//**********************************************************************************************************************
vector<string> GetCoreMicroBiomeCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(pshared);
- CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(prelabund);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter poutput("output", "Multiple", "fraction-count", "fraction", "", "", "",false,false); parameters.push_back(poutput);
- CommandParameter pabund("abundance", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pabund);
- CommandParameter psamples("samples", "Number", "", "-1", "", "", "",false,false); parameters.push_back(psamples);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none","coremicrobiom",false,false, true); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none","coremicrobiom",false,false, true); parameters.push_back(prelabund);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter poutput("output", "Multiple", "fraction-count", "fraction", "", "", "","",false,false); parameters.push_back(poutput);
+ CommandParameter pabund("abundance", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pabund);
+ CommandParameter psamples("samples", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(psamples);
+ 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 GetCoreMicroBiomeCommand::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string GetCoreMicroBiomeCommand::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 == "coremicrobiome") { outputFileName = "core.microbiome"; }
- 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, "GetCoreMicroBiomeCommand", "getOutputFileNameTag");
- exit(1);
- }
+ if (type == "coremicrobiome") { pattern = "[filename],[tag],core.microbiome"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetCoreMicroBiomeCommand", "getOutputPattern");
+ exit(1);
+ }
}
-
//**********************************************************************************************************************
GetCoreMicroBiomeCommand::GetCoreMicroBiomeCommand(){
try {
int GetCoreMicroBiomeCommand::createTable(vector<SharedRAbundFloatVector*>& lookup){
try {
-
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("coremicrobiome");
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+ variables["[tag]"] = lookup[0]->getLabel();
+ string outputFileName = getOutputFileName("coremicrobiome", variables);
outputNames.push_back(outputFileName); outputTypes["coremicrobiome"].push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
for (int k = 0; k < counts[j]; k++) { table[j][k]++; }
if ((abund == -1) && (samples != -1)) { //we want all OTUs with this number of samples
- if (counts[j] >= samples) { otuNames[j].push_back(m->currentBinLabels[i]); }
+ if (counts[j] >= samples) { otuNames[j].push_back(m->currentSharedBinLabels[i]); }
}else if ((abund != -1) && (samples == -1)) { //we want all OTUs with this relabund
if (j == abund) {
- for (int k = 0; k < counts[j]; k++) { otuNames[k+1].push_back(m->currentBinLabels[i]); }
+ for (int k = 0; k < counts[j]; k++) { otuNames[k+1].push_back(m->currentSharedBinLabels[i]); }
}
}else if ((abund != -1) && (samples != -1)) { //we want only OTUs with this relabund for this number of samples
if ((j == abund) && (counts[j] >= samples)) {
- otuNames[j].push_back(m->currentBinLabels[i]);
+ otuNames[j].push_back(m->currentSharedBinLabels[i]);
}
}
}