string MakeBiomCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The make.biom command parameters are shared, groups, matrixtype and label. shared is required, unless you have a valid current file.\n";
+ helpString += "The make.biom command parameters are shared, contaxonomy, groups, matrixtype and label. shared is required, unless you have a valid current file.\n";
helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n";
helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";
helpString += "The matrixtype parameter allows you to select what type you would like to make. Choices are sparse and dense, default is sparse.\n";
+ helpString += "The contaxonomy file is the taxonomy file outputted by classify.otu(list=yourListfile, taxonomy=yourTaxonomyFile). Be SURE that the you are the constaxonomy file distance matches the shared file distance. ie, for *.0.03.cons.taxonomy set label=0.03. Mothur is smart enough to handle shared files that have been subsampled.\n";
helpString += "The make.biom command should be in the following format: make.biom(shared=yourShared, groups=yourGroups, label=yourLabels).\n";
- helpString += "The contaxonomy file is the taxonomy file outputted by classify.otu(list=yourListfile, taxonomy=yourTaxonomyFile). Be SURE that the you are the constaxonomy file distance matches the shared file distance. ie, for *.0.03.cons.taxonomy set label=0.03. Mothur is smart enough to handle shared files that have been subsampled after the classify.otu command was run on the list and taxonomy file.\n";
helpString += "Example make.biom(shared=abrecovery.an.shared, groups=A-B-C).\n";
helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
helpString += "The make.biom command outputs a .biom file.\n";
exit(1);
}
}
+//**********************************************************************************************************************
+string MakeBiomCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //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 == "biom") { outputFileName = "biom"; }
+ 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, "MakeBiomCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
MakeBiomCommand::MakeBiomCommand(){
try {
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
-
+
//initialize outputTypes
vector<string> tempOutNames;
- outputTypes["relabund"] = tempOutNames;
+ outputTypes["biom"] = tempOutNames;
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+ //set sabund file as new current sabundfile
+ string current = "";
+ itTypes = outputTypes.find("biom");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setBiomFile(current); }
+ }
+
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
int MakeBiomCommand::getBiom(vector<SharedRAbundVector*>& lookup){
try {
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + ".biom";
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + lookup[0]->getLabel() + "." + getOutputFileNameTag("biom");
ofstream out;
m->openOutputFile(outputFileName, out);
outputNames.push_back(outputFileName); outputTypes["biom"].push_back(outputFileName);
if (m->control_pressed) { return metadata; }
//if there is a bin label use it otherwise make one
- string binLabel = binTag;
- string sbinNumber = otuLabels[i];
- if (sbinNumber.length() < snumBins.length()) {
- int diff = snumBins.length() - sbinNumber.length();
- for (int h = 0; h < diff; h++) { binLabel += "0"; }
- }
- binLabel += sbinNumber;
-
- labelTaxMap[binLabel] = taxs[i];
+ if (m->isContainingOnlyDigits(otuLabels[i])) {
+ string binLabel = binTag;
+ string sbinNumber = otuLabels[i];
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { binLabel += "0"; }
+ }
+ binLabel += sbinNumber;
+ labelTaxMap[binLabel] = taxs[i];
+ }else { labelTaxMap[otuLabels[i]] = taxs[i]; }
}
scores.push_back(confidenceScore);
}else{ scores.push_back("null"); }
}
- }
+ }else{ scores.push_back("null"); }
//strip "" if they are there
pos = taxon.find("\"");
projects / mothur.git / blobdiff