back(countOutputFileName);
sampledCt.printTable(countOutputFileName);
}
string countOutputDir = outputDir;
if (outputDir == "") { countOutputDir += m->hasPath(countfile); }
- string countOutputFileName = countOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+ map<string, string> variables;
+ variables["[filename]"] = countOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string countOutputFileName = getOutputFileName("count", variables);
outputTypes["count"].push_back(countOutputFileName); outputNames.push_back(countOutputFileName);
sampledCt.printTable(countOutputFileName);
}
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta", fastafile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+ variables["[extension]"] = m->getExtension(fastafile);
+ string outputFileName = getOutputFileName("fasta", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
if (namefile != "") {
m->mothurOut("Deconvoluting subsampled fasta file... "); m->mothurOutEndLine();
-
- string outputNameFileName = 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 outputNameFileName = getOutputFileName("name", variables);
//use unique.seqs to create new name and fastafile
string inputString = "fasta=" + outputFileName;
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
string groupOutputDir = outputDir;
if (outputDir == "") { groupOutputDir += m->hasPath(groupfile); }
- string groupOutputFileName = groupOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+ map<string, string> variables;
+ variables["[filename]"] = groupOutputDir + m->getRootName(m->getSimpleName(groupfile));
+ variables["[extension]"] = m->getExtension(groupfile);
+ string groupOutputFileName = getOutputFileName("group", variables);
ofstream outGroup;
m->openOutputFile(groupOutputFileName, outGroup);
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + thislookup[0]->getLabel() + "." +getOutputFileNameTag("shared", sharedfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile));
+ variables["[extension]"] = m->getExtension(sharedfile);
+ variables["[distance]"] = thislookup[0]->getLabel();
+ string outputFileName = getOutputFileName("shared", variables);
SubSample sample;
vector<string> subsampledLabels = sample.getSample(thislookup, size);
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
+ variables["[extension]"] = m->getExtension(listfile);
+ string outputFileName = getOutputFileName("list", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
string countOutputDir = outputDir;
if (outputDir == "") { countOutputDir += m->hasPath(countfile); }
- string countOutputFileName = countOutputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+ map<string, string> variables;
+ variables["[filename]"] = countOutputDir + m->getRootName(m->getSimpleName(countfile));
+ variables["[extension]"] = m->getExtension(countfile);
+ string countOutputFileName = getOutputFileName("count", variables);
outputTypes["count"].push_back(countOutputFileName); outputNames.push_back(countOutputFileName);
sampledCt.printTable(countOutputFileName);
}
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(rabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + getOutputFileNameTag("rabund", rabundfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile));
+ variables["[extension]"] = m->getExtension(rabundfile);
+ string outputFileName = getOutputFileName("rabund", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
outputTypes["rabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sabundfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + getOutputFileNameTag("sabund", sabundfile);
+ map<string, string> variables;
+ variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile));
+ variables["[extension]"] = m->getExtension(sabundfile);
+ string outputFileName = getOutputFileName("sabund", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
outputTypes["sabund"].push_back(outputFileName); outputNames.push_back(outputFileName);